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Zinc in PDB 3o9x: Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter

Protein crystallography data

The structure of Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter, PDB code: 3o9x was solved by B.L.Brown, W.Peti, R.Page, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.15 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 60.996, 60.996, 148.612, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter (pdb code 3o9x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter, PDB code: 3o9x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3o9x

Go back to Zinc Binding Sites List in 3o9x
Zinc binding site 1 out of 2 in the Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn132

b:31.5
occ:1.00
SG A:CYS6 2.2 29.9 1.0
SG A:CYS40 2.3 31.0 1.0
SG A:CYS3 2.3 35.3 1.0
SG A:CYS37 2.3 28.5 1.0
CB A:CYS3 3.0 31.8 1.0
CB A:CYS37 3.2 27.6 1.0
CB A:CYS6 3.3 34.3 1.0
CB A:CYS40 3.3 34.7 1.0
N A:CYS40 3.5 33.1 1.0
N A:CYS6 3.7 34.5 1.0
CA A:CYS40 3.9 31.4 1.0
CA A:CYS6 4.0 34.8 1.0
CB A:GLU42 4.2 33.5 1.0
CB A:HIS39 4.2 32.7 1.0
C A:CYS40 4.5 29.9 1.0
C A:HIS39 4.5 32.2 1.0
CA A:CYS3 4.5 32.9 1.0
N A:GLY9 4.5 32.5 1.0
N A:HIS7 4.7 35.5 1.0
CA A:CYS37 4.7 26.4 1.0
C A:CYS6 4.7 34.3 1.0
CA A:HIS39 4.7 31.4 1.0
N A:HIS39 4.8 31.6 1.0
CB A:VAL5 4.8 30.4 1.0
O A:CYS40 4.8 28.3 1.0
CA A:GLY9 4.9 30.2 1.0
ND1 A:HIS39 4.9 41.5 1.0
C A:VAL5 4.9 38.2 1.0
N A:GLU42 4.9 34.4 1.0
CG A:HIS39 5.0 38.9 1.0

Zinc binding site 2 out of 2 in 3o9x

Go back to Zinc Binding Sites List in 3o9x
Zinc binding site 2 out of 2 in the Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the E. Coli Antitoxin Mqsa (Ygit/B3021) in Complex with Its Gene Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn132

b:33.7
occ:1.00
SG B:CYS3 2.0 34.0 1.0
SG B:CYS40 2.3 34.8 1.0
SG B:CYS6 2.4 34.6 1.0
SG B:CYS37 2.4 25.7 1.0
CB B:CYS3 2.9 32.0 1.0
CB B:CYS37 3.2 27.9 1.0
CB B:CYS6 3.4 35.5 1.0
CB B:CYS40 3.4 33.3 1.0
N B:CYS6 3.6 34.9 1.0
N B:CYS40 3.7 31.6 1.0
CB B:GLU42 3.9 34.1 1.0
CA B:CYS40 4.0 31.6 1.0
CA B:CYS6 4.1 34.6 1.0
CA B:CYS3 4.3 34.1 1.0
C B:CYS40 4.5 30.8 1.0
CB B:VAL5 4.6 32.2 1.0
CB B:HIS39 4.6 31.8 1.0
N B:HIS7 4.6 35.2 1.0
CA B:CYS37 4.7 26.2 1.0
C B:CYS6 4.7 34.2 1.0
N B:GLY9 4.7 32.1 1.0
N B:GLU42 4.7 31.9 1.0
C B:VAL5 4.7 39.5 1.0
C B:HIS39 4.8 31.3 1.0
CG B:GLU42 4.8 31.5 1.0
C B:CYS3 4.9 37.4 1.0
O B:CYS40 4.9 29.5 1.0
N B:VAL5 4.9 37.1 1.0
CA B:GLU42 5.0 32.4 1.0
CA B:VAL5 5.0 35.0 1.0
O B:CYS3 5.0 37.1 1.0

Reference:

B.L.Brown, T.K.Wood, W.Peti, R.Page. Structure of the Escherichia Coli Antitoxin Mqsa (Ygit/B3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation. J.Biol.Chem. V. 286 2285 2011.
ISSN: ISSN 0021-9258
PubMed: 21068382
DOI: 10.1074/JBC.M110.172643
Page generated: Wed Dec 16 04:40:08 2020

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