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Rhodium 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:

Magnesium (Mg) 2 atoms

Rhodium Binding Sites:

The binding sites of Rhodium 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 Rhodium atom.
In total only one binding site of Rhodium was determined in the Mycobacterium Tuberculosis Pduo-Type Atp:Cobalamin Adenosyltransferase Bound to 5-Deoxyadenosylrhodibalamin and Pppi, PDB code: 8d32:

Rhodium binding site 1 out of 1 in 8d32

Go back to Rhodium Binding Sites List in 8d32
Rhodium binding site 1 out of 1 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 Rhodium with other atoms in the Rh 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:Rh201

b:30.8
occ:1.00
 RH01 A:SF0201 0.0 30.8 1.0
N22 A:SF0201 2.0 29.2 1.0
N17 A:SF0201 2.0 32.9 1.0
N20 A:SF0201 2.0 27.1 1.0
N19 A:SF0201 2.0 30.4 1.0
C5' A:5AD202 2.2 28.7 1.0
C68 A:SF0201 2.9 33.4 1.0
HE1 A:PHE117 2.9 41.5 1.0
C53 A:SF0201 2.9 29.4 1.0
C56 A:SF0201 2.9 27.9 1.0
C32 A:SF0201 3.0 31.6 1.0
C40 A:SF0201 3.0 31.4 1.0
C64 A:SF0201 3.0 32.1 1.0
C62 A:SF0201 3.0 27.1 1.0
C46 A:SF0201 3.0 30.6 1.0
C4' A:5AD202 3.2 29.6 1.0
HZ A:PHE117 3.2 38.8 1.0
H311 A:SF0201 3.2 42.8 1.0
C54 A:SF0201 3.3 28.5 1.0
H681 A:SF0201 3.3 40.1 1.0
C63 A:SF0201 3.4 28.5 1.0
C43 A:SF0201 3.4 32.6 1.0
CE1 A:PHE117 3.6 34.6 1.0
C31 A:SF0201 3.6 35.7 1.0
CZ A:PHE117 3.7 32.3 1.0
H313 A:SF0201 3.9 42.8 1.0
O4' A:5AD202 4.0 27.8 1.0
H541 A:SF0201 4.0 34.2 1.0
H691 A:SF0201 4.1 39.6 1.0
C67 A:SF0201 4.1 33.8 1.0
C35 A:SF0201 4.2 32.9 1.0
C38 A:SF0201 4.2 34.7 1.0
C51 A:SF0201 4.3 29.3 1.0
C65 A:SF0201 4.3 32.5 1.0
C58 A:SF0201 4.3 27.1 1.0
C48 A:SF0201 4.3 32.0 1.0
H671 A:SF0201 4.3 40.6 1.0
C61 A:SF0201 4.3 26.2 1.0
H851 A:SF0201 4.3 42.5 1.0
C3' A:5AD202 4.4 28.2 1.0
H312 A:SF0201 4.4 42.8 1.0
H751 A:SF0201 4.5 33.8 1.0
O3' A:5AD202 4.6 29.6 1.0
C69 A:SF0201 4.6 33.0 1.0
H381 A:SF0201 4.7 41.7 1.0
O2G A:3PO203 4.7 31.0 1.0
O1G A:3PO203 4.8 28.6 1.0
H611 A:SF0201 4.8 31.4 1.0
H593 A:SF0201 4.8 31.9 1.0
HH22 A:ARG137 4.8 29.9 1.0
CD1 A:PHE117 4.8 35.3 1.0
H772 A:SF0201 4.8 38.0 1.0
C74 A:SF0201 4.9 32.1 1.0
C83 A:SF0201 4.9 28.7 1.0
C75 A:SF0201 4.9 28.2 1.0
H511 A:SF0201 4.9 35.1 1.0
H811 A:SF0201 4.9 35.6 1.0
H692 A:SF0201 4.9 39.6 1.0
H812 A:SF0201 4.9 35.6 1.0
H752 A:SF0201 5.0 33.8 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: Tue Aug 19 00:44:25 2025

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