metal cations are constituents of approximately 40% of all proteins ( 1 ) , they take part in enzymatic reactions and they are the essential partners in assembly of the functional ribonucleic acid ( rna ) structures ( 2,3 ) . for example , presence of magnesium di - cations is essential for the formation and stabilization of the transfer rna tertiary structure ( 4,5 ) . removal or replacement of one metal by another is accompanied by loss , reduction or even alteration of the enzyme catalytic potency [ see for example ( 6 ) ] . the knowledge of the metal ions environment , especially the electron donor types and number , is important to clarify how specific a metal - binding site is and how we can tune the desired chemical reaction . to the best of our knowledge , currently , there are several databases available for researchers to view the information on metals and metal - binding sites in proteins [ metligdb ( 7 ) , mespeus ( 8) , mips ( 9 ) , mdb ( 10 ) and come ( 11 ) ] and rnas [ merna ( 12 ) ] . however , they are typically limited to simple retrieval of protein data bank ( pdb ) structures for specified metal and donor atoms . the main contribution of biome is that , unlike the databases discussed earlier , it generates statistical reports for predefined or user - defined pdb subsets . this approach allows the users to find characteristics of particular metal - biding sites in a simple and straightforward manner . in addition , to the best of our knowledge , biome is the only website that distinguishes between various chain types [ i.e. protein , rna and deoxyribonucleic acid ( dna ) ] , thus enabling the user to easily focus on the chain of their interest . our website additionally provides information about the binuclear metal centers , the occurrence of certain combination of molecules ( 13 ) in metal ion coordination sphere and about the metal coordination geometry ( 14 ) , for coordination numbers ranging from 3 to 14 . finally , the mysql database dump of biome underlying database is publicly available . among the existing databases , as far as we know , only mdb ( the time of the last update was in 2003 ) has the dump available , whereas querying mespeus sql database is available only on request ( by sending an email to author ) . the main motivations for setting up biome are exponentially growing number of three - dimensional ( 3d ) structures deposited in the pdb ( 15 ) , the green chemistry requirements for increasing efficiency of existing metaloenzymes and design of the new ones . this is a continuation of our earlier work on structure of the metal - binding sites in proteins ( 13 ) . a user - friendly interface enables scientists to perform their own statistics and to easily extrapolate the relevant data . in addition , the website enables the retrieval of information concerning natural , as well as toxic metal cations , precisely the all metal ions found in pdb to be tightly bound either to a protein or / and to a nucleic acid are considered . in comparison with the other mentioned databases , biome enables queries for a multiple selection of metals and ligands . furthermore , for the purpose of getting more general picture of the metal ions distribution in different types of proteins , the pre - calculated nonredundant pdb set is also available . biome underlying database is built from the 3d structures ( pdb files ) in which the metal ions are coordinated with at least either two donor atoms from a protein chain or alternatively one donor atom from a nucleic acid chain . the purpose of these constraints is try to eliminate metals added for the crystallization purposes . for each pdb entry , we have extracted the pdb code , title , information about the method used to derive the 3d structure , resolution and the release date . distances between the metal ions and the electron donor atoms ( o , n , s , cl and f ) , as well as those between the metals ions themselves , are calculated from the atomic coordinates . in the cases where either the metal ion and/or some of its electron donors have multiple positions within the crystal structure , the position with higher occupancy was selected . in this study , we distinguish protein , rna , dna ,  other chains and water . protein chains and nucleic acid chains ( rna and dna ) are defined as chains with at least 50 amino acid residues and five nucleotides , respectively . we use the distance limit of 3   for defining the coordination bond as in ( 13 ) . this high threshold was used to account for the natural flexibility of a metal coordination sphere and for the possible coordination errors in structure determination . a metal coordination number was calculated by summing the number of all electronegative atoms within the 3   range ( o , n , s , cl and f ) . the calculation of the coordination geometry ( 14 ) is based on the geometrical pattern of the coordinating atoms l1 , l2 ,    ,  ln , which is described by the list w of all bond angles around the metal ion m sorted in ascending order : 
