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Zinc in PDB 1ynn: Taq Rna Polymerase-Rifampicin Complex

Enzymatic activity of Taq Rna Polymerase-Rifampicin Complex

All present enzymatic activity of Taq Rna Polymerase-Rifampicin Complex:
2.7.7.6;

Protein crystallography data

The structure of Taq Rna Polymerase-Rifampicin Complex, PDB code: 1ynn was solved by E.A.Campbell, O.Pavlova, N.Zenkin, F.Leon, H.Irschik, R.Jansen, K.Severinov, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 200.760, 200.760, 292.938, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 33.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Taq Rna Polymerase-Rifampicin Complex (pdb code 1ynn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Taq Rna Polymerase-Rifampicin Complex, PDB code: 1ynn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ynn

Go back to Zinc Binding Sites List in 1ynn
Zinc binding site 1 out of 2 in the Taq Rna Polymerase-Rifampicin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Taq Rna Polymerase-Rifampicin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1525

b:90.3
occ:1.00
N D:ALA59 2.6 0.4 1.0
O D:CYS76 2.8 0.8 1.0
CB D:CYS58 3.0 0.9 1.0
C D:CYS58 3.1 0.1 1.0
CB D:ALA59 3.2 0.6 1.0
CA D:ALA59 3.4 0.7 1.0
CA D:CYS58 3.5 0.0 1.0
SG D:CYS58 3.6 0.9 1.0
N D:CYS60 3.7 1.0 1.0
C D:CYS76 3.9 0.9 1.0
CB D:CYS76 3.9 1.0 1.0
O D:CYS58 4.0 0.2 1.0
C D:ALA59 4.1 0.7 1.0
SG D:CYS76 4.2 0.7 1.0
CG2 D:VAL78 4.3 95.8 1.0
CA D:CYS76 4.5 0.9 1.0
N D:CYS58 4.9 0.6 1.0
CA D:CYS60 4.9 0.3 1.0
N D:GLY77 4.9 0.6 1.0
CB D:CYS73 5.0 0.0 1.0

Zinc binding site 2 out of 2 in 1ynn

Go back to Zinc Binding Sites List in 1ynn
Zinc binding site 2 out of 2 in the Taq Rna Polymerase-Rifampicin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Taq Rna Polymerase-Rifampicin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1526

b:52.6
occ:1.00
SG D:CYS1112 1.9 40.4 1.0
SG D:CYS1194 2.1 36.4 1.0
SG D:CYS1204 2.6 34.4 1.0
SG D:CYS1201 2.7 36.0 1.0
CB D:CYS1112 3.2 40.2 1.0
CB D:CYS1194 3.2 37.2 1.0
CB D:CYS1204 3.5 33.9 1.0
CA D:CYS1194 3.6 37.3 1.0
CB D:CYS1201 3.7 36.3 1.0
NH1 D:ARG1189 3.9 35.0 1.0
N D:CYS1112 4.0 40.1 1.0
N D:GLN1195 4.1 40.0 1.0
CA D:CYS1112 4.2 40.2 1.0
C D:CYS1194 4.4 38.5 1.0
N D:CYS1204 4.5 34.6 1.0
CA D:CYS1204 4.6 34.1 1.0
N D:CYS1201 4.6 36.8 1.0
CA D:CYS1201 4.7 36.3 1.0
N D:CYS1194 4.7 36.2 1.0
O D:THR1193 5.0 35.2 1.0
C D:CYS1112 5.0 40.2 1.0
CG2 D:THR1114 5.0 39.5 1.0
O D:CYS1201 5.0 35.6 1.0

Reference:

E.A.Campbell, O.Pavlova, N.Zenkin, F.Leon, H.Irschik, R.Jansen, K.Severinov, S.A.Darst. Structural, Functional, and Genetic Analysis of Sorangicin Inhibition of Bacterial Rna Polymerase Embo J. V. 24 674 2005.
ISSN: ISSN 0261-4189
PubMed: 15692574
DOI: 10.1038/SJ.EMBOJ.7600499
Page generated: Wed Dec 16 03:14:48 2020

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