Atomistry » Magnesium » PDB 6vzq-6whe » 6wh5
Atomistry »
  Magnesium »
    PDB 6vzq-6whe »
      6wh5 »

Magnesium 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
Cobalt (Co) 3 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 6wh5

Go back to Magnesium Binding Sites List in 6wh5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg202

b:21.0
occ:1.00
 O2G C:3PO203 2.0 21.6 1.0
OD1 A:ASN163 2.1 18.6 1.0
O A:HOH326 2.1 20.8 1.0
O1A C:3PO203 2.1 25.4 1.0
O A:HOH317 2.2 22.7 1.0
O1B C:3PO203 2.3 28.4 1.0
PB C:3PO203 3.1 22.4 1.0
HH12 A:ARG137 3.1 30.6 1.0
CG A:ASN163 3.2 19.1 1.0
O3A C:3PO203 3.3 24.1 1.0
PG C:3PO203 3.3 24.1 1.0
PA C:3PO203 3.3 21.5 1.0
HZ2 C:LYS28 3.4 25.4 1.0
HD21 A:ASN163 3.4 27.0 1.0
O3B C:3PO203 3.5 26.0 1.0
ND2 A:ASN163 3.7 22.5 1.0
K A:K201 3.8 25.6 1.0
HZ1 C:LYS28 3.9 25.4 1.0
NH1 A:ARG137 3.9 25.5 1.0
NZ C:LYS28 4.0 21.1 1.0
HA A:ASN163 4.1 22.7 1.0
O A:HOH310 4.1 26.2 1.0
O2A C:3PO203 4.1 27.2 1.0
O A:ASN163 4.1 19.0 1.0
HH11 A:ARG137 4.2 30.6 1.0
O1G C:3PO203 4.2 24.6 1.0
O3G C:3PO203 4.3 20.1 1.0
HE2 C:LYS28 4.3 32.4 1.0
HH22 A:ARG137 4.3 36.5 1.0
OE1 A:GLU140 4.3 22.2 1.0
O C:HOH371 4.4 28.5 1.0
CB A:ASN163 4.4 18.9 1.0
OD1 A:ASP167 4.5 25.1 1.0
HA3 C:GLY13 4.5 33.4 1.0
HG A:SER166 4.5 29.1 1.0
O5' C:3PO203 4.5 26.9 1.0
O2B C:3PO203 4.5 24.4 1.0
CA A:ASN163 4.6 18.9 1.0
HD22 A:ASN163 4.6 27.0 1.0
C A:ASN163 4.6 19.5 1.0
OD2 A:ASP167 4.6 30.8 1.0
HZ3 C:LYS28 4.7 25.4 1.0
CE C:LYS28 4.7 26.9 1.0
OE2 A:GLU140 4.8 21.9 1.0
OG A:SER166 4.8 24.3 1.0
CZ A:ARG137 4.8 27.7 1.0
HB2 A:ASN163 4.9 22.6 1.0
NH2 A:ARG137 4.9 30.4 1.0
CG A:ASP167 4.9 29.3 1.0
CD A:GLU140 5.0 21.2 1.0
H371 C:B12205 5.0 23.6 1.0

Magnesium binding site 2 out of 3 in 6wh5

Go back to Magnesium Binding Sites List in 6wh5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg202