  in the same way , a set of angle lists of ideal coordination geometries was developed . the root mean square deviation ( rmsd ) is calculated between the angle list of the particular metal ion and each of the ideal geometry lists of the same length . the list that shows smallest rmsd is used as the best fitting coordination geometry ( 16 ) . currently , the web server calculates 22 different geometries for coordination numbers ranging from 4 to 14 . table 1.coordination geometries used in biome web servercoordination numbergeometry4tetrahedron4square planar5trigonal bipyramid5square pyramid ( tetragonal bipyramid)6octahedron6trigonal prism7octahedron , face capped7trigonal prism , square face monocapped7pentagonal bipyramid8dodecahedron ( bisdisphenoid)8cube8hexagonal bipyramid8trigonal prism , square face bicapped8square antiprism8trigonal prism , triangular face bicapped9square antiprism , monocapped9trigonal prism , square face tricapped10square antiprism , bicapped12cuboctahedron12anticuboctahedron12icosahedron14hexagonal antiprism , bicapped coordination geometries used in biome web server although in our previous work ( 13 ) , we used only a set of most representative metals , in this study , we have taken into account all the metals found in the pdb structures . after parsing the whole pdb , we found 20  307 files with structures that satisfied our conditions . among those , there are 43  326 protein chains , 650 dna chains and 734 rna chains . hence , for the purpose of getting an unbiased picture of the metal ions distribution in proteins , the list of metals in the nonredundant , representative selection of structures is also available . the representative set of the protein chains and the corresponding pdb files was extracted from the pdb ( april 2012 ) according to a pre - calculated nonredundant set of , we chose the best - ranked chain and checked whether it contains a metal cation that satisfies defined conditions . if such a metal was not found in the best ranked chain , we chose the second one on the list and repeated the procedure recursively until we found a structure with a bound metal ion or reached the end of the list . the database is implemented with mysql on a gentoo linux operating system ( intel core2 quad cpu q6600 at 2.40  ghz , 4 gb ) . the main purpose of the user interface is to create a query and to present the results ( statistics ) in an appropriate form . the starting page offers a large number of options , so users can easily tailor their queries . they can refine their search by type of the metal ions , the structure determination method ( x - ray crystallography , nmr or both ) and resolution , by the type of chain and combination of ligands , by the coordination number , maximum rmsd for a metal coordination geometry ( the default value is 15 ) and by the threshold distance between the selected metal ions . the search can be performed on the prepared list of all pdbs that fulfilled the requirements ( metal ions with at least two donor atoms from a protein chain or at least one from a nucleic acid chain ) and/or on the representative cluster-70 list . currently , users can select up to 25 most representative kinds of ions ( mg , zn , ca , fe , na , mn , k , sr , cu , cd , ni , hg , co , w , os , mo , ba , al , tl , au , pt , pb , v , yb and sm ) . however , using the publicly available database dump , users can perform search for any metal available in the pdb . biome distinguishes between five different types of ligands : amino acid residues , rna and dna nucleotides , water and  others. in the output statistics , ligands belonging to the first four types are presented with their names , whereas those from the last group are presented just as others. we found that using the original names from pdb files for the last group of ligands introduces a poorly legible graphical representation of the results , especially when the search is performed for a large number of structures . therefore , the results for them are available on a separate page that can be accessed by  other list button . among the available results , we distinguish between two types of statistics : statistics associated with the selected metals and statistics associated with the selected amino acids and nucleotides . for each metal , seven statistics are available ( i ) relative presence of selected ligands in the metal coordination sphere , ( ii ) relative distribution of the coordination numbers , ( iii ) percentage of metal ions with the selected coordination number coordinated by combination of selected ligands , ( iv ) distribution of monodentate and bidentate metal - carboxyl bindings for asp and glu , ( v ) number of particular binuclear metal centers , ( vi ) distribution of coordination geometries and ( vii ) average distances and standard deviations for selected metal and donor atoms . the last statistics , statistics 8 , is performed if more than one metal is selected . for each metal ion , it gives information on how often it is coordinated with each of the selected ligands . with the exception of statistics 3 and statistics 7 , all the remaining statistics are presented numerically and graphically . , the query includes mg ions in any coordination number bound to any type of rna nucleotide ( in the rna chain ) . as can be seen from figure 1 , mg is mostly bound to g , followed by a and c and u base . concurrent binding to g and a corresponds to binding to the shared g a pairs , as described in stefan et al . figure 1.a screenshot displaying results of statistics number 1 showing the number of each type of rna nucleotide that binds to mg . a screenshot displaying results of statistics number 1 showing the number of each type of rna nucleotide that binds to mg . examples of the outputs for statistics 3 , 4 and 5 are presented in figures 2 , 3 and 4 , respectively . the query specified zn as a metal of interest , asp and glu amino acid residues as ligand types , protein as a chain type , 4 as a desired coordination number and the entire database as a set of structures to be searched . figure 2.a screenshot displaying results of statistics number 3 showing the number of the zn ions with the coordination number 4 coordinated by the given combination of ligands . in the query , the following selections were made : entire pdb , zn , asp and glu amino acid residues , protein chain type and