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Cobalt in PDB 6wh5: Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi

Enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi

All present enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi:
2.5.1.17;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi, PDB code: 6wh5 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) 39.81 / 1.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.428, 62.678, 103.071, 90, 119.04, 90
R / Rfree (%) 17.6 / 21.7

Other elements in 6wh5:

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi also contains other interesting chemical elements:

Potassium (K) 3 atoms
Magnesium (Mg) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi (pdb code 6wh5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi, PDB code: 6wh5:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 6wh5

Go back to Cobalt Binding Sites List in 6wh5
Cobalt binding site 1 out of 3 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin 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 Cob(II)Alamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co204

b:23.0
occ:1.00
CO A:B12204 0.0 23.0 1.0
N23 A:B12204 1.8 22.6 1.0
N21 A:B12204 1.9 26.5 1.0
N24 A:B12204 1.9 28.7 1.0
N22 A:B12204 1.9 21.9 1.0
C11 A:B12204 2.8 26.1 1.0
C9 A:B12204 2.8 21.6 1.0
C19 A:B12204 2.9 32.3 1.0
C4 A:B12204 2.9 24.3 1.0
C1 A:B12204 2.9 27.4 1.0
HE1 B:PHE117 2.9 32.0 1.0
C16 A:B12204 2.9 29.5 1.0
C14 A:B12204 2.9 25.2 1.0
C6 A:B12204 3.0 22.9 1.0
HZ B:PHE117 3.0 32.7 1.0
C10 A:B12204 3.2 21.9 1.0
H91 A:B12204 3.2 38.8 1.0
O A:HOH303 3.2 36.1 1.0
H203 A:B12204 3.3 35.7 1.0
C5 A:B12204 3.4 23.7 1.0
C15 A:B12204 3.4 27.1 1.0
CE1 B:PHE117 3.5 26.7 1.0
CZ B:PHE117 3.6 27.2 1.0
C20 A:B12204 3.6 29.8 1.0
H262 A:B12204 3.8 30.9 1.0
C18 A:B12204 4.1 36.8 1.0
H10 A:B12204 4.1 26.3 1.0
C2 A:B12204 4.1 24.7 1.0
C12 A:B12204 4.2 26.9 1.0
C17 A:B12204 4.2 33.8 1.0
H202 A:B12204 4.2 35.7 1.0
C3 A:B12204 4.2 23.6 1.0
H562 A:B12204 4.2 47.4 1.0
C13 A:B12204 4.2 25.2 1.0
C8 A:B12204 4.2 21.6 1.0
O2A A:3PO203 4.3 23.5 1.0
C7 A:B12204 4.3 22.4 1.0
H201 A:B12204 4.4 35.7 1.0
H18 A:B12204 4.4 44.2 1.0
H372 A:B12204 4.4 26.1 1.0
C26 A:B12204 4.4 25.7 1.0
H412 A:B12204 4.5 24.8 1.0
HD21 A:LEU5 4.6 38.1 1.0
H492 A:B12204 4.6 34.3 1.0
H13 A:B12204 4.6 30.2 1.0
H261 A:B12204 4.7 30.9 1.0
H3 A:B12204 4.7 28.4 1.0
H541 A:B12204 4.7 36.7 1.0
O1A A:3PO203 4.7 22.0 1.0
H471 A:B12204 4.8 34.6 1.0
CD1 B:PHE117 4.8 25.6 1.0
O A:HOH357 4.8 45.4 1.0
C37 A:B12204 4.8 21.8 1.0
H422 A:B12204 4.9 27.8 1.0
C35 A:B12204 4.9 26.1 1.0
C41 A:B12204 4.9 20.7 1.0
H463 A:B12204 4.9 35.8 1.0
CE2 B:PHE117 4.9 27.5 1.0
C53 A:B12204 4.9 24.8 1.0
H8 A:B12204 4.9 26.0 1.0
C56 A:B12204 5.0 39.5 1.0

Cobalt binding site 2 out of 3 in 6wh5

Go back to Cobalt Binding Sites List in 6wh5
Cobalt binding site 2 out of 3 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co204