b:21.6
occ:1.00
 O1G A:3PO203 2.1 18.4 1.0
O5' A:3PO203 2.1 22.2 1.0
OD1 B:ASN163 2.1 18.5 1.0
O B:HOH329 2.1 19.5 1.0
O B:HOH317 2.2 20.9 1.0
O1B A:3PO203 2.3 22.8 1.0
HH12 B:ARG137 3.2 25.3 1.0
PB A:3PO203 3.2 22.3 1.0
O3A A:3PO203 3.2 23.0 1.0
CG B:ASN163 3.2 21.2 1.0
PG A:3PO203 3.2 19.4 1.0
PA A:3PO203 3.3 24.8 1.0
HZ1 A:LYS28 3.4 28.9 1.0
HD21 B:ASN163 3.5 25.8 1.0
O3B A:3PO203 3.6 21.4 1.0
HZ3 A:LYS28 3.8 28.9 1.0
K B:K201 3.8 23.0 1.0
ND2 B:ASN163 3.8 21.4 1.0
NH1 B:ARG137 3.9 21.1 1.0
NZ A:LYS28 4.0 24.1 1.0
HA B:ASN163 4.1 23.2 1.0
O B:ASN163 4.1 22.0 1.0
O2G A:3PO203 4.1 19.7 1.0
HH11 B:ARG137 4.1 25.3 1.0
O B:HOH307 4.2 28.4 1.0
O1A A:3PO203 4.2 22.0 1.0
O2A A:3PO203 4.3 23.5 1.0
HE2 A:LYS28 4.3 28.9 1.0
OE1 B:GLU140 4.4 19.3 1.0
O B:HOH363 4.4 33.6 1.0
OD1 B:ASP167 4.4 22.0 1.0
HH22 B:ARG137 4.4 28.8 1.0
HG B:SER166 4.4 25.2 1.0
CB B:ASN163 4.5 18.8 1.0
O3G A:3PO203 4.5 20.8 1.0
O2B A:3PO203 4.5 24.9 1.0
CA B:ASN163 4.6 19.4 1.0
HA3 A:GLY13 4.6 31.8 1.0
HD22 B:ASN163 4.6 25.8 1.0
C B:ASN163 4.6 19.1 1.0
OD2 B:ASP167 4.7 24.4 1.0
HZ2 A:LYS28 4.7 28.9 1.0
OG B:SER166 4.7 21.0 1.0
CE A:LYS28 4.8 24.1 1.0
CZ B:ARG137 4.8 24.0 1.0
OE2 B:GLU140 4.8 20.6 1.0
CG B:ASP167 4.9 24.6 1.0
NH2 B:ARG137 4.9 23.9 1.0
HB2 B:ASN163 4.9 22.5 1.0
H371 A:B12204 5.0 26.1 1.0

Magnesium binding site 3 out of 3 in 6wh5

Go back to Magnesium Binding Sites List in 6wh5
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg202

b:20.4
occ:1.00
 O3G B:3PO203 2.0 19.8 1.0
OD1 C:ASN163 2.1 21.1 1.0
O1A B:3PO203 2.1 20.2 1.0
O C:HOH307 2.1 21.0 1.0
O C:HOH326 2.1 19.2 1.0
O1B B:3PO203 2.2 21.6 1.0
PB B:3PO203 3.1 20.3 1.0
HH12 C:ARG137 3.1 28.5 1.0
CG C:ASN163 3.2 20.8 1.0
O3A B:3PO203 3.3 23.4 1.0
HZ2 B:LYS28 3.3 25.2 1.0
PA B:3PO203 3.3 19.8 1.0
PG B:3PO203 3.3 22.0 1.0
HD21 C:ASN163 3.4 28.1 1.0
O3B B:3PO203 3.5 23.6 1.0
HZ1 B:LYS28 3.7 25.2 1.0
ND2 C:ASN163 3.7 23.4 1.0
K C:K201 3.8 23.2 1.0
NH1 C:ARG137 3.9 23.7 1.0
NZ B:LYS28 3.9 21.0 1.0
O2A B:3PO203 4.1 24.3 1.0
HA C:ASN163 4.1 25.5 1.0
O C:ASN163 4.1 19.1 1.0
O C:HOH309 4.1 25.9 1.0
HH11 C:ARG137 4.2 28.5 1.0
O2G B:3PO203 4.2 22.5 1.0
O1G B:3PO203 4.3 22.0 1.0
OE1 C:GLU140 4.3 21.9 1.0
HE2 B:LYS28 4.3 29.7 1.0
HH22 C:ARG137 4.4 29.2 1.0
HG C:SER166 4.4 23.5 1.0
CB C:ASN163 4.4 19.8 1.0
O B:HOH362 4.5 28.0 1.0
OD1 C:ASP167 4.5 22.9 1.0
O2B B:3PO203 4.5 24.5 1.0
O5' B:3PO203 4.5 25.1 1.0
HA3 B:GLY13 4.6 29.5 1.0
HZ3 B:LYS28 4.6 25.2 1.0
HD22 C:ASN163 4.6 28.1 1.0
CA C:ASN163 4.6 21.2 1.0
C C:ASN163 4.6 20.1 1.0
OD2 C:ASP167 4.7 24.1 1.0
CE B:LYS28 4.7 24.8 1.0
OG C:SER166 4.7 19.6 1.0
OE2 C:GLU140 4.8 19.7 1.0
HB2 C:ASN163 4.8 23.7 1.0
CZ C:ARG137 4.8 24.1 1.0
CG C:ASP167 4.9 24.7 1.0
NH2 C:ARG137 4.9 24.3 1.0
CD C:GLU140 4.9 21.1 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: Tue Oct 1 22:58:44 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy