Cobalt in PDB 3nvl: Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei

All present enzymatic activity of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei:
5.4.2.1;

The structure of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei, PDB code: 3nvl was solved by G.F.Mercaldi, H.M.Pereira, A.T.Cordeiro, A.D.Andricopulo, O.H.Thiemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.55 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.670, 85.660, 109.110, 90.00, 102.20, 90.00
R / Rfree (%)	16.6 / 21.7

The binding sites of Cobalt atom in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei (pdb code 3nvl). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei, PDB code: 3nvl:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Co553 b:23.4 occ:1.00 OD1 A:ASP22 1.9 26.6 1.0 OD2 A:ASP465 2.1 21.5 1.0 OG A:SER74 2.2 33.3 1.0 NE2 A:HIS466 2.2 28.6 1.0 CG A:ASP22 2.6 31.2 1.0 OD2 A:ASP22 2.7 35.9 1.0 CD2 A:HIS466 2.8 23.6 1.0 CG A:ASP465 2.9 30.2 1.0 OD1 A:ASP465 3.0 31.4 1.0 CB A:SER74 3.2 32.1 1.0 CA A:SER74 3.3 27.1 1.0 CE1 A:HIS466 3.4 27.7 1.0 NZ A:LYS356 3.6 29.4 1.0 N A:SER74 3.6 22.7 1.0 O A:HOH695 3.9 29.5 1.0 CG A:HIS466 4.0 22.6 1.0 OD2 A:ASP424 4.0 29.7 1.0 CB A:ASP22 4.0 25.9 1.0 CG A:ASP424 4.1 31.8 1.0 N A:GLY23 4.2 29.2 1.0 ND1 A:HIS466 4.2 23.6 1.0 CB A:ASP465 4.3 27.7 1.0 CE A:LYS356 4.3 26.2 1.0 C A:ASN73 4.4 22.1 1.0 OD1 A:ASP424 4.4 30.1 1.0 CA A:ASP22 4.4 28.4 1.0 CB A:ASP424 4.6 30.2 1.0 CE1 A:HIS78 4.6 18.8 1.0 C A:ASP22 4.7 27.9 1.0 C A:SER74 4.8 25.0 1.0 CO A:CO554 4.8 29.7 1.0 O A:ASN73 4.8 25.3 1.0 CA A:GLY23 5.0 32.0 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ A:Co554 b:29.7 occ:1.00 NE2 A:HIS428 2.1 19.2 1.0 NE2 A:HIS495 2.2 31.8 1.0 OD2 A:ASP424 2.3 29.7 1.0 OD2 A:ASP319 2.6 53.9 1.0 O A:HOH695 2.6 29.5 1.0 OD1 A:ASP319 2.8 53.4 1.0 OD1 A:ASP424 2.8 30.1 1.0 CG A:ASP424 2.9 31.8 1.0 CE1 A:HIS428 2.9 23.5 1.0 CG A:ASP319 3.0 49.6 1.0 CE1 A:HIS495 3.1 30.4 1.0 CD2 A:HIS428 3.2 23.7 1.0 CD2 A:HIS495 3.2 31.3 1.0 NZ A:LYS356 4.1 29.4 1.0 ND1 A:HIS428 4.1 24.6 1.0 CE1 A:HIS466 4.1 27.7 1.0 NE2 A:HIS466 4.2 28.6 1.0 ND1 A:HIS495 4.2 34.6 1.0 CG A:HIS428 4.2 25.0 1.0 OG A:SER74 4.3 