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Zinc in PDB 2o5i: Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex

Enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex, PDB code: 2o5i was solved by D.G.Vassylyev, T.H.Tahirov, M.N.Vassylyeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 156.211, 156.211, 499.229, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.7

Other elements in 2o5i:

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex (pdb code 2o5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex, PDB code: 2o5i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2o5i

Go back to Zinc Binding Sites List in 2o5i
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4058

b:82.8
occ:1.00
 SG D:CYS76 2.3 78.4 1.0
SG D:CYS60 2.4 79.1 1.0
SG D:CYS73 2.5 78.8 1.0
SG D:CYS58 2.5 82.0 1.0
CB D:CYS76 3.4 73.6 1.0
CB D:CYS73 3.4 78.1 1.0
CB D:ALA59 3.6 78.3 1.0
N D:CYS60 3.7 79.2 1.0
CB D:CYS58 3.9 81.7 1.0
CB D:CYS60 3.9 79.5 1.0
N D:GLY61 4.1 79.4 1.0
N D:ALA59 4.2 80.4 1.0
N D:LYS62 4.3 81.4 1.0
CA D:CYS60 4.3 79.2 1.0
O D:CYS76 4.3 72.1 1.0
CA D:ALA59 4.4 78.8 1.0
CB D:LYS62 4.4 81.4 1.0
CA D:CYS76 4.4 71.2 1.0
CG D:LYS62 4.4 79.9 1.0
N D:CYS76 4.5 71.8 1.0
CG2 D:VAL78 4.5 71.1 1.0
C D:ALA59 4.6 78.8 1.0
C D:CYS60 4.7 79.1 1.0
C D:CYS76 4.7 71.6 1.0
CA D:CYS73 5.0 77.8 1.0
CA D:LYS62 5.0 83.0 1.0

Zinc binding site 2 out of 4 in 2o5i

Go back to Zinc Binding Sites List in 2o5i
Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn6112

b:65.8
occ:1.00
 SG D:CYS1112 2.3 68.0 1.0
SG D:CYS1201 2.3 63.7 1.0
SG D:CYS1194 2.3 64.6 1.0
SG D:CYS1204 2.3 63.2 1.0
CB D:CYS1204 3.2 59.8 1.0
CB D:CYS1112 3.4 67.5 1.0
CB D:CYS1194 3.4 62.7 1.0
CB D:CYS1201 3.6 65.5 1.0
CA D:CYS1194 3.7 61.3 1.0
N D:CYS1201 3.8 67.6 1.0
N D:GLN1195 4.2 62.9 1.0
CA D:CYS1201 4.3 66.2 1.0
CA D:CYS1204 4.4 61.1 1.0
C D:CYS1194 4.5 61.8 1.0
N D:CYS1204 4.6 63.9 1.0
CA D:CYS1112 4.6 69.6 1.0
N D:CYS1112 4.7 71.0 1.0
N D:CYS1194 4.9 60.5 1.0
C D:VAL1200 4.9 68.5 1.0
O D:CYS1112 4.9 69.3 1.0
C D:CYS1201 5.0 67.0 1.0
OG1 D:THR1196 5.0 70.7 1.0

Zinc binding site 3 out of 4 in 2o5i

Go back to Zinc Binding Sites List in 2o5i
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn5058

b:71.5
occ:1.00
 SG N:CYS76 2.3 75.7 1.0
SG N:CYS60 2.3 72.5 1.0
SG N:CYS58 2.4 72.0 1.0
SG N:CYS73 2.5 76.4 1.0
CB N:CYS76 3.3 76.6 1.0
OG D:SER1300 3.4 90.7 1.0
N N:CYS60 3.5 66.2 1.0
CB N:CYS73 3.6 75.7 1.0
CB N:ALA59 3.6 68.2 1.0
CB N:CYS60 3.8 69.0 1.0
CB N:CYS58 3.9 70.1 1.0
N N:GLY61 4.1 71.0 1.0
N N:ALA59 4.1 66.8 1.0
CA N:CYS60 4.2 68.1 1.0
CA N:ALA59 4.3 67.3 1.0
N N:LYS62 4.3 74.0 1.0
O N:CYS76 4.4 78.7 1.0
CA N:CYS76 4.4 77.7 1.0
C N:ALA59 4.5 66.7 1.0
CB D:SER1300 4.5 91.8 1.0
CB N:LYS62 4.5 72.3 1.0
N N:CYS76 4.6 77.1 1.0
C N:CYS60 4.6 69.6 1.0
CE2 D:PHE1293 4.7 90.4 1.0
CG2 N:VAL78 4.7 73.5 1.0
C N:CYS76 4.7 78.7 1.0
CG N:LYS62 4.7 70.5 1.0
CD2 D:PHE1293 4.9 91.0 1.0

Zinc binding site 4 out of 4 in 2o5i

Go back to Zinc Binding Sites List in 2o5i
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the T. Thermophilus Rna Polymerase Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7112

b:73.9
occ:1.00
 SG N:CYS1194 2.3 72.1 1.0
SG N:CYS1112 2.4 74.8 1.0
SG N:CYS1204 2.4 69.8 1.0
SG N:CYS1201 2.4 71.2 1.0
CB N:CYS1112 3.3 76.6 1.0
CB N:CYS1204 3.3 63.9 1.0
CB N:CYS1194 3.4 76.9 1.0
CB N:CYS1201 3.7 65.0 1.0
CA N:CYS1194 3.7 78.7 1.0
N N:CYS1201 4.0 63.4 1.0
N N:GLN1195 4.2 80.2 1.0
NH1 N:ARG1189 4.3 87.5 1.0
CA N:CYS1201 4.4 62.6 1.0
OG1 N:THR1196 4.5 81.2 1.0
CA N:CYS1204 4.5 61.9 1.0
CA N:CYS1112 4.5 77.6 1.0
C N:CYS1194 4.5 79.7 1.0
N N:CYS1204 4.6 62.5 1.0
N N:CYS1112 4.6 78.6 1.0
O N:CYS1112 4.8 77.8 1.0
N N:CYS1194 4.9 78.9 1.0
CZ N:ARG1189 5.0 87.3 1.0
O N:HOH8129 5.0 41.8 1.0

Reference:

D.G.Vassylyev, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, I.Artsimovitch. Structural Basis For Transcription Elongation By Bacterial Rna Polymerase. Nature V. 448 157 2007.
ISSN: ISSN 0028-0836
PubMed: 17581590
DOI: 10.1038/NATURE05932
Page generated: Thu Oct 17 02:27:58 2024

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