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Sodium in PDB 3ifz: Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution

Enzymatic activity of Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution

All present enzymatic activity of Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution, PDB code: 3ifz was solved by J.Piton, A.Aubry, M.Delarue, C.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.915, 109.660, 101.996, 90.00, 120.40, 90.00
R / Rfree (%) 19.2 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution (pdb code 3ifz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution, PDB code: 3ifz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ifz

Go back to Sodium Binding Sites List in 3ifz
Sodium binding site 1 out of 2 in the Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:54.9
occ:1.00
 NE2 A:GLN431 3.5 71.0 1.0
NZ A:LYS396 3.7 0.9 1.0
CE A:LYS396 4.2 93.0 1.0
OE1 A:GLN431 4.3 81.9 1.0
CD A:GLN431 4.3 82.7 1.0
CB A:ARG392 4.4 46.4 1.0
CD A:ARG392 4.6 53.2 1.0
CD2 A:HIS389 4.9 58.0 1.0

Sodium binding site 2 out of 2 in 3ifz

Go back to Sodium Binding Sites List in 3ifz
Sodium binding site 2 out of 2 in the Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the First Part of the Mycobacterium Tuberculosis Dna Gyrase Reaction Core: the Breakage and Reunion Domain at 2.7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na510

b:77.5
occ:1.00
 NE2 B:GLN431 3.3 71.2 1.0
NZ B:LYS396 3.3 94.8 1.0
OE1 B:GLN431 3.9 75.1 1.0
CE B:LYS396 4.0 83.5 1.0
CD B:GLN431 4.1 79.1 1.0
O B:ASP426 4.6 63.1 1.0
CB B:ARG392 4.7 53.5 1.0
CG2 B:ILE427 4.7 61.3 1.0
CD B:LYS396 4.9 72.0 1.0
CD2 B:HIS389 5.0 62.1 1.0

Reference:

J.Piton, S.Petrella, M.Delarue, G.Andre-Leroux, V.Jarlier, A.Aubry, C.Mayer. Structural Insights Into the Quinolone Resistance Mechanism of Mycobacterium Tuberculosis Dna Gyrase. Plos One V. 5 12245 2010.
ISSN: ESSN 1932-6203
PubMed: 20805881
DOI: 10.1371/JOURNAL.PONE.0012245
Page generated: Sun Aug 17 15:45:54 2025

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