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Zinc in PDB 3eql: Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin

Enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin

All present enzymatic activity of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin, PDB code: 3eql was solved by D.G.Vassylyev, M.N.Vassylyeva, I.Artsimovitch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 235.001, 235.001, 254.947, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 27

Other elements in 3eql:

The structure of Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin 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 Holoenzyme in Complex with Antibiotic Myxopyronin (pdb code 3eql). 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 Holoenzyme in Complex with Antibiotic Myxopyronin, PDB code: 3eql:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3eql

Go back to Zinc Binding Sites List in 3eql
Zinc binding site 1 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin


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 Holoenzyme in Complex with Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1525

b:62.4
occ:1.00
 SG D:CYS60 2.3 60.7 1.0
SG D:CYS73 2.3 60.1 1.0
SG D:CYS58 2.4 54.4 1.0
SG D:CYS76 2.4 62.8 1.0
O D:HOH1539 3.0 36.1 1.0
N D:CYS60 3.2 55.2 1.0
CB D:CYS73 3.3 59.5 1.0
O D:HOH2023 3.4 49.7 1.0
CB D:CYS60 3.4 58.5 1.0
CB D:CYS58 3.7 48.1 1.0
CA D:CYS60 3.7 57.0 1.0
N D:GLY61 3.9 58.1 1.0
CB D:CYS76 3.9 63.2 1.0
O D:CYS76 4.0 64.0 1.0
N D:ALA59 4.0 47.6 1.0
N D:LYS62 4.1 60.3 1.0
CB D:LYS62 4.2 61.7 1.0
C D:CYS60 4.2 57.5 1.0
C D:ALA59 4.2 54.0 1.0
N D:CYS76 4.4 65.8 1.0
CA D:ALA59 4.5 51.6 1.0
CA D:CYS76 4.6 63.9 1.0
C D:CYS58 4.7 45.9 1.0
CA D:CYS73 4.7 59.5 1.0
C D:CYS76 4.7 62.3 1.0
CA D:LYS62 4.8 62.0 1.0
CA D:CYS58 4.8 45.7 1.0
CB D:ALA59 4.8 50.6 1.0
O D:HOH1735 4.9 34.4 1.0
N D:TYR63 5.0 62.2 1.0

Zinc binding site 2 out of 4 in 3eql

Go back to Zinc Binding Sites List in 3eql
Zinc binding site 2 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin


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 Holoenzyme in Complex with Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1526

b:48.9
occ:1.00
 SG D:CYS1112 2.3 54.3 1.0
SG D:CYS1204 2.3 49.6 1.0
SG D:CYS1194 2.3 51.2 1.0
SG D:CYS1201 2.3 48.2 1.0
CB D:CYS1204 3.1 50.2 1.0
CB D:CYS1112 3.2 56.7 1.0
CB D:CYS1194 3.5 49.3 1.0
CB D:CYS1201 3.6 42.7 1.0
O D:HOH1762 3.7 33.8 1.0
CA D:CYS1194 3.8 51.1 1.0
N D:CYS1201 4.1 36.9 1.0
N D:GLN1195 4.3 56.6 1.0
CA D:CYS1204 4.3 50.5 1.0
N D:CYS1204 4.4 48.8 1.0
CA D:CYS1112 4.4 59.9 1.0
CA D:CYS1201 4.4 39.5 1.0
N D:CYS1112 4.5 59.6 1.0
NH1 D:ARG1189 4.5 54.0 1.0
O D:CYS1112 4.6 63.5 1.0
C D:CYS1194 4.7 53.7 1.0
C D:CYS1112 4.9 62.4 1.0
N D:CYS1194 5.0 48.3 1.0

Zinc binding site 3 out of 4 in 3eql

Go back to Zinc Binding Sites List in 3eql
Zinc binding site 3 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin


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 Holoenzyme in Complex with Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1525

b:58.4
occ:1.00
 SG N:CYS73 2.3 57.2 1.0
SG N:CYS60 2.3 57.0 1.0
SG N:CYS76 2.4 58.9 1.0
SG N:CYS58 2.4 57.1 1.0
CB N:CYS73 3.2 59.3 1.0
N N:CYS60 3.3 53.2 1.0
CB N:CYS60 3.4 55.2 1.0
O N:HOH1921 3.4 62.7 1.0
CA N:CYS60 3.8 55.4 1.0
CB N:CYS58 3.8 53.5 1.0
CB N:CYS76 3.9 57.9 1.0
O N:CYS76 3.9 59.5 1.0
N N:GLY61 4.0 58.1 1.0
N N:ALA59 4.1 48.5 1.0
N N:LYS62 4.2 60.4 1.0
CB N:LYS62 4.2 61.6 1.0
N N:CYS76 4.3 57.0 1.0
C N:CYS60 4.3 56.7 1.0
C N:ALA59 4.3 51.5 1.0
CA N:CYS76 4.5 57.6 1.0
CA N:ALA59 4.6 50.0 1.0
C N:CYS76 4.6 57.2 1.0
CA N:CYS73 4.7 59.1 1.0
C N:CYS58 4.7 49.1 1.0
CA N:LYS62 4.9 61.0 1.0
CB N:ALA59 4.9 48.8 1.0
CA N:CYS58 4.9 50.4 1.0

Zinc binding site 4 out of 4 in 3eql

Go back to Zinc Binding Sites List in 3eql
Zinc binding site 4 out of 4 in the Crystal Structure of the T. Thermophilus Rna Polymerase Holoenzyme in Complex with Antibiotic Myxopyronin


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 Holoenzyme in Complex with Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1526

b:66.7
occ:1.00
 SG N:CYS1112 2.3 67.2 1.0
SG N:CYS1194 2.3 64.9 1.0
SG N:CYS1204 2.4 65.7 1.0
SG N:CYS1201 2.4 65.7 1.0
O N:HOH1595 3.1 39.8 1.0
CB N:CYS1112 3.2 65.3 1.0
CB N:CYS1204 3.3 61.8 1.0
CB N:CYS1194 3.4 63.5 1.0
CA N:CYS1194 3.7 63.2 1.0
CB N:CYS1201 3.7 61.0 1.0
N N:GLN1195 4.1 68.1 1.0
N N:CYS1201 4.1 57.0 1.0
CA N:CYS1112 4.4 66.7 1.0
CA N:CYS1204 4.5 58.7 1.0
C N:CYS1194 4.5 64.7 1.0
CA N:CYS1201 4.5 58.0 1.0
N N:CYS1204 4.5 60.5 1.0
N N:CYS1112 4.6 67.1 1.0
O N:CYS1112 4.7 69.9 1.0
NH1 N:ARG1189 4.8 47.2 1.0
N N:CYS1194 4.8 61.5 1.0
C N:CYS1112 4.9 67.8 1.0

Reference:

G.A.Belogurov, M.N.Vassylyeva, A.Sevostyanova, J.R.Appleman, A.X.Xiang, R.Lira, S.E.Webber, S.Klyuyev, E.Nudler, I.Artsimovitch, D.G.Vassylyev. Transcription Inactivation Through Local Refolding of the Rna Polymerase Structure. Nature V. 457 332 2009.
ISSN: ISSN 0028-0836
PubMed: 18946472
DOI: 10.1038/NATURE07510
Page generated: Thu Oct 24 12:54:11 2024

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