Cobalt in PDB 3igz: Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration

All present enzymatic activity of Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration:
5.4.2.1;

The structure of Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration, PDB code: 3igz was solved by M.W.Nowicki, B.Kuaprasert, I.W.Mcnae, H.P.Morgan, M.M.Harding, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.464, 72.267, 129.678, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.3

The structure of Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration (pdb code 3igz). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration, PDB code: 3igz:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration within 5.0Å range: probe atom residue distance (Å) B Occ B:Co562 b:5.3 occ:1.00 O2P B:3PG564 2.0 6.1 0.5 O2P B:2PG565 2.0 6.1 0.5 OD1 B:ASP425 2.0 6.6 1.0 NE2 B:HIS429 2.1 5.7 1.0 NE2 B:HIS496 2.1 4.0 1.0 O1P B:3PG564 2.6 7.7 0.5 O1P B:2PG565 2.7 7.6 0.5 CG B:ASP425 2.7 11.0 1.0 OD2 B:ASP425 2.7 7.6 1.0 P B:3PG564 2.9 5.1 0.5 P B:2PG565 3.0 5.0 0.5 CD2 B:HIS429 3.0 5.3 1.0 CD2 B:HIS496 3.1 3.2 1.0 CE1 B:HIS496 3.1 4.9 1.0 CE1 B:HIS429 3.1 3.5 1.0 O B:HOH624 3.6 4.5 1.0 CE1 B:HIS467 3.6 9.8 1.0 C3 B:3PG564 3.7 5.2 0.5 O4P B:2PG565 3.8 3.7 0.5 O4P B:3PG564 3.9 3.7 0.5 C2 B:2PG565 3.9 6.4 0.5 NE2 B:HIS467 4.0 11.8 1.0 O3P B:3PG564 4.0 5.3 0.5 ND2 B:ASN469 4.0 4.1 1.0 CB B:ASP425 4.1 6.2 1.0 ND1 B:HIS429 4.1 3.3 1.0 C3 B:2PG565 4.2 8.0 0.5 CG B:HIS429 4.2 3.3 1.0 ND1 B:HIS496 4.2 4.4 1.0 CG B:HIS496 4.2 1.9 1.0 O3P B:2PG565 4.2 6.3 0.5 NZ B:LYS357 4.3 10.4 1.0 C2 B:3PG564 4.4 7.5 0.5 CO B:CO563 4.6 9.4 0.1 OD1 B:ASP23 4.6 6.3 1.0 O2 B:2PG565 4.6 6.5 0.5 ND1 B:HIS467 4.7 8.7 1.0 OG B:SER75 4.7 4.1 0.5 O B:ASP425 4.8 5.3 1.0 C1 B:2PG565 4.8 5.7 0.5 O2 B:3PG564 4.8 5.5 0.5 CA B:ASP425 4.9 6.0 1.0 O B:HOH668 5.0 8.5 1.0 C B:ASP425 5.0 8.7 1.0 C1 B:3PG564 5.0 5.2 0.5

Cobalt binding site 2 out of 2 in the Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase at Low Cobalt Concentration within 5.0Å range: probe atom residue distance (Å) B Occ B:Co563 b:9.4 occ:0.06 OG B:SER75 1.4 4.1 0.5 OG B:SER75 1.9 6.0 0.1 NE2 B:HIS467 2.0 11.8 1.0 OD1 B:ASP23 2.2 6.3 1.0 OD1 B:ASP466 2.2 10.1 1.0 CB B:SER75 2.5 6.3 0.5 CD2 B:HIS467 2.6 5.3 1.0 CB B:SER75 2.7 6.2 0.5 CG B:ASP23 2.8 6.4 1.0 OD2 B:ASP23 2.8 9.8 1.0 OG B:SER75 2.8 9.5 0.5 CB B:SER75 2.8 6.2 0.1 O2P B:3PG564 3.0 6.1 0.5 CG B:ASP466 3.0 9.2 1.0 OD2 B:ASP466 3.1 6.5 1.0 O2P B:2PG565 3.2 6.1 0.5 CE1 B:HIS467 3.2 9.8 1.0 CA B:SER75 3.2 5.9 0.5 CA B:SER75 3.2 5.9 0.1 CA B:SER75 3.2 5.9 0.5 NZ B:LYS357 3.3 10.4 1.0 N B:SER75 3.6 3.8 0.5 N B:SER75 3.6 3.8 0.5 N B:SER75 3.6 3.8 0.1 CG B:HIS467 3.9 9.1 1.0 P B:3PG564 3.9 5.1 0.5 P B:2PG565 4.1 5.0 0.5 ND1 B:HIS467 4.1 8.7 1.0 O4P B:3PG564 4.2 3.7 0.5 CB B:ASP23 4.2 3.2 1.0 CB B:ASP466 4.4 4.9 1.0 O3P B:3PG564 4.4 5.3 0.5 O4P B:2PG565 4.4 3.7 0.5 OD1 B:ASP425 4.4 6.6 1.0 CG B:ASP425 4.4 11.0 1.0 N B:GLY24 4.4 3.9 1.0 C B:ASN74 4.5 6.4 1.0 CE B:LYS357 4.5 9.3 1.0 CE1 B:HIS79 4.6 7.2 1.0 CO B:CO562 4.6 5.3 1.0 CA B:ASP23 4.6 3.2 1.0 CD2 B:HIS360 4.6 11.4 1.0 O3P B:2PG565 4.6 6.3 0.5 C B:SER75 4.7 5.6 0.5 C B:SER75 4.7 5.6 0.5 C B:SER75 4.7 5.6 0.1 OD2 B:ASP425 4.7 7.6 1.0 ND1 B:HIS79 4.8 6.2 1.0 CB B:ASP425 4.9 6.2 1.0 C B:ASP23 4.9 4.6 1.0 CD B:LYS357 5.0 8.7 1.0

M.W.Nowicki, B.Kuaprasert, I.W.Mcnae, H.P.Morgan, M.M.Harding, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Crystal Structures of Leishmania Mexicana Phosphoglycerate Mutase Suggest A One-Metal Mechanism and A New Enzyme Subclass J.Mol.Biol. V. 394 535 2009.
ISSN: ISSN 0022-2836
PubMed: 19781556
DOI: 10.1016/J.JMB.2009.09.041