coordination number 4 . figure 3.a screen shot of statistic number 4 ( distribution of monodentate and bidentate metal - carboxyl bindings for asp and glu ) obtained from a query that included all available pdb structures , zn atom , asp and glu amino acid residues , protein chain type and coordination number 4 . figure 4.a screenshot displaying results of statistics number 5 which revealing the number of binuclear metal centers containing the zn ion together with the percentage of metals that together with the zinc dication form a binuclear metal center . in the query , the following selections were made : entire pdb , zn , asp and glu amino acid residues , protein chain type and coordination number 4 . a screenshot displaying results of statistics number 3 showing the number of the zn ions with the coordination number 4 coordinated by the given combination of ligands . in the query , the following selections were made : entire pdb , zn , asp and glu amino acid residues , protein chain type and coordination number 4 . a screen shot of statistic number 4 ( distribution of monodentate and bidentate metal - carboxyl bindings for asp and glu ) obtained from a query that included all available pdb structures , zn atom , asp and glu amino acid residues , protein chain type and coordination number 4 . a screenshot displaying results of statistics number 5 which revealing the number of binuclear metal centers containing the zn ion together with the percentage of metals that together with the zinc dication form a binuclear metal center . in the query , the following selections were made : entire pdb , zn , asp and glu amino acid residues , protein chain type and coordination number 4 . the statistics 4 classifies the carboxyl binding as monodentate , in the case where only one of its o atoms participates in the coordination of a particular metal ion and bidentate in the case where both oxygen atoms are involved in the metal coordination . for the purpose of further processing , furthermore , for each of the statistics , there is a list of pdb files that satisfy the query with links to their entries in pdb . the dump of the underlying database is publicly available in a separate window that can be accessed from the starting page , and it gives users the opportunity to perform their own analysis . the user interface was built as a web application using gwt development toolkit ( http://code.google.com/webtoolkit/ ) . the statistics obtained using the presented databases may help in the identification and modeling of the metal - binding sites in the protein structures derived by homology modeling and in design of proteins with a specific affinity for a certain metal ( so - called metal biosorbents ) with potential application in the environmental chemistry . carefully designed and performed statistics could provide a clue about which metal ion and/or environment would be the best choice for a certain reaction . thus , it should also help to improve catalytic performances of existing and aid the design of new ones . the website allows scientists to perform a number of different searches and to obtain useful information about the selected metal ions in biological macromolecules and their ligands . users can choose to retrieve information from all structures available in pdb , from a nonredundant set of protein chains or from their own list of structures . the search can be performed either for proteins or nucleic acids , rnas and dnas or both . for each selection , information about the coordination numbers , distances , percentage of monodentately and bidentately bound asp and glu carboxyl groups , percentage of metal ions with selected coordination number coordinated by combination of selected ligands , coordination geometry and population of particular binuclear metal centers users can retrieve . we believe that biome will prove a valuable tool for all research related to metal ions in proteins and nucleic acids . ministry of education science and sports of the republic of croatia [ 098 - 1191344 - 2860 to s.t . and m. . ] and [ 036 - 0362214 - 1987 to m. . ] ; biomedical research council of a*star , singapore to m. . funding for open access charge : biomedical research council of a*star , singapore .
in this article , we introduce biome ( biologically relevant metals ) , a web - based platform for calculation of various statistical properties of metal - binding sites . 
 users can obtain the following statistical properties : presence of selected ligands in metal coordination sphere , distribution of coordination numbers , percentage of metal ions coordinated by the combination of selected ligands , distribution of monodentate and bidentate metal - carboxyl , bindings for asp and glu , percentage of particular binuclear metal centers , distribution of coordination geometry , descriptive statistics for a metal ion 
 donor distance and percentage of the selected metal ions coordinated by each of the selected ligands . 
 statistics is presented in numerical and graphical forms . 
 the underlying database contains information about all contacts within the range of 3   from a metal ion found in the asymmetric crystal unit . 
 the stored information for each metal ion includes protein data bank code , structure determination method , types of metal - binding chains [ protein , ribonucleic acid ( rna ) , deoxyribonucleic acid ( dna ) , water and other ] and names of the bounded ligands ( amino acid residue , rna nucleotide , dna nucleotide , water and other ) and the coordination number , the coordination geometry and , if applicable , another metal(s ) . 
 biome is on a regular weekly update schedule . 
 it is accessible at http://metals.zesoi.fer.hr .