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Zinc in PDB 2ppb: Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin

Enzymatic activity of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin, PDB code: 2ppb was solved by D.G.Vassylyev, M.N.Vassylyeva, I.Artsimovitch, R.Landick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 155.379, 155.379, 496.992, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.6

Other elements in 2ppb:

The structure of Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin (pdb code 2ppb). 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 Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin, PDB code: 2ppb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ppb

Go back to Zinc Binding Sites List in 2ppb
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin


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 Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn7058

b:87.6
occ:1.00
 SG D:CYS76 2.4 84.6 1.0
SG D:CYS73 2.4 84.8 1.0
SG D:CYS58 2.4 86.1 1.0
SG D:CYS60 2.5 86.9 1.0
CB D:CYS73 3.3 81.1 1.0
CB D:CYS76 3.5 80.6 1.0
O D:HOH9344 3.6 38.5 1.0
N D:CYS60 3.8 86.5 1.0
CB D:CYS58 3.8 84.9 1.0
CB D:CYS60 3.9 85.7 1.0
N D:LYS62 4.0 78.5 1.0
N D:GLY61 4.0 83.2 1.0
CB D:LYS62 4.2 75.4 1.0
CA D:CYS60 4.3 85.5 1.0
CB D:ALA59 4.3 86.6 1.0
N D:ALA59 4.3 86.3 1.0
CG D:LYS62 4.5 71.8 1.0
O D:CYS76 4.5 76.6 1.0
C D:CYS60 4.6 84.8 1.0
CA D:CYS76 4.6 78.3 1.0
CA D:ALA59 4.7 86.8 1.0
C D:ALA59 4.7 86.9 1.0
CA D:LYS62 4.7 77.5 1.0
N D:CYS76 4.7 77.7 1.0
CA D:CYS73 4.8 79.1 1.0
CG2 D:VAL78 4.9 70.0 1.0
C D:CYS76 4.9 77.0 1.0
C D:GLY61 5.0 80.4 1.0
CA D:GLY61 5.0 81.6 1.0

Zinc binding site 2 out of 4 in 2ppb

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Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin


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 Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn8112

b:58.0
occ:1.00
 SG D:CYS1112 2.3 54.2 1.0
SG D:CYS1201 2.4 52.5 1.0
SG D:CYS1194 2.4 55.2 1.0
SG D:CYS1204 2.4 50.4 1.0
CB D:CYS1204 3.2 49.4 1.0
CB D:CYS1112 3.3 55.1 1.0
CB D:CYS1194 3.6 55.6 1.0
CB D:CYS1201 3.6 50.9 1.0
CA D:CYS1194 3.9 56.8 1.0
N D:CYS1201 4.1 52.0 1.0
N D:CYS1204 4.3 48.3 1.0
CA D:CYS1204 4.3 49.2 1.0
CA D:CYS1201 4.4 50.5 1.0
CA D:CYS1112 4.5 55.9 1.0
N D:GLN1195 4.6 60.1 1.0
N D:CYS1112 4.6 53.3 1.0
CG1 D:VAL1200 4.7 54.6 1.0
O D:HOH9117 4.8 34.4 1.0
C D:CYS1194 4.8 58.8 1.0
O D:CYS1112 4.9 57.5 1.0
O D:HOH9016 4.9 10.1 1.0
C D:CYS1201 5.0 49.2 1.0

Zinc binding site 3 out of 4 in 2ppb

Go back to Zinc Binding Sites List in 2ppb
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin


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 Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn7158

b:70.1
occ:1.00
 SG N:CYS76 2.3 70.7 1.0
SG N:CYS58 2.4 66.7 1.0
SG N:CYS73 2.4 70.4 1.0
SG N:CYS60 2.5 71.7 1.0
CB N:CYS73 3.3 67.0 1.0
CB N:CYS76 3.4 69.3 1.0
CB N:CYS58 3.7 61.9 1.0
N N:CYS60 3.7 67.8 1.0
OG D:SER1300 3.9 62.8 1.0
CB N:CYS60 3.9 70.2 1.0
N N:GLY61 4.1 71.7 1.0
N N:ALA59 4.1 62.7 1.0
N N:LYS62 4.2 75.5 1.0
CB N:ALA59 4.3 64.3 1.0
CB N:LYS62 4.3 76.0 1.0
CA N:CYS60 4.3 69.8 1.0
O N:CYS76 4.5 69.0 1.0
CA N:CYS76 4.5 67.8 1.0
CA N:ALA59 4.6 63.9 1.0
C N:ALA59 4.7 64.7 1.0
C N:CYS60 4.7 70.9 1.0
N N:CYS76 4.8 66.8 1.0
CA N:CYS73 4.8 65.9 1.0
C N:CYS76 4.9 69.2 1.0
CA N:LYS62 4.9 76.8 1.0
CG2 N:VAL78 4.9 66.9 1.0
C N:CYS58 4.9 61.2 1.0
CA N:CYS58 4.9 59.9 1.0
O N:HOH9267 4.9 3.4 1.0
CB D:SER1300 5.0 64.6 1.0

Zinc binding site 4 out of 4 in 2ppb

Go back to Zinc Binding Sites List in 2ppb
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin


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 Rnap Polymerase Elongation Complex with the Ntp Substrate Analog and Antibiotic Streptolydigin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn8212

b:54.5
occ:1.00
 SG N:CYS1204 2.3 52.7 1.0
SG N:CYS1201 2.4 47.5 1.0
SG N:CYS1112 2.4 53.0 1.0
SG N:CYS1194 2.4 56.7 1.0
CB N:CYS1204 3.1 50.2 1.0
CB N:CYS1112 3.4 55.1 1.0
CB N:CYS1194 3.6 61.0 1.0
CB N:CYS1201 3.6 43.6 1.0
CA N:CYS1194 3.9 62.9 1.0
N N:CYS1201 4.1 39.7 1.0
NH1 N:ARG1189 4.2 41.9 1.0
CA N:CYS1204 4.3 46.8 1.0
N N:CYS1204 4.3 45.0 1.0
CA N:CYS1201 4.4 40.5 1.0
N N:GLN1195 4.5 62.2 1.0
CA N:CYS1112 4.6 55.5 1.0
N N:CYS1112 4.7 55.0 1.0
CG1 N:VAL1200 4.7 36.2 1.0
C N:CYS1194 4.8 63.3 1.0
O N:CYS1112 4.9 55.2 1.0
O N:HOH9103 4.9 2.8 1.0
CZ N:ARG1189 5.0 42.6 1.0
N N:CYS1194 5.0 64.4 1.0

Reference:

D.G.Vassylyev, M.N.Vassylyeva, J.Zhang, M.Palangat, I.Artsimovitch, R.Landick. Structural Basis For Substrate Loading in Bacterial Rna Polymerase. Nature V. 448 163 2007.
ISSN: ISSN 0028-0836
PubMed: 17581591
DOI: 10.1038/NATURE05931
Page generated: Wed Aug 20 05:12:08 2025

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