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Cobalt in PDB 8dyj: Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin

Enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin

All present enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin:
5.4.99.2;

Protein crystallography data

The structure of Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin, PDB code: 8dyj was solved by R.N.Mascarenhas, H.Gouda, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.11 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 61.025, 129.358, 188.422, 90, 90, 90
R / Rfree (%) 19.5 / 22.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin (pdb code 8dyj). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin, PDB code: 8dyj:

Cobalt binding site 1 out of 1 in 8dyj

Go back to Cobalt Binding Sites List in 8dyj
Cobalt binding site 1 out of 1 in the Crystal Structure of Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin


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 Human Methylmalonyl-Coa Mutase in Complex with Adp and Cob(II)Alamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co801

b:47.2
occ:1.00
 CO B:B12801 0.0 47.2 1.0
N23 B:B12801 1.8 46.8 1.0
N21 B:B12801 1.9 45.7 1.0
N24 B:B12801 1.9 47.2 1.0
N22 B:B12801 1.9 47.7 1.0
NE2 B:HIS590 2.3 52.5 1.0
C9 B:B12801 2.8 47.8 1.0
C11 B:B12801 2.8 47.3 1.0
C1 B:B12801 2.9 47.3 1.0
C19 B:B12801 2.9 47.1 1.0
C4 B:B12801 2.9 46.6 1.0
C14 B:B12801 2.9 46.9 1.0
C16 B:B12801 2.9 44.8 1.0
C6 B:B12801 3.0 49.1 1.0
CD2 B:HIS590 3.1 50.5 1.0
C10 B:B12801 3.2 48.2 1.0
CE1 B:HIS590 3.3 51.1 1.0
C5 B:B12801 3.3 47.1 1.0
C15 B:B12801 3.4 45.4 1.0
C20 B:B12801 3.6 49.1 1.0
O3' B:ADP802 3.8 59.4 1.0
C3' B:ADP802 4.0 58.3 1.0
C2 B:B12801 4.1 43.2 1.0
C18 B:B12801 4.1 47.7 1.0
C13 B:B12801 4.1 48.5 1.0
C12 B:B12801 4.2 45.5 1.0
C3 B:B12801 4.2 46.1 1.0
C17 B:B12801 4.2 45.3 1.0
C8 B:B12801 4.2 46.5 1.0
C5' B:ADP802 4.2 60.1 1.0
C7 B:B12801 4.3 49.6 1.0
CG B:HIS590 4.3 50.4 1.0
ND1 B:HIS590 4.4 51.3 1.0
C26 B:B12801 4.5 46.5 1.0
C42 B:B12801 4.7 48.7 1.0
C4' B:ADP802 4.7 57.8 1.0
C48 B:B12801 4.7 49.8 1.0
C54 B:B12801 4.7 40.6 1.0
C46 B:B12801 4.7 44.9 1.0
C35 B:B12801 4.9 48.8 1.0
O B:HOH904 4.9 71.5 1.0
O5' B:ADP802 4.9 63.0 1.0
C53 B:B12801 4.9 47.7 1.0

Reference:

H.Gouda, R.Mascarenhas, M.Ruetz, M.Yaw, R.Banerjee. Allosteric Control of Metal Redox State Regulates Coenzyme B12 Repair To Be Published.
Page generated: Sun Jul 13 21:55:21 2025

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