33.3 1.0 CG A:HIS495 4.3 35.9 1.0 CB A:ASP424 4.4 30.2 1.0 CB A:ASP319 4.4 44.5 1.0 ND2 A:ASN468 4.5 24.4 1.0 O A:HOH680 4.7 51.9 1.0 O A:HOH597 4.7 45.6 1.0 O A:HOH694 4.8 30.0 1.0 CO A:CO553 4.8 23.4 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Co553 b:27.5 occ:1.00 OG B:SER74 2.0 23.2 1.0 OD1 B:ASP22 2.0 25.0 1.0 OD1 B:ASP465 2.0 25.9 1.0 NE2 B:HIS466 2.2 18.4 1.0 CG B:ASP22 2.6 25.2 1.0 OD2 B:ASP22 2.7 26.5 1.0 CG B:ASP465 2.8 27.1 1.0 CD2 B:HIS466 2.9 21.2 1.0 CB B:SER74 3.0 22.8 1.0 OD2 B:ASP465 3.0 24.7 1.0 CA B:SER74 3.2 28.5 1.0 CE1 B:HIS466 3.3 22.6 1.0 N B:SER74 3.5 30.5 1.0 NZ B:LYS356 3.7 28.6 1.0 OD2 B:ASP424 4.0 37.7 1.0 CG B:HIS466 4.1 24.0 1.0 CB B:ASP22 4.1 18.2 1.0 CG B:ASP424 4.2 36.6 1.0 ND1 B:HIS466 4.2 26.8 1.0 CB B:ASP465 4.2 25.6 1.0 N B:GLY23 4.3 26.2 1.0 C B:ASN73 4.4 30.7 1.0 CE B:LYS356 4.4 28.7 1.0 CA B:ASP22 4.5 25.7 1.0 CE1 B:HIS78 4.6 29.3 1.0 C B:SER74 4.6 30.9 1.0 CB B:ASP424 4.6 35.6 1.0 OD1 B:ASP424 4.6 31.0 1.0 C B:ASP22 4.8 27.2 1.0 O B:ASN73 4.9 33.5 1.0 CD B:LYS356 4.9 29.0 1.0 ND1 B:HIS78 4.9 26.5 1.0 CO B:CO554 4.9 35.1 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei within 5.0Å range: probe atom residue distance (Å) B Occ B:Co554 b:35.1 occ:1.00 OD2 B:ASP424 2.1 37.7 1.0 NE2 B:HIS428 2.1 29.9 1.0 NE2 B:HIS495 2.1 31.7 1.0 OD1 B:ASP319 2.5 49.9 1.0 OD2 B:ASP319 2.5 52.5 1.0 CG B:ASP319 2.7 50.5 1.0 CG B:ASP424 2.8 36.6 1.0 OD1 B:ASP424 2.9 31.0 1.0 CE1 B:HIS495 3.0 33.3 1.0 CD2 B:HIS428 3.1 29.4 1.0 CE1 B:HIS428 3.1 33.4 1.0 CD2 B:HIS495 3.2 30.4 1.0 O B:HOH612 4.0 55.4 1.0 NZ B:LYS356 4.0 28.6 1.0 CB B:ASP319 4.2 48.9 1.0 ND1 B:HIS495 4.2 37.6 1.0 ND1 B:HIS428 4.2 36.5 1.0 CG B:HIS428 4.2 25.4 1.0 O B:HOH619 4.2 62.5 1.0 CB B:ASP424 4.3 35.6 1.0 CG B:HIS495 4.3 31.3 1.0 CE1 B:HIS466 4.3 22.6 1.0 NE2 B:HIS466 4.4 18.4 1.0 OG B:SER74 4.4 23.2 1.0 ND2 B:ASN468 4.7 22.3 1.0 O B:ASP424 4.9 31.9 1.0 O B:HOH648 4.9 30.0 1.0 CO B:CO553 4.9 27.5 1.0

G.F.Mercaldi, H.M.Pereira, A.T.Cordeiro, P.A.Michels, O.H.Thiemann. Crystal Structure of Phosphoglycerate Mutase From Trypanosoma Brucei. Febs J. V. 279 2012 2012.
ISSN: ISSN 1742-464X
PubMed: 22458781
DOI: 10.1111/J.1742-4658.2012.08586.X