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Zinc in PDB 5x22: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp, PDB code: 5x22 was solved by Y.Zhang, R.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 3.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 186.410, 104.320, 297.290, 90.00, 98.36, 90.00
R / Rfree (%) 20.8 / 25

Other elements in 5x22:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp also contains other interesting chemical elements:

Magnesium (Mg) 14 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp (pdb code 5x22). 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 Transcription Initiation Complex with Gpa and Cmpcpp, PDB code: 5x22:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5x22

Go back to Zinc Binding Sites List in 5x22
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 Transcription Initiation Complex with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:11.0
occ:1.00
 SG D:CYS1204 2.3 11.1 1.0
SG D:CYS1112 2.3 18.8 1.0
SG D:CYS1201 2.3 11.0 1.0
SG D:CYS1194 2.3 7.7 1.0
CB D:CYS1204 2.9 9.2 1.0
CB D:CYS1194 3.3 9.7 1.0
CB D:CYS1201 3.4 10.8 1.0
CB D:CYS1112 3.5 15.1 1.0
CA D:CYS1194 3.7 9.7 1.0
OG1 D:THR1196 3.9 13.3 1.0
N D:CYS1201 3.9 10.0 1.0
N D:GLN1195 4.1 12.6 1.0
CA D:CYS1204 4.2 9.6 1.0
N D:CYS1112 4.2 14.9 1.0
NH2 D:ARG1189 4.2 13.7 1.0
CA D:CYS1201 4.2 10.0 1.0
CG2 D:THR1114 4.2 14.4 1.0
N D:CYS1204 4.3 10.7 1.0
C D:CYS1194 4.4 11.7 1.0
CA D:CYS1112 4.4 14.3 1.0
N D:THR1196 4.7 11.3 1.0
N D:CYS1194 4.9 9.6 1.0
C D:CYS1201 4.9 10.4 1.0

Zinc binding site 2 out of 4 in 5x22

Go back to Zinc Binding Sites List in 5x22
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 Transcription Initiation Complex with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:73.1
occ:1.00
 SG D:CYS60 2.3 64.1 1.0
SG D:CYS58 2.3 78.8 1.0
SG D:CYS76 2.3 60.1 1.0
SG D:CYS73 2.3 74.6 1.0
CB D:CYS58 2.7 64.7 1.0
CB D:CYS73 2.7 66.9 1.0
N D:LYS62 3.9 71.6 1.0
CB D:LYS62 4.0 72.5 1.0
CB D:CYS60 4.0 65.4 1.0
CB D:CYS76 4.0 63.5 1.0
N D:GLY61 4.2 66.1 1.0
N D:CYS76 4.2 74.4 1.0
CA D:CYS58 4.2 60.5 1.0
N D:CYS60 4.2 68.5 1.0
CA D:CYS73 4.2 64.1 1.0
CD2 D:TYR63 4.5 75.0 1.0
CA D:LYS62 4.5 72.6 1.0
CA D:CYS60 4.5 66.4 1.0
N D:ALA59 4.6 59.9 1.0
CA D:CYS76 4.6 70.7 1.0
C D:CYS58 4.6 59.8 1.0
N D:TYR63 4.7 76.4 1.0
C D:CYS60 4.8 68.3 1.0
CB D:ARG75 4.8 69.3 1.0
CE2 D:TYR63 4.8 70.9 1.0
C D:CYS73 4.9 67.2 1.0
C D:GLY61 4.9 74.4 1.0
N D:CYS58 4.9 58.3 1.0
CA D:GLY61 5.0 70.9 1.0

Zinc binding site 3 out of 4 in 5x22

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Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 Transcription Initiation Complex with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2001

b:15.7
occ:1.00
 SG N:CYS1201 2.2 25.3 1.0
SG N:CYS1112 2.2 23.3 1.0
SG N:CYS1204 2.3 19.6 1.0
SG N:CYS1194 2.3 23.1 1.0
CB N:CYS1204 3.0 20.1 1.0
CB N:CYS1201 3.2 25.1 1.0
CB N:CYS1194 3.3 21.8 1.0
CA N:CYS1194 3.8 20.3 1.0
CB N:CYS1112 3.8 28.2 1.0
OG1 N:THR1196 3.9 26.6 1.0
CG2 N:THR1114 4.0 28.9 1.0
N N:CYS1201 4.0 23.1 1.0
NH2 N:ARG1189 4.0 23.4 1.0
CA N:CYS1204 4.2 21.4 1.0
CA N:CYS1201 4.2 22.9 1.0
N N:CYS1204 4.2 22.8 1.0
N N:CYS1112 4.3 29.2 1.0
N N:GLN1195 4.3 19.9 1.0
C N:CYS1194 4.5 21.4 1.0
CA N:CYS1112 4.6 27.6 1.0
NE N:ARG1189 4.9 27.5 1.0
N N:CYS1194 4.9 15.5 1.0
N N:THR1196 4.9 21.7 1.0
CZ N:ARG1189 4.9 26.1 1.0
C N:CYS1201 5.0 21.1 1.0

Zinc binding site 4 out of 4 in 5x22

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Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with Gpa and Cmpcpp


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 Transcription Initiation Complex with Gpa and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2002

b:25.9
occ:1.00
 SG N:CYS76 2.3 38.5 1.0
SG N:CYS60 2.3 41.1 1.0
SG N:CYS73 2.3 35.9 1.0
SG N:CYS58 2.4 42.4 1.0
CB N:CYS73 3.2 38.2 1.0
CB N:CYS76 3.3 36.8 1.0
CB N:CYS58 3.3 37.6 1.0
N N:CYS60 3.6 44.4 1.0
CB N:CYS60 3.7 43.1 1.0
N N:CYS76 3.9 47.8 1.0
CB N:LYS62 3.9 50.4 1.0
N N:LYS62 4.0 53.6 1.0
CA N:CYS60 4.1 44.7 1.0
N N:ALA59 4.1 33.0 1.0
N N:GLY61 4.1 51.0 1.0
CA N:CYS76 4.2 41.1 1.0
C N:CYS58 4.5 37.2 1.0
CA N:CYS58 4.5 37.4 1.0
C N:CYS60 4.5 49.6 1.0
CA N:LYS62 4.6 51.4 1.0
C N:ALA59 4.6 42.8 1.0
CA N:CYS73 4.7 36.5 1.0
CB N:ARG75 4.7 44.7 1.0
CA N:ALA59 4.8 33.0 1.0
CD2 N:TYR63 4.9 48.3 1.0
N N:TYR63 4.9 49.0 1.0
C N:ARG75 5.0 49.4 1.0

Reference:

S.I.Maffioli, Y.Zhang, D.Degen, T.Carzaniga, G.Del Gatto, S.Serina, P.Monciardini, C.Mazzetti, P.Guglierame, G.Candiani, A.I.Chiriac, G.Facchetti, P.Kaltofen, H.G.Sahl, G.Deho, S.Donadio, R.H.Ebright. Antibacterial Nucleoside-Analog Inhibitor of Bacterial Rna Polymerase. Cell V. 169 1240 2017.
ISSN: ISSN 1097-4172
PubMed: 28622509
DOI: 10.1016/J.CELL.2017.05.042
Page generated: Mon Oct 28 14:46:16 2024

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