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Zinc in PDB 3dxj: Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin

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

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

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin, PDB code: 3dxj was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 235.090, 235.090, 250.880, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 28.9

Other elements in 3dxj:

The structure of Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 3dxj

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Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the 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 Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1525

b:92.0
occ:1.00
SG D:CYS73 2.3 65.4 1.0
SG D:CYS60 2.5 71.9 1.0
SG D:CYS76 2.5 62.7 1.0
SG D:CYS58 2.5 84.8 1.0
CB D:CYS58 3.1 84.8 1.0
CB D:CYS73 3.4 79.0 1.0
CB D:LYS62 3.5 80.8 1.0
CG D:LYS62 3.5 82.7 1.0
N D:LYS62 3.7 80.9 1.0
CB D:CYS76 3.7 71.5 1.0
CD1 D:TYR63 3.9 91.1 1.0
CB D:CYS60 3.9 74.8 1.0
N D:CYS60 3.9 76.5 1.0
N D:CYS76 3.9 80.1 1.0
N D:GLY61 4.0 80.0 1.0
CA D:LYS62 4.1 80.3 1.0
N D:ALA59 4.2 79.6 1.0
CA D:CYS60 4.3 76.7 1.0
N D:TYR63 4.4 82.4 1.0
CA D:CYS58 4.4 83.9 1.0
C D:CYS60 4.4 78.7 1.0
CE1 D:TYR63 4.4 95.1 1.0
CA D:CYS76 4.4 75.3 1.0
CB D:ARG75 4.5 89.9 1.0
C D:CYS58 4.6 81.4 1.0
C D:GLY61 4.6 81.2 1.0
CA D:CYS73 4.6 81.7 1.0
C D:LYS62 4.6 80.2 1.0
C D:ALA59 4.7 77.3 1.0
CA D:GLY61 4.8 80.8 1.0
CG D:TYR63 4.9 90.9 1.0
CA D:ALA59 4.9 78.0 1.0
CD D:LYS62 4.9 82.1 1.0
CG D:ARG75 4.9 95.2 1.0

Zinc binding site 2 out of 4 in 3dxj

Go back to Zinc Binding Sites List in 3dxj
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the 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 Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1526

b:77.2
occ:1.00
SG D:CYS1194 2.4 69.5 1.0
SG D:CYS1112 2.5 71.6 1.0
SG D:CYS1201 2.5 47.1 1.0
SG D:CYS1204 2.5 71.6 1.0
CB D:CYS1194 3.0 67.3 1.0
CB D:CYS1204 3.0 66.5 1.0
CA D:CYS1194 3.2 67.2 1.0
CB D:CYS1112 3.3 72.1 1.0
N D:GLN1195 3.5 72.2 1.0
CB D:CYS1201 3.6 52.3 1.0
N D:CYS1201 3.6 54.6 1.0
OG1 D:THR1196 3.7 77.2 1.0
C D:CYS1194 3.8 69.6 1.0
CA D:CYS1201 4.1 55.0 1.0
N D:CYS1204 4.2 66.4 1.0
CA D:CYS1204 4.2 65.6 1.0
N D:THR1196 4.4 76.3 1.0
O D:CYS1201 4.4 54.2 1.0
N D:CYS1112 4.5 70.0 1.0
CG1 D:VAL1200 4.5 44.8 1.0
CA D:CYS1112 4.5 71.5 1.0
N D:CYS1194 4.5 65.5 1.0
CA D:GLN1195 4.7 75.3 1.0
CG2 D:THR1114 4.7 77.9 1.0
C D:CYS1201 4.7 57.0 1.0
C D:VAL1200 4.7 53.6 1.0
CB D:THR1196 4.8 75.3 1.0
CA D:VAL1200 4.9 52.0 1.0
C D:GLN1195 4.9 75.8 1.0
O D:CYS1194 5.0 69.7 1.0

