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Potassium 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:

Magnesium (Mg) 3 atoms
Cobalt (Co) 3 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 3 in 6wh5

Go back to Potassium Binding Sites List in 6wh5
Potassium 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 Potassium with other atoms in the K 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:K201

b:25.6
occ:1.00
 O1G C:3PO203 2.7 24.6 1.0
O C:ILE8 2.7 29.8 1.0
O1A C:3PO203 2.7 25.4 1.0
OD2 A:ASP167 2.8 30.8 1.0
OD1 A:ASP167 2.9 25.1 1.0
O5' C:3PO203 3.0 26.9 1.0
H353 C:B12205 3.0 29.4 1.0
H352 C:B12205 3.0 29.4 1.0
HA C:TYR9 3.2 29.4 1.0
CG A:ASP167 3.2 29.3 1.0
O2G C:3PO203 3.2 21.6 1.0
PA C:3PO203 3.3 21.5 1.0
PG C:3PO203 3.4 24.1 1.0
C35 C:B12205 3.4 24.5 1.0
H291 C:B12205 3.4 29.4 1.0
H371 C:B12205 3.7 23.6 1.0
O A:HOH317 3.7 22.7 1.0
H C:THR10 3.7 31.0 1.0
C C:ILE8 3.8 27.7 1.0
MG A:MG202 3.8 21.0 1.0
O3A C:3PO203 3.9 24.1 1.0
HG23 C:THR10 3.9 34.8 1.0
H292 C:B12205 3.9 29.4 1.0
N29 C:B12205 4.0 24.5 1.0
CA C:TYR9 4.1 24.5 1.0
H351 C:B12205 4.1 29.4 1.0
HG22 C:ILE8 4.1 31.4 1.0
H401 C:B12205 4.1 26.4 1.0
O A:HOH310 4.2 26.2 1.0
H3 C:B12205 4.2 28.7 1.0
HG1 C:THR10 4.3 34.9 1.0
H312 C:B12205 4.4 38.9 1.0
N C:TYR9 4.4 24.7 1.0
N C:THR10 4.4 25.8 1.0
O3B C:3PO203 4.4 26.0 1.0
C5 C:B12205 4.5 23.0 1.0
HG23 C:ILE8 4.6 31.4 1.0
HH12 A:ARG137 4.6 30.6 1.0
PB C:3PO203 4.7 22.4 1.0
C37 C:B12205 4.7 19.6 1.0
CB A:ASP167 4.7 28.2 1.0
HA C:ILE8 4.7 33.8 1.0
O3G C:3PO203 4.7 20.1 1.0
C C:TYR9 4.8 25.1 1.0
H362 C:B12205 4.8 28.5 1.0
O2A C:3PO203 4.8 27.2 1.0
CG2 C:ILE8 4.8 26.2 1.0
CA C:ILE8 4.9 28.2 1.0
CG2 C:THR10 4.9 29.0 1.0
HB3 A:ASP167 4.9 33.9 1.0
N40 C:B12205 4.9 22.0 1.0

Potassium binding site 2 out of 3 in 6wh5

Go back to Potassium Binding Sites List in 6wh5
Potassium 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 Potassium with other atoms in the K 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
B:K201

