Zinc in PDB 6woy: Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp

Enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp, PDB code: 6woy 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) 29.98 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.977, 102.465, 296.043, 90.00, 98.87, 90.00
R / Rfree (%) 20.6 / 21.9

Other elements in 6woy:

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp (pdb code 6woy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp, PDB code: 6woy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6woy

Go back to Zinc Binding Sites List in 6woy
Zinc binding site 1 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:96.5
occ:1.00
SG D:CYS76 2.3 86.8 1.0
SG D:CYS73 2.4 0.0 1.0
SG D:CYS58 2.4 0.0 1.0
SG D:CYS60 2.4 96.3 1.0
CB D:LYS62 3.1 0.3 1.0
CB D:CYS73 3.2 0.7 1.0
CB D:CYS58 3.6 98.7 1.0
CG D:LYS62 3.7 0.9 1.0
N D:LYS62 3.8 0.3 1.0
CB D:CYS76 3.8 93.2 1.0
N D:CYS60 3.9 0.2 1.0
N D:CYS76 3.9 97.9 1.0
CB D:CYS60 3.9 93.1 1.0
CA D:LYS62 4.1 0.5 1.0
N D:GLY61 4.3 98.5 1.0
N D:ALA59 4.4 82.6 1.0
CA D:CYS60 4.4 0.4 1.0
CA D:CYS76 4.4 92.9 1.0
CB D:ARG75 4.4 96.3 1.0
C D:CYS58 4.6 88.9 1.0
CA D:CYS73 4.7 98.8 1.0
N D:GLY77 4.7 95.6 1.0
CA D:CYS58 4.7 92.4 1.0
N D:ARG75 4.8 98.1 1.0
C D:CYS60 4.9 97.3 1.0
C D:ARG75 4.9 99.1 1.0
C D:ALA59 4.9 90.2 1.0
CA D:ARG75 4.9 98.0 1.0
C D:GLY61 5.0 0.8 1.0

Zinc binding site 2 out of 2 in 6woy

Go back to Zinc Binding Sites List in 6woy
Zinc binding site 2 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex with 3'Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:76.2
occ:1.00
SG D:CYS1201 2.1 64.8 1.0
SG D:CYS1112 2.1 69.6 1.0
SG D:CYS1194 2.3 71.6 1.0
SG D:CYS1204 2.6 76.3 1.0
CB D:CYS1194 3.0 62.0 1.0
CB D:CYS1204 3.2 61.2 1.0
CA D:CYS1194 3.3 59.5 1.0
CB D:CYS1201 3.5 60.4 1.0
CB D:CYS1112 3.6 67.1 1.0
CG2 D:THR1114 3.9 64.4 1.0
N D:GLN1195 3.9 64.6 1.0
N D:CYS1201 4.0 65.6 1.0
C D:CYS1194 4.1 62.5 1.0
N D:CYS1112 4.2 73.9 1.0
CA D:CYS1201 4.3 60.3 1.0
NH2 D:ARG1189 4.4 75.6 1.0
N D:CYS1204 4.4 64.4 1.0
N D:CYS1194 4.4 58.3 1.0
CA D:CYS1204 4.4 63.4 1.0
CA D:CYS1112 4.5 67.7 1.0
N D:THR1196 4.6 57.7 1.0
OG1 D:THR1196 4.8 69.8 1.0
OD1 D:ASP1111 4.8 69.6 1.0
CZ D:ARG1189 4.9 70.9 1.0
C D:CYS1201 4.9 61.3 1.0

Reference:

Y.Shin, K.S.Murakami. The Mechanism of Discrimination Against 2DNTPS By the Multisubunit Rna Polymerases To Be Published.
Page generated: Wed Dec 16 13:06:06 2020

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