Zinc binding site 3 out of 4 in 3dxj

Go back to Zinc Binding Sites List in 3dxj
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the 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 Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1525

b:50.2
occ:1.00
SG N:CYS60 2.4 52.2 1.0
SG N:CYS76 2.4 69.4 1.0
SG N:CYS73 2.5 68.8 1.0
SG N:CYS58 2.5 57.0 1.0
CB N:CYS58 2.9 75.4 1.0
N N:CYS60 3.3 76.8 1.0
CB N:CYS73 3.4 76.5 1.0
CB N:CYS76 3.5 76.5 1.0
N N:GLY61 3.5 82.3 1.0
N N:ALA59 3.6 79.4 1.0
N N:LYS62 3.6 89.6 1.0
CB N:CYS60 3.7 71.0 1.0
CG N:LYS62 3.7 95.7 1.0
CB N:LYS62 3.8 91.8 1.0
CA N:CYS60 3.8 75.4 1.0
C N:CYS58 3.9 80.3 1.0
C N:CYS60 3.9 78.6 1.0
N N:CYS76 4.0 82.8 1.0
CA N:CYS58 4.0 80.2 1.0
C N:ALA59 4.0 77.7 1.0
CA N:ALA59 4.3 78.1 1.0
C N:GLY61 4.3 88.5 1.0
CA N:LYS62 4.3 90.2 1.0
CA N:GLY61 4.3 85.6 1.0
CA N:CYS76 4.3 78.7 1.0
N N:TYR63 4.6 91.7 1.0
O N:CYS58 4.6 80.4 1.0
CB N:ALA59 4.6 79.0 1.0
CA N:CYS73 4.7 77.5 1.0
O N:CYS60 4.8 78.3 1.0
CD1 N:TYR63 4.8 0.5 1.0
CB N:ARG75 4.8 91.0 1.0
CD N:LYS62 4.8 100.0 1.0
O N:ALA59 5.0 77.8 1.0
C N:LYS62 5.0 90.2 1.0

Zinc binding site 4 out of 4 in 3dxj

Go back to Zinc Binding Sites List in 3dxj
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the 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 Thermus Thermophilus Rna Polymerase Holoenzyme in Complex with the Antibiotic Myxopyronin within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1526

b:55.7
occ:1.00
SG N:CYS1112 2.3 59.3 1.0
SG N:CYS1201 2.3 46.1 1.0
SG N:CYS1204 2.4 60.5 1.0
SG N:CYS1194 2.5 62.4 1.0
CB N:CYS1201 2.6 56.3 1.0
CB N:CYS1204 3.0 66.4 1.0
CB N:CYS1112 3.0 62.8 1.0
CB N:CYS1194 3.2 64.4 1.0
N N:CYS1201 3.4 65.5 1.0
CA N:CYS1201 3.5 61.9 1.0
CA N:CYS1194 3.6 66.8 1.0
N N:CYS1112 3.6 65.2 1.0
N N:CYS1204 3.7 71.0 1.0
O N:CYS1201 3.9 60.1 1.0
CA N:CYS1112 3.9 64.0 1.0
CA N:CYS1204 4.0 68.0 1.0
C N:CYS1201 4.0 62.4 1.0
N N:GLN1195 4.2 70.5 1.0
OG1 N:THR1196 4.3 67.6 1.0
C N:CYS1194 4.4 68.6 1.0
C N:VAL1200 4.7 67.2 1.0
N N:CYS1194 4.7 67.2 1.0
C N:CYS1112 4.7 63.9 1.0
N N:GLY1113 4.8 64.0 1.0
C N:ASP1111 4.8 65.4 1.0
CG2 N:THR1114 4.8 68.6 1.0
C N:LYS1203 4.9 71.8 1.0
OE1 N:GLU1109 5.0 84.2 1.0

Reference:

J.Mukhopadhyay, K.Das, S.Ismail, D.Koppstein, M.Jang, B.Hudson, S.Sarafianos, S.Tuske, J.Patel, R.Jansen, H.Irschik, E.Arnold, R.H.Ebright. The Rna Polymerase "Switch Region" Is A Target For Inhibitors. Cell(Cambridge,Mass.) V. 135 295 2008.
ISSN: ISSN 0092-8674
PubMed: 18957204
DOI: 10.1016/J.CELL.2008.09.033
Page generated: Thu Oct 24 12:22:05 2024

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