b:23.0
occ:1.00
 O A:ILE8 2.7 23.4 1.0
OD2 B:ASP167 2.8 24.4 1.0
O1A A:3PO203 2.8 22.0 1.0
O1G A:3PO203 2.8 18.4 1.0
OD1 B:ASP167 2.8 22.0 1.0
H352 A:B12204 2.9 31.3 1.0
H353 A:B12204 3.1 31.3 1.0
O5' A:3PO203 3.1 22.2 1.0
O3G A:3PO203 3.1 20.8 1.0
HA A:TYR9 3.1 30.3 1.0
CG B:ASP167 3.1 24.6 1.0
PG A:3PO203 3.4 19.4 1.0
C35 A:B12204 3.4 26.1 1.0
PA A:3PO203 3.4 24.8 1.0
H291 A:B12204 3.5 35.1 1.0
O B:HOH317 3.6 20.9 1.0
HG22 A:ILE8 3.6 29.8 1.0
H371 A:B12204 3.7 26.1 1.0
H A:THR10 3.7 31.9 1.0
C A:ILE8 3.8 25.1 1.0
MG B:MG202 3.8 21.6 1.0
H292 A:B12204 4.0 35.1 1.0
H351 A:B12204 4.0 31.3 1.0
CA A:TYR9 4.0 25.2 1.0
O3B A:3PO203 4.0 21.4 1.0
HG23 A:THR10 4.0 34.3 1.0
N29 A:B12204 4.0 29.2 1.0
O3A A:3PO203 4.1 23.0 1.0
O B:HOH307 4.1 28.4 1.0
H401 A:B12204 4.3 29.4 1.0
H3 A:B12204 4.3 28.4 1.0
HG1 A:THR10 4.3 33.0 1.0
N A:TYR9 4.3 22.9 1.0
N A:THR10 4.4 26.6 1.0
H312 A:B12204 4.4 31.0 1.0
C5 A:B12204 4.5 23.7 1.0
HH12 B:ARG137 4.5 25.3 1.0
CG2 A:ILE8 4.6 24.9 1.0
CB B:ASP167 4.6 24.4 1.0
PB A:3PO203 4.6 22.3 1.0
C37 A:B12204 4.6 21.8 1.0
HA A:ILE8 4.7 31.1 1.0
C A:TYR9 4.8 24.5 1.0
O2G A:3PO203 4.8 19.7 1.0
H362 A:B12204 4.8 29.9 1.0
HB3 B:ASP167 4.8 29.2 1.0
CA A:ILE8 4.8 25.9 1.0
O2A A:3PO203 4.9 23.5 1.0
HG23 A:ILE8 4.9 29.8 1.0
HB3 A:TYR9 5.0 31.0 1.0
O1B A:3PO203 5.0 22.8 1.0
HB2 A:TYR9 5.0 31.0 1.0
CB A:TYR9 5.0 25.8 1.0

Potassium binding site 3 out of 3 in 6wh5

Go back to Potassium Binding Sites List in 6wh5
Potassium 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 Potassium with other atoms in the K 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:K201

b:23.2
occ:1.00
 O B:ILE8 2.7 20.9 1.0
O1A B:3PO203 2.7 20.2 1.0
O1G B:3PO203 2.8 22.0 1.0
OD2 C:ASP167 2.8 24.1 1.0
OD1 C:ASP167 2.8 22.9 1.0
O5' B:3PO203 3.0 25.1 1.0
O3G B:3PO203 3.2 19.8 1.0
CG C:ASP167 3.2 24.7 1.0
H353 C:B12204 3.2 24.2 1.0
HA B:TYR9 3.2 32.1 1.0
H352 C:B12204 3.3 24.2 1.0
PA B:3PO203 3.3 19.8 1.0
PG B:3PO203 3.4 22.0 1.0
H291 C:B12204 3.6 30.1 1.0
C35 C:B12204 3.7 20.1 1.0
O C:HOH307 3.7 21.0 1.0
H371 C:B12204 3.7 25.5 1.0
C B:ILE8 3.7 23.6 1.0
O3A B:3PO203 3.8 23.4 1.0
MG C:MG202 3.8 20.4 1.0
H B:THR10 3.8 30.9 1.0
HG22 B:ILE8 4.0 30.7 1.0
HG23 B:THR10 4.0 35.8 1.0
H292 C:B12204 4.1 30.1 1.0
CA B:TYR9 4.1 26.7 1.0
N29 C:B12204 4.1 25.1 1.0
O C:HOH309 4.2 25.9 1.0
H401 C:B12204 4.2 22.1 1.0
H3 C:B12204 4.2 26.0 1.0
N B:TYR9 4.4 24.8 1.0
H312 C:B12204 4.4 29.0 1.0
O3B B:3PO203 4.4 23.6 1.0
HG23 B:ILE8 4.4 30.7 1.0
HG1 B:THR10 4.4 34.5 1.0
H351 C:B12204 4.4 24.2 1.0
C5 C:B12204 4.5 23.0 1.0
N B:THR10 4.5 25.8 1.0
HH12 C:ARG137 4.5 28.5 1.0
PB B:3PO203 4.6 20.3 1.0
HA B:ILE8 4.6 29.8 1.0
CG2 B:ILE8 4.6 25.6 1.0
CB C:ASP167 4.6 23.3 1.0
C37 C:B12204 4.7 21.3 1.0
O2G B:3PO203 4.7 22.5 1.0
O2A B:3PO203 4.8 24.3 1.0
CA B:ILE8 4.8 24.8 1.0
C B:TYR9 4.8 29.1 1.0
H362 C:B12204 4.9 27.1 1.0
HB3 C:ASP167 4.9 27.9 1.0
N40 C:B12204 4.9 18.4 1.0
CG2 B:THR10 5.0 29.8 1.0
O1B B:3PO203 5.0 21.6 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: Mon Aug 12 18:15:47 2024

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