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Zinc in PDB 1ynj: Taq Rna Polymerase-Sorangicin Complex

Enzymatic activity of Taq Rna Polymerase-Sorangicin Complex

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

Protein crystallography data

The structure of Taq Rna Polymerase-Sorangicin Complex, PDB code: 1ynj 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) 40.00 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 199.190, 199.190, 289.306, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 34.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Taq Rna Polymerase-Sorangicin Complex (pdb code 1ynj). 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-Sorangicin Complex, PDB code: 1ynj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ynj

Go back to Zinc Binding Sites List in 1ynj
Zinc binding site 1 out of 2 in the Taq Rna Polymerase-Sorangicin 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-Sorangicin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1525

b:77.2
occ:1.00
SG D:CYS58 2.0 0.4 1.0
SG D:CYS73 2.4 0.6 1.0
SG D:CYS76 2.8 0.4 1.0
CB D:CYS73 2.8 1.0 1.0
SG D:CYS60 2.9 0.2 1.0
CB D:CYS58 3.4 0.9 1.0
N D:ALA59 4.0 0.4 1.0
N D:CYS60 4.0 0.4 1.0
CB D:CYS60 4.1 0.0 1.0
CA D:CYS73 4.3 0.0 1.0
CB D:CYS76 4.4 0.5 1.0
N D:GLY61 4.5 0.1 1.0
C D:ALA59 4.6 0.6 1.0
CA D:CYS60 4.6 0.1 1.0
CA D:CYS58 4.6 0.1 1.0
O D:CYS76 4.6 1.0 1.0
CA D:ALA59 4.7 0.3 1.0
N D:GLU74 4.7 0.2 1.0
C D:CYS58 4.8 0.6 1.0
N D:CYS76 5.0 0.3 1.0

Zinc binding site 2 out of 2 in 1ynj

Go back to Zinc Binding Sites List in 1ynj
Zinc binding site 2 out of 2 in the Taq Rna Polymerase-Sorangicin 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-Sorangicin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1526

b:64.6
occ:1.00
SG D:CYS1201 2.1 47.4 1.0
SG D:CYS1112 2.1 51.5 1.0
SG D:CYS1194 2.3 48.0 1.0
SG D:CYS1204 3.1 48.5 1.0
CB D:CYS1201 3.3 48.1 1.0
CB D:CYS1194 3.3 48.3 1.0
CB D:CYS1112 3.6 51.1 1.0
CB D:CYS1204 3.6 45.0 1.0
CA D:CYS1194 3.6 48.4 1.0
N D:CYS1112 3.8 50.6 1.0
N D:GLN1195 3.9 50.8 1.0
N D:CYS1201 4.1 49.3 1.0
OG1 D:THR1196 4.2 55.2 1.0
N D:CYS1204 4.2 45.2 1.0
CA D:CYS1201 4.3 48.2 1.0
CA D:CYS1112 4.3 51.0 1.0
C D:CYS1194 4.3 49.4 1.0
NH1 D:ARG1189 4.4 38.6 1.0
CA D:CYS1204 4.5 45.1 1.0
OD1 D:ASP1111 4.6 51.0 1.0
C D:ASP1111 4.8 50.4 1.0
N D:CYS1194 4.9 47.3 1.0
CA D:ASP1111 4.9 50.2 1.0
N D:GLY1113 4.9 51.3 1.0
C D:CYS1201 5.0 47.5 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: Sat Sep 26 00:34:51 2020
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