Cobalt in PDB 6oxc: Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin

Enzymatic activity of Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin

All present enzymatic activity of Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin:
5.4.99.2;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin, PDB code: 6oxc was solved by M.Purchal, M.Ruetz, R.Banerjee, M.Koutmos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.802, 103.561, 211.197, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin (pdb code 6oxc). 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 Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin, PDB code: 6oxc:

Cobalt binding site 1 out of 1 in 6oxc

Go back to Cobalt Binding Sites List in 6oxc
Cobalt binding site 1 out of 1 in the Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Mycobacterium Tuberculosis Methylmalonyl-Coa Mutase with Adenosyl Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1000

b:18.4
occ:1.00
 CO A:B121000 0.0 18.4 1.0
H5'1 A:5AD1001 1.9 34.9 1.0
N23 A:B121000 1.9 16.2 1.0
N21 A:B121000 1.9 16.8 1.0
N24 A:B121000 1.9 21.0 1.0
N22 A:B121000 1.9 20.6 1.0
NE2 A:HIS629 2.3 19.2 1.0
H5'3 A:5AD1001 2.5 34.9 1.0
C5' A:5AD1001 2.5 29.1 1.0
C19 A:B121000 2.8 21.9 1.0
C1 A:B121000 2.9 19.6 1.0
C14 A:B121000 2.9 16.5 1.0
C11 A:B121000 2.9 20.7 1.0
C4 A:B121000 2.9 18.2 1.0
C9 A:B121000 2.9 22.9 1.0
C6 A:B121000 3.0 19.6 1.0
C16 A:B121000 3.0 17.4 1.0
H4' A:5AD1001 3.0 37.2 1.0
H201 A:B121000 3.0 20.3 1.0
CE1 A:HIS629 3.2 21.3 1.0
C4' A:5AD1001 3.2 31.0 1.0
CD2 A:HIS629 3.3 19.3 1.0
C10 A:B121000 3.3 17.2 1.0
HE1 A:HIS629 3.3 25.6 1.0
H5'2 A:5AD1001 3.3 34.9 1.0
C5 A:B121000 3.4 20.9 1.0
C15 A:B121000 3.4 20.9 1.0
C20 A:B121000 3.5 16.9 1.0
HD2 A:HIS629 3.5 23.1 1.0
O4' A:5AD1001 3.7 33.5 1.0
H202 A:B121000 3.9 20.3 1.0
H261 A:B121000 4.1 23.9 1.0
C2 A:B121000 4.1 22.5 1.0
C13 A:B121000 4.1 18.9 1.0
H421 A:B121000 4.1 27.9 1.0
C18 A:B121000 4.2 17.5 1.0
C3 A:B121000 4.2 19.4 1.0
H463 A:B121000 4.2 21.4 1.0
C12 A:B121000 4.2 19.8 1.0
C8 A:B121000 4.3 22.2 1.0
C17 A:B121000 4.3 17.9 1.0
C7 A:B121000 4.3 22.0 1.0
ND1 A:HIS629 4.3 17.9 1.0
H203 A:B121000 4.3 20.3 1.0
H10 A:B121000 4.4 20.7 1.0
CG A:HIS629 4.4 24.9 1.0
H543 A:B121000 4.4 24.7 1.0
H482 A:B121000 4.6 21.4 1.0
H481 A:B121000 4.6 21.4 1.0
C26 A:B121000 4.6 20.0 1.0
C3' A:5AD1001 4.7 31.5 1.0
C48 A:B121000 4.8 17.9 1.0
H3' A:5AD1001 4.8 37.8 1.0
C46 A:B121000 4.8 17.8 1.0
H422 A:B121000 4.8 27.9 1.0
H561 A:B121000 4.8 18.3 1.0
H3 A:B121000 4.8 23.3 1.0
H371 A:B121000 4.9 28.1 1.0
C35 A:B121000 4.9 27.5 1.0
C54 A:B121000 4.9 20.6 1.0
C42 A:B121000 4.9 23.3 1.0
C53 A:B121000 4.9 17.7 1.0
H262 A:B121000 4.9 23.9 1.0
H8 A:B121000 4.9 26.7 1.0
H13 A:B121000 5.0 22.7 1.0

Reference:

M.Ruetz, G.C.Campanello, M.Purchal, H.Shen, L.Mcdevitt, H.Gouda, S.Wakabayashi, J.Zhu, E.J.Rubin, K.Warncke, V.K.Mootha, M.Koutmos, R.Banerjee. Itaconyl-Coa Forms A Stable Biradical in Methylmalonyl-Coa Mutase and Derails Its Activity and Repair. Science V. 366 589 2019.
ISSN: ESSN 1095-9203
PubMed: 31672889
DOI: 10.1126/SCIENCE.AAY0934
Page generated: Sun Dec 13 10:51:25 2020

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