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Cobalt in PDB 1cb7: Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin

Enzymatic activity of Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin

All present enzymatic activity of Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin:
5.4.99.1;

Protein crystallography data

The structure of Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin, PDB code: 1cb7 was solved by K.Gruber, R.Reitzer, C.Kratky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.330, 113.140, 108.610, 90.00, 95.62, 90.00
R / Rfree (%) 16 / 21.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin (pdb code 1cb7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin, PDB code: 1cb7:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1cb7

Go back to Cobalt Binding Sites List in 1cb7
Cobalt binding site 1 out of 2 in the Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co800

b:11.6
occ:1.00
CO A:COB800 0.0 11.6 1.0
N21 A:COB800 1.9 9.5 1.0
N24 A:COB800 1.9 8.7 1.0
N23 A:COB800 1.9 10.7 1.0
N22 A:COB800 1.9 9.9 1.0
C1A A:COB800 2.0 11.1 0.7
NE2 A:HIS16 2.3 16.1 1.0
C19 A:COB800 2.8 9.3 1.0
C9 A:COB800 2.8 9.6 1.0
C1 A:COB800 2.9 12.2 1.0
C11 A:COB800 2.9 11.8 1.0
C4 A:COB800 2.9 10.8 1.0
C14 A:COB800 2.9 11.2 1.0
C16 A:COB800 2.9 10.9 1.0
C6 A:COB800 3.0 10.3 1.0
CE1 A:HIS16 3.2 13.9 1.0
C10 A:COB800 3.2 14.3 1.0
C5 A:COB800 3.3 9.4 1.0
C15 A:COB800 3.4 8.4 1.0
C1A A:COB800 3.4 11.1 0.4
CD2 A:HIS16 3.4 14.4 1.0
C20 A:COB800 3.6 10.9 1.0
C18 A:COB800 4.1 9.0 1.0
C2 A:COB800 4.1 13.2 1.0
C3 A:COB800 4.1 11.7 1.0
C8 A:COB800 4.2 8.7 1.0
C13 A:COB800 4.2 11.4 1.0
C17 A:COB800 4.2 9.2 1.0
C12 A:COB800 4.2 12.4 1.0
C7 A:COB800 4.2 12.8 1.0
ND1 A:HIS16 4.4 14.5 1.0
O A:HOH863 4.4 39.2 1.0
C26 A:COB800 4.5 15.4 1.0
CG A:HIS16 4.5 13.7 1.0
C37 A:COB800 4.6 16.6 1.0
O39 A:COB800 4.7 18.3 1.0
C48 A:COB800 4.8 13.5 1.0
C53 A:COB800 4.9 9.2 1.0
C46 A:COB800 4.9 7.5 1.0
C35 A:COB800 4.9 15.3 1.0
O B:HOH942 4.9 11.6 1.0
C54 A:COB800 4.9 12.1 1.0
C41 A:COB800 4.9 12.4 1.0

Cobalt binding site 2 out of 2 in 1cb7

Go back to Cobalt Binding Sites List in 1cb7
Cobalt binding site 2 out of 2 in the Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Glutamate Mutase From Clostridium Cochlearium Reconstituted with Methyl-Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co800

b:12.4
occ:1.00
CO C:COB800 0.0 12.4 1.0
N21 C:COB800 1.9 8.7 1.0
N24 C:COB800 1.9 9.3 1.0
N23 C:COB800 1.9 9.3 1.0
N22 C:COB800 1.9 10.3 1.0
C1A C:COB800 2.0 11.1 0.7
NE2 C:HIS16 2.3 15.9 1.0
C19 C:COB800 2.8 8.5 1.0
C9 C:COB800 2.8 9.7 1.0
C11 C:COB800 2.9 12.0 1.0
C1 C:COB800 2.9 11.2 1.0
C4 C:COB800 2.9 10.6 1.0
C14 C:COB800 2.9 9.6 1.0
C16 C:COB800 2.9 9.9 1.0
C6 C:COB800 3.0 10.9 1.0
C10 C:COB800 3.2 12.3 1.0
CE1 C:HIS16 3.2 20.2 1.0
C5 C:COB800 3.3 9.6 1.0
C15 C:COB800 3.3 8.1 1.0
C1A C:COB800 3.4 11.1 0.4
CD2 C:HIS16 3.4 13.6 1.0
C20 C:COB800 3.6 10.3 1.0
C2 C:COB800 4.1 12.8 1.0
C18 C:COB800 4.1 10.0 1.0
C8 C:COB800 4.1 10.3 1.0
C3 C:COB800 4.2 11.4 1.0
C13 C:COB800 4.2 10.9 1.0
C12 C:COB800 4.2 10.4 1.0
C7 C:COB800 4.2 13.9 1.0
C17 C:COB800 4.2 10.3 1.0
ND1 C:HIS16 4.4 16.9 1.0
C26 C:COB800 4.5 14.5 1.0
CG C:HIS16 4.5 14.1 1.0
C37 C:COB800 4.6 15.9 1.0
O39 C:COB800 4.6 18.8 1.0
O C:HOH826 4.7 25.7 1.0
C48 C:COB800 4.8 14.1 1.0
C46 C:COB800 4.8 7.2 1.0
C53 C:COB800 4.8 8.3 1.0
C35 C:COB800 4.9 15.3 1.0
C54 C:COB800 4.9 13.1 1.0
C38 C:COB800 4.9 20.4 1.0
C41 C:COB800 4.9 12.8 1.0
O D:HOH927 4.9 12.2 1.0

Reference:

R.Reitzer, K.Gruber, G.Jogl, U.G.Wagner, H.Bothe, W.Buckel, C.Kratky. Glutamate Mutase From Clostridium Cochlearium: the Structure of A Coenzyme B12-Dependent Enzyme Provides New Mechanistic Insights. Structure Fold.Des. V. 7 891 1999.
ISSN: ISSN 0969-2126
PubMed: 10467146
DOI: 10.1016/S0969-2126(99)80116-6
Page generated: Sun Dec 13 10:34:23 2020

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