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: Sun Jan 24 17:54:08 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy