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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

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