QUICK GUIDE TO CHARACTERISTICS OF METAL SITES IN PROTEINS

metal	Na sodium	Mg ** magnesium	K potassium	Ca calcium	Mn manganese
atomic no. (= no. of electrons)	11	12	19	20	25
usual ion	Na+	Mg^2+	K^+	Ca^2+	Mn^2+ (Mn^3+)
usual donor atoms^1 (for more detail see )	O m.chain O of asp,glu	O of asp,glu O m.chain	O m.chain O of asp,glu,	O of asp,glu, O m.chain	O of asp,glu N of his
other donors sometimes found (and occasionally found)	O of ser,thr O of asn,gln (N of his)	O of ser,thr O of asn,gln N of his	O of ser,thr O of asn,gln (N of his)	O of asn,gln O of ser,thr (N of his)	O m.chain O of asn,gln O of ser,thr
usual coordination number(s)^2	5,6	6	5,6	6	5,6
other coordination numbers^3	4,7	3,4,5	4,7,8	4,5,7,8	4,7
typical^4 distance Å) M-O more info M-N M-S	2.35-2.45 ..... .....	2.05-2.15 ..... .....	2.75-2.85 ?+ ..... .....	2.35-2.45 ...... ......	2.15-2.20 2.21 2.35
relative abundance^5 in PDB	96	177	72	358	109
link to lists of examples^6	Na groups	Mg groups	K groups	Ca groups	Mn groups

** chlorophyll groups, containing Mg, are common, but not included here

metal	Fe *** iron	Co cobalt	Ni nickel	Cu copper	Zn zinc
atomic no. (= no. of electrons)	26	27	28	29	30
usual ion (s)	Fe^2+, Fe^3+	Co^2+ (Co^3+)	Ni^2+	Cu^2 + (Cu^+)	Zn^2+
usual donor atoms^1 (for more detail see)	N of his, O fo asp,glu	O of asp,glu N of his	N of his O if asp,glu	N of cys S of cys	N of his S of cys O of asp,glu
other donors sometimes found (and very occasionally found)	S of cys	O of ser,thr O m.chain (S of cys)	S of cys O m.chain	O of asp,glu (O m.chain) (O asn,gln)	O m.chain O of asn,gln (O of ser,thr)
usual coordination number(s)^2	5,6	6	6	3,4	4
other coordination numbers^3	4	4,5	4,5	5,6	3,5,6
typical^4 distance (Å) M-O more info M-N M-S	2.04-2.09 2.16 2.30	2.04-2.09 2.14 2.25		2.00 but see^4 2.02 2.15	2.00-2.10 2.03 2.31
relative abundance^5 in PDB	55	30	30	58	309
link to lists of sites^6	Fe groups	Co groups	Ni groups	Cu groups	Zn groups

*** Haem groups, containing Fe, are very common, and Fe/S clusters are common; neither are included here.

metal see note 7	V vanadium	Mo molybdenum
atomic no. (= no. of electrons)	23	42
usual forms	VO4^3- or polymeric	within cofactors, linked to S, e.g. Fe7MoS9 , or to O.
typical distance (Å) M-O in MO4^2-	1.6 (up to 1.8 bridging)	1.7 (1.9 bridging)
relative abundance^5 in PDB	(very low)	(low)

Notes:

1. Donor group preferences (relative frequencies) are given below.

m.chain signifies main chain carbonyl oxygen.

2. Coordination number is total number of donor atoms within bonding distance around metal. Ideal stereochemistry for coordination numbers 6 is octahedral, for 5 is trigonal bipyramidal or square pyramidal, and for 4 normally tetrahedral, but square planar for Cu and possibly Ni. In real metalloproteins it may be substantially distorted from these ideals. For coordinaiton numbers 7 and 8 (as for 5 and 6) the main consideration is an even distribution of the donor atoms in the space around the metal ion.

For each metal, tables summarising the frequency of different coordination numbers, donor groups, etc are available.

3. Lower coordination numbers may be reported when water molecules have not been identified in the metal coordination sphere.

4. True distances are not likely to be more than 0.10Å from this - but experimental error in determining distances from a medium resolution electron density map can be much more. Further information .

5. Number of metal sites in a representative set of proteins in the PDB at September 2003. In these the metal is bound to one or more atoms of a protein molecule; sites with disorder are excluded, and so are redundant copies when there are two or more protein molecules in the crystal asymmetric unit.

6. For explanation of tables of metal sites.

7. Because these metals (V, Mo) are usually present in anionic forms, and often in association with cofactors, their interaction with the protein structure and its amino-acid side chains is quite different from the other metals for which information is assembled and tabulated above. The M-O distances given are from the Cambridge Structural Database (CSD).

Donor group preferences and relative frequencies:

Numbers of different kinds of donor groups (amino-acid side chains, main chain carbonyl oxygen) found in representative structures in the PDB (to Oct 2003) with different metals, and within chemical bonding distance plus a tolerance of 0.75Å . For Na,K the interactions are almost entirely electrostatic, but the geometry is relevant. For Fe**, only the metal sites which are not haem groups or Fe/S clusters are included. Disordered groups and redundant groups are excluded.

	Na	Mg	K	Ca	Mn	Fe**	Co	Ni	Cu	Zn
D,E	52	245	70	722	212	60	44	20	9	254
N,Q	14	33	30	134	19	1	1	1	2	13
S,T	19	64	44	61	10	0	4	0	0	7
Om.ch.	200	108	297	545	22	0	3	4	3	19
H	8	23	3	8	64	93	37	44	122	362
C	0	0	0	0	1	22	2	8	30	282

(distance information updated Jan 2008)

back to main page