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Zinc in PDB 6oy7: X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min

Enzymatic activity of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min

All present enzymatic activity of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min, PDB code: 6oy7 was solved by Y.Shin, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 3.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.684, 101.609, 295.796, 90.00, 98.76, 90.00
R / Rfree (%) 20.7 / 24.8

Other elements in 6oy7:

The structure of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min (pdb code 6oy7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min, PDB code: 6oy7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6oy7

Go back to Zinc Binding Sites List in 6oy7
Zinc binding site 1 out of 2 in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1603

b:0.4
occ:1.00
SG D:CYS76 2.1 0.6 1.0
SG D:CYS60 2.2 0.2 1.0
SG D:CYS73 2.3 0.5 1.0
SG D:CYS58 2.6 0.5 1.0
CB D:CYS76 3.2 99.2 1.0
CB D:CYS73 3.2 0.5 1.0
N D:CYS60 3.5 0.2 1.0
CB D:CYS58 3.5 0.5 1.0
CB D:CYS60 3.6 0.8 1.0
N D:CYS76 3.7 0.6 1.0
N D:GLY61 3.9 0.7 1.0
CA D:CYS60 3.9 0.3 1.0
N D:LYS62 4.0 0.8 1.0
CA D:CYS76 4.1 0.0 1.0
N D:ALA59 4.1 87.4 1.0
C D:CYS60 4.3 0.7 1.0
CB D:LYS62 4.3 0.1 1.0
C D:CYS58 4.5 94.9 1.0
C D:ALA59 4.5 0.6 1.0
CA D:CYS58 4.6 97.2 1.0
CA D:CYS73 4.7 0.4 1.0
CA D:ALA59 4.7 88.6 1.0
CB D:ARG75 4.8 0.3 1.0
CA D:LYS62 4.8 0.2 1.0
C D:CYS76 4.8 96.5 1.0
C D:ARG75 4.9 0.4 1.0
CA D:GLY61 4.9 0.6 1.0
N D:GLY77 4.9 97.5 1.0
CD2 D:TYR63 5.0 0.6 1.0
C D:GLY61 5.0 0.8 1.0

Zinc binding site 2 out of 2 in 6oy7

Go back to Zinc Binding Sites List in 6oy7
Zinc binding site 2 out of 2 in the X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of A Bacterial Reiterative Transcription Complex of Pyrg Promoter at 7 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1604

b:84.4
occ:1.00
SG D:CYS1194 2.2 78.5 1.0
SG D:CYS1204 2.3 67.2 1.0
SG D:CYS1112 2.3 66.7 1.0
SG D:CYS1201 2.3 67.4 1.0
CB D:CYS1194 3.0 67.9 1.0
CB D:CYS1204 3.1 65.7 1.0
CA D:CYS1194 3.4 60.9 1.0
CB D:CYS1112 3.7 66.0 1.0
CB D:CYS1201 3.7 65.8 1.0
N D:GLN1195 4.0 65.5 1.0
OG1 D:THR1196 4.1 78.2 1.0
CG2 D:THR1114 4.1 80.3 1.0
NH2 D:ARG1189 4.2 76.3 1.0
C D:CYS1194 4.2 61.7 1.0
N D:CYS1204 4.2 65.0 1.0
N D:CYS1201 4.2 69.2 1.0
N D:CYS1112 4.3 74.2 1.0
CA D:CYS1204 4.3 63.1 1.0
CA D:CYS1201 4.5 67.7 1.0
N D:CYS1194 4.6 57.4 1.0
CA D:CYS1112 4.6 67.8 1.0
N D:THR1196 4.8 62.1 1.0
O D:CYS1201 5.0 65.7 1.0

Reference:

Y.Shin, K.S.Murakami. Structural Basis of Reiterative Transcription From the Pyrg Promoter To Be Published.
Page generated: Wed Dec 16 12:28:30 2020

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