Magnesium in PDB 8d32: Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi

Enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi

All present enzymatic activity of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi:
2.5.1.17;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi, PDB code: 8d32 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) 38.05 / 1.85
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 62.618, 62.618, 266.997, 90, 90, 120
R / Rfree (%) 21.9 / 24.6

Other elements in 8d32:

The structure of Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi also contains other interesting chemical elements:

Rhodium (Rh) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi (pdb code 8d32). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi, PDB code: 8d32:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8d32

Go back to Magnesium Binding Sites List in 8d32
Magnesium binding site 1 out of 2 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin 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 5-Deoxyadenosylrhodibalamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:28.2
occ:1.00
 O3G A:3PO203 1.9 28.6 1.0
OD1 A:ASN163 2.1 27.2 1.0
O A:HOH315 2.2 26.2 1.0
O A:HOH309 2.2 29.2 1.0
O2B A:3PO203 2.3 30.4 1.0
O5' A:3PO203 2.4 35.4 1.0
PB A:3PO203 3.0 28.6 1.0
O3A A:3PO203 3.0 35.7 1.0
CG A:ASN163 3.2 29.0 1.0
PG A:3PO203 3.3 28.7 1.0
HD21 A:ASN163 3.4 36.2 1.0
PA A:3PO203 3.4 34.4 1.0
O3B A:3PO203 3.4 27.9 1.0
HH12 A:ARG137 3.5 32.7 1.0
MG A:MG205 3.6 24.6 1.0
ND2 A:ASN163 3.7 30.1 1.0
O1G A:3PO203 3.9 28.6 1.0
O A:HOH302 4.0 31.9 1.0
O1A A:3PO203 4.1 30.8 1.0
O A:ASN163 4.1 27.9 1.0
HA A:ASN163 4.1 31.6 1.0
NH1 A:ARG137 4.2 27.3 1.0
HH11 A:ARG137 4.4 32.7 1.0
O2G A:3PO203 4.4 31.0 1.0
OD1 A:ASP167 4.4 30.4 1.0
O1B A:3PO203 4.4 27.2 1.0
OE2 A:GLU140 4.4 22.3 1.0
CB A:ASN163 4.4 27.5 1.0
HG A:SER166 4.4 32.3 1.0
N7 A:5AD202 4.5 26.9 1.0
OD2 A:ASP167 4.5 33.0 1.0
HD22 A:ASN163 4.5 36.2 1.0
O2A A:3PO203 4.6 33.6 1.0
CA A:ASN163 4.6 26.3 1.0
C A:ASN163 4.6 27.4 1.0
OG A:SER166 4.7 26.9 1.0
CG A:ASP167 4.7 32.9 1.0
OE1 A:GLU140 4.9 23.5 1.0
C8 A:5AD202 4.9 26.1 1.0
HB2 A:ASN163 4.9 33.0 1.0

Magnesium binding site 2 out of 2 in 8d32

Go back to Magnesium Binding Sites List in 8d32
Magnesium binding site 2 out of 2 in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin 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 5-Deoxyadenosylrhodibalamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:24.6
occ:1.00
 OD2 A:ASP167 2.3 33.0 1.0
OD1 A:ASP167 2.5 30.4 1.0
O5' A:3PO203 2.6 35.4 1.0
CG A:ASP167 2.8 32.9 1.0
O3G A:3PO203 2.8 28.6 1.0
O2G A:3PO203 3.1 31.0 1.0
H743 A:SF0201 3.2 38.5 1.0
O2A A:3PO203 3.4 33.6 1.0
H742 A:SF0201 3.4 38.5 1.0
PA A:3PO203 3.4 34.4 1.0
PG A:3PO203 3.5 28.7 1.0
O A:HOH309 3.5 29.2 1.0
MG A:MG204 3.6 28.2 1.0
C74 A:SF0201 3.7 32.1 1.0
H752 A:SF0201 3.8 33.8 1.0
O3A A:3PO203 3.8 35.7 1.0
O A:HOH302 3.9 31.9 1.0
H232 A:SF0201 3.9 41.4 1.0
H741 A:SF0201 4.3 38.5 1.0
CB A:ASP167 4.3 32.4 1.0
N23 A:SF0201 4.4 34.5 1.0
O3B A:3PO203 4.5 27.9 1.0
H231 A:SF0201 4.5 41.4 1.0
HB3 A:ASP167 4.6 38.9 1.0
H381 A:SF0201 4.6 41.7 1.0
HH12 A:ARG137 4.6 32.7 1.0
PB A:3PO203 4.6 28.6 1.0
O1G A:3PO203 4.7 28.6 1.0
O12 A:SF0201 4.7 29.9 1.0
C75 A:SF0201 4.7 28.2 1.0
HB2 A:ASP167 4.7 38.9 1.0
H721 A:SF0201 4.8 46.3 1.0
H492 A:SF0201 4.8 37.1 1.0
C43 A:SF0201 4.8 32.6 1.0
HA A:ASP167 4.9 36.3 1.0
O1A A:3PO203 4.9 30.8 1.0

Reference:

M.Ruetz, R.N.Mascarenhas, M.Koutmos, B.Krautler, R.Banerjee. A Noble Substitution Leads to the Cofactor Mimicry By Rhodibalamin To Be Published.
Page generated: Thu Jul 27 23:28:13 2023

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