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Cobalt in PDB 6wgv: Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi

Enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi

All present enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi:
2.5.1.17;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi, PDB code: 6wgv was solved by R.N.Mascarenhas, M.Ruetz, M.Koutmos, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.68 / 2.15
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.631, 87.631, 46.554, 90, 90, 120
R / Rfree (%) 18.8 / 22.1

Other elements in 6wgv:

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi (pdb code 6wgv). 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 Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi, PDB code: 6wgv:

Cobalt binding site 1 out of 1 in 6wgv

Go back to Cobalt Binding Sites List in 6wgv
Cobalt binding site 1 out of 1 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Adenosylcobalamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:26.6
occ:1.00
CO A:B12201 0.0 26.6 1.0
N23 A:B12201 1.8 28.3 1.0
N21 A:B12201 1.9 34.6 1.0
N24 A:B12201 1.9 30.4 1.0
N22 A:B12201 1.9 30.1 1.0
H5'2 A:5AD202 2.1 51.4 1.0
HE1 A:PHE117 2.8 41.0 1.0
C11 A:B12201 2.8 27.6 1.0
C9 A:B12201 2.9 28.7 1.0
C1 A:B12201 2.9 25.8 1.0
C5' A:5AD202 2.9 42.8 1.0
C4 A:B12201 2.9 36.9 1.0
C19 A:B12201 2.9 25.9 1.0
C16 A:B12201 2.9 29.9 1.0
C14 A:B12201 2.9 27.1 1.0
C6 A:B12201 3.0 32.6 1.0
H4' A:5AD202 3.0 51.1 1.0
H5'1 A:5AD202 3.1 51.4 1.0
H201 A:B12201 3.1 30.6 1.0
C10 A:B12201 3.2 26.8 1.0
HZ A:PHE117 3.2 32.6 1.0
H91 A:B12201 3.3 31.1 1.0
C5 A:B12201 3.3 32.9 1.0
C15 A:B12201 3.4 27.8 1.0
C4' A:5AD202 3.4 42.5 1.0
C20 A:B12201 3.5 25.4 1.0
CE1 A:PHE117 3.5 34.1 1.0
H5'3 A:5AD202 3.6 51.4 1.0
H202 A:B12201 3.7 30.6 1.0
CZ A:PHE117 3.7 27.2 1.0
H261 A:B12201 4.0 46.0 1.0
O4' A:5AD202 4.1 33.6 1.0
H10 A:B12201 4.1 32.2 1.0
C18 A:B12201 4.1 37.6 1.0
C17 A:B12201 4.2 26.6 1.0
C2 A:B12201 4.2 37.1 1.0
C12 A:B12201 4.2 29.1 1.0
C3 A:B12201 4.2 34.4 1.0
C13 A:B12201 4.2 30.6 1.0
C8 A:B12201 4.2 29.5 1.0
C7 A:B12201 4.2 28.7 1.0
H371 A:B12201 4.3 36.7 1.0
H203 A:B12201 4.3 30.6 1.0
H18 A:B12201 4.4 45.2 1.0
H562 A:B12201 4.4 33.2 1.0
HM62 A:B12201 4.5 46.3 1.0
H412 A:B12201 4.5 33.8 1.0
H462 A:B12201 4.5 34.9 1.0
H491 A:B12201 4.5 36.2 1.0
C26 A:B12201 4.6 38.4 1.0
H13 A:B12201 4.7 36.7 1.0
C3' A:5AD202 4.7 39.3 1.0
H492 A:B12201 4.7 36.2 1.0
C37 A:B12201 4.8 30.5 1.0
CD1 A:PHE117 4.8 29.3 1.0
H3 A:B12201 4.8 41.2 1.0
H543 A:B12201 4.8 38.0 1.0
C35 A:B12201 4.8 29.8 1.0
C46 A:B12201 4.9 29.0 1.0
O3' A:5AD202 4.9 39.1 1.0
H8 A:B12201 4.9 35.4 1.0
C41 A:B12201 4.9 28.1 1.0
H372 A:B12201 4.9 36.7 1.0
C53 A:B12201 4.9 24.2 1.0
C54 A:B12201 4.9 31.7 1.0
H541 A:B12201 4.9 38.0 1.0
HO3' A:5AD202 5.0 46.9 1.0
HH22 A:ARG137 5.0 38.3 1.0

Reference:

R.Mascarenhas, M.Ruetz, L.Mcdevitt, M.Koutmos, R.Banerjee. Mobile Loop Dynamics in Adenosyltransferase Control Binding and Reactivity of Coenzyme B 12 . Proc.Natl.Acad.Sci.Usa V. 117 30412 2020.
ISSN: ESSN 1091-6490
PubMed: 33199623
DOI: 10.1073/PNAS.2007332117
Page generated: Sun Jan 24 14:52:41 2021

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