Magnesium in PDB 6gau: Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert

All present enzymatic activity of Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert:
5.99.1.3;

The structure of Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert, PDB code: 6gau was solved by S.Petrella, E.Capton, P.M.Alzari, A.Aubry, C.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 3.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	91.523, 96.782, 105.791, 75.64, 64.44, 65.80
R / Rfree (%)	17.3 / 25.1

The binding sites of Magnesium atom in the Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert (pdb code 6gau). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert, PDB code: 6gau:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:0.0 occ:1.00 O2A A:ANP1601 1.9 0.8 1.0 OD1 A:ASN52 2.3 0.5 1.0 O3G A:ANP1601 2.7 0.9 1.0 CG A:ASN52 2.7 0.7 1.0 ND2 A:ASN52 2.9 0.6 1.0 O A:GLU48 3.1 0.3 1.0 OE2 A:GLU48 3.4 0.9 1.0 PA A:ANP1601 3.5 0.5 1.0 O2B A:ANP1601 3.7 0.5 1.0 PG A:ANP1601 3.9 0.7 1.0 CB A:ASN52 3.9 0.7 1.0 CB A:VAL125 4.1 0.1 1.0 O5' A:ANP1601 4.1 0.8 1.0 O3A A:ANP1601 4.2 0.7 1.0 C A:GLU48 4.2 0.9 1.0 N A:VAL125 4.3 0.6 1.0 O1A A:ANP1601 4.4 0.3 1.0 N3B A:ANP1601 4.4 0.2 1.0 CD A:GLU48 4.4 1.0 1.0 PB A:ANP1601 4.4 0.3 1.0 O2G A:ANP1601 4.4 0.4 1.0 CG A:GLU48 4.5 0.7 1.0 CA A:ASN52 4.6 0.0 1.0 CA A:VAL125 4.6 0.9 1.0 N A:ASN52 4.6 0.6 1.0 CA A:GLU48 4.7 0.6 1.0 CG1 A:VAL125 4.8 0.4 1.0 C A:GLY124 4.9 0.2 1.0 CG2 A:VAL125 4.9 0.4 1.0

Magnesium binding site 2 out of 2 in the Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Extremely 'Open' Clamp Structure of Dna Gyrase: Role of the Corynebacteriales Gyrb Specific Insert within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1602 b:0.4 occ:1.00 OD1 B:ASN52 1.9 0.2 1.0 O1G B:ANP1601 2.1 0.7 1.0 O1A B:ANP1601 2.2 0.1 1.0 CG B:ASN52 3.0 0.3 1.0 O B:GLU48 3.0 0.2 1.0 CG2 B:VAL125 3.1 0.2 1.0 OE2 B:GLU48 3.3 1.0 1.0 PG B:ANP1601 3.4 0.3 1.0 ND2 B:ASN52 3.5 0.7 1.0 PA B:ANP1601 3.6 0.8 1.0 O2G B:ANP1601 3.7 0.0 1.0 O1B B:ANP1601 3.8 0.5 1.0 N B:VAL125 3.9 0.2 1.0 C B:GLU48 4.1 0.9 1.0 O5' B:ANP1601 4.1 0.2 1.0 N3B B:ANP1601 4.2 0.8 1.0 CB B:ASN52 4.2 0.4 1.0 C B:GLY124 4.3 0.8 1.0 CA B:GLY124 4.3 0.2 1.0 CB B:VAL125 4.4 0.9 1.0 O3A B:ANP1601 4.4 0.7 1.0 PB B:ANP1601 4.4 0.2 1.0 CA B:GLU48 4.5 0.9 1.0 CA B:VAL125 4.5 0.4 1.0 CD B:GLU48 4.5 0.5 1.0 O3G B:ANP1601 4.5 0.5 1.0 O2A B:ANP1601 4.6 0.4 1.0 N B:ASN52 4.7 0.6 1.0 CB B:GLU48 4.8 0.3 1.0 CA B:ASN52 4.9 0.7 1.0

S.Petrella, E.Capton, B.Raynal, C.Giffard, A.Thureau, F.Bonnete, P.M.Alzari, A.Aubry, C.Mayer. Overall Structures of Mycobacterium Tuberculosis Dna Gyrase Reveal the Role of A Corynebacteriales Gyrb-Specific Insert in Atpase Activity. Structure V. 27 579 2019.
ISSN: ISSN 0969-2126
PubMed: 30744994
DOI: 10.1016/J.STR.2019.01.004