b:22.7
occ:1.00
CO C:B12204 0.0 22.7 1.0
N23 C:B12204 1.9 21.9 1.0
N21 C:B12204 1.9 21.8 1.0
N24 C:B12204 1.9 24.7 1.0
N22 C:B12204 1.9 21.5 1.0
C11 C:B12204 2.8 24.8 1.0
C9 C:B12204 2.9 24.2 1.0
C4 C:B12204 2.9 21.9 1.0
C19 C:B12204 2.9 28.6 1.0
C16 C:B12204 2.9 27.9 1.0
C1 C:B12204 2.9 21.8 1.0
C14 C:B12204 2.9 23.2 1.0
HE1 C:PHE117 2.9 29.1 1.0
C6 C:B12204 3.0 21.1 1.0
HZ C:PHE117 3.1 28.5 1.0
O B:HOH330 3.1 32.5 1.0
C10 C:B12204 3.2 24.0 1.0
H91 C:B12204 3.3 34.3 1.0
H203 C:B12204 3.3 29.4 1.0
C5 C:B12204 3.3 23.0 1.0
C15 C:B12204 3.4 24.9 1.0
CE1 C:PHE117 3.6 24.2 1.0
CZ C:PHE117 3.6 23.8 1.0
C20 C:B12204 3.6 24.5 1.0
H262 C:B12204 3.8 26.4 1.0
C18 C:B12204 4.1 34.0 1.0
H202 C:B12204 4.1 29.4 1.0
C2 C:B12204 4.1 20.4 1.0
H10 C:B12204 4.1 28.8 1.0
C17 C:B12204 4.2 31.9 1.0
C3 C:B12204 4.2 21.6 1.0
C12 C:B12204 4.2 26.3 1.0
C13 C:B12204 4.2 24.0 1.0
C8 C:B12204 4.2 21.8 1.0
H18 C:B12204 4.2 40.9 1.0
C7 C:B12204 4.3 21.0 1.0
O2G B:3PO203 4.3 22.5 1.0
H562 C:B12204 4.3 48.2 1.0
H372 C:B12204 4.4 25.5 1.0
C26 C:B12204 4.4 22.0 1.0
H412 C:B12204 4.4 23.2 1.0
H201 C:B12204 4.4 29.4 1.0
H13 C:B12204 4.6 28.8 1.0
H261 C:B12204 4.6 26.4 1.0
H492 C:B12204 4.6 34.4 1.0
H3 C:B12204 4.7 26.0 1.0
HD21 B:LEU5 4.7 34.3 1.0
H541 C:B12204 4.7 36.7 1.0
H471 C:B12204 4.7 37.3 1.0
O1G B:3PO203 4.7 22.0 1.0
CD1 C:PHE117 4.8 25.2 1.0
C37 C:B12204 4.8 21.3 1.0
C41 C:B12204 4.9 19.4 1.0
C53 C:B12204 4.9 21.8 1.0
C35 C:B12204 4.9 20.1 1.0
H8 C:B12204 4.9 26.2 1.0
C54 C:B12204 4.9 30.6 1.0
CE2 C:PHE117 4.9 24.4 1.0
H371 C:B12204 5.0 25.5 1.0

Cobalt binding site 3 out of 3 in 6wh5

Go back to Cobalt Binding Sites List in 6wh5
Cobalt binding site 3 out of 3 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to Cob(II)Alamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co205

b:23.8
occ:1.00
CO C:B12205 0.0 23.8 1.0
N21 C:B12205 1.9 24.9 1.0
N23 C:B12205 1.9 24.1 1.0
N24 C:B12205 1.9 26.2 1.0
N22 C:B12205 1.9 25.0 1.0
C11 C:B12205 2.8 27.1 1.0
C19 C:B12205 2.8 29.4 1.0
C9 C:B12205 2.9 23.4 1.0
C1 C:B12205 2.9 24.3 1.0
C4 C:B12205 2.9 22.6 1.0
C16 C:B12205 2.9 27.0 1.0
HE1 A:PHE117 2.9 32.6 1.0
C14 C:B12205 2.9 26.8 1.0
C6 C:B12205 3.0 21.9 1.0
HZ A:PHE117 3.0 30.2 1.0
H203 C:B12205 3.2 32.5 1.0
H91 C:B12205 3.2 35.2 1.0
C10 C:B12205 3.2 23.8 1.0
O C:HOH310 3.3 36.1 1.0
C5 C:B12205 3.4 23.0 1.0
C15 C:B12205 3.4 26.9 1.0
CE1 A:PHE117 3.5 27.2 1.0
C20 C:B12205 3.6 27.1 1.0
CZ A:PHE117 3.6 25.1 1.0
H262 C:B12205 3.8 27.8 1.0
H202 C:B12205 4.1 32.5 1.0
C2 C:B12205 4.1 22.6 1.0
C18 C:B12205 4.1 34.7 1.0
H10 C:B12205 4.1 28.6 1.0
C3 C:B12205 4.1 23.9 1.0
C17 C:B12205 4.2 31.1 1.0
C12 C:B12205 4.2 26.7 1.0
C8 C:B12205 4.2 23.4 1.0
C13 C:B12205 4.2 25.1 1.0
H562 C:B12205 4.2 46.3 1.0
C7 C:B12205 4.3 22.1 1.0
H201 C:B12205 4.3 32.5 1.0
O3G C:3PO203 4.3 20.1 1.0
H18 C:B12205 4.4 41.6 1.0
H372 C:B12205 4.4 23.6 1.0
C26 C:B12205 4.4 23.2 1.0
H412 C:B12205 4.4 25.5 1.0
HD21 C:LEU5 4.6 44.6 1.0
H13 C:B12205 4.6 30.2 1.0
H261 C:B12205 4.6 27.8 1.0
H492 C:B12205 4.6 33.7 1.0
H3 C:B12205 4.6 28.7 1.0
H541 C:B12205 4.7 37.9 1.0
O A:HOH356 4.7 40.5 1.0
H471 C:B12205 4.8 36.6 1.0
CD1 A:PHE117 4.8 27.9 1.0
C37 C:B12205 4.8 19.6 1.0
O1G C:3PO203 4.8 24.6 1.0
C41 C:B12205 4.9 21.2 1.0
C35 C:B12205 4.9 24.5 1.0
CE2 A:PHE117 4.9 24.5 1.0
C53 C:B12205 4.9 25.8 1.0
H8 C:B12205 4.9 28.1 1.0
H422 C:B12205 5.0 27.2 1.0
H463 C:B12205 5.0 34.8 1.0
H371 C:B12205 5.0 23.6 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 14:52:44 2021

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