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Zinc in PDB 5d4c: Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp, PDB code: 5d4c was solved by Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.20 / 3.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.960, 103.640, 297.420, 90.00, 98.30, 90.00
R / Rfree (%) 21.2 / 25.7

Other elements in 5d4c:

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp (pdb code 5d4c). 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 Product Complex For Transcription Initiation with Atp and Ctp, PDB code: 5d4c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5d4c

Go back to Zinc Binding Sites List in 5d4c
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp


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 Product Complex For Transcription Initiation with Atp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:10.4
occ:1.00
SG D:CYS1204 2.2 10.2 1.0
SG D:CYS1201 2.2 16.7 1.0
SG D:CYS1112 2.3 29.6 1.0
SG D:CYS1194 2.5 12.3 1.0
CB D:CYS1201 3.0 11.8 1.0
CB D:CYS1112 3.3 21.0 1.0
CB D:CYS1194 3.3 16.5 1.0
CA D:CYS1194 3.5 12.8 1.0
CB D:CYS1204 3.6 14.4 1.0
N D:GLN1195 3.8 14.1 1.0
OG1 D:THR1196 4.0 19.6 1.0
N D:CYS1112 4.0 19.2 1.0
N D:CYS1201 4.0 13.9 1.0
CG2 D:THR1114 4.1 21.5 1.0
CA D:CYS1201 4.1 11.2 1.0
NH2 D:ARG1189 4.1 14.3 1.0
C D:CYS1194 4.2 14.6 1.0
CA D:CYS1112 4.2 18.8 1.0
N D:THR1196 4.5 12.1 1.0
N D:CYS1204 4.7 10.1 1.0
CA D:CYS1204 4.7 12.1 1.0
N D:CYS1194 4.8 8.0 1.0
CA D:GLN1195 4.9 14.9 1.0
C D:CYS1112 5.0 22.4 1.0
OD1 D:ASP1111 5.0 27.8 1.0
CB D:THR1196 5.0 14.8 1.0

Zinc binding site 2 out of 4 in 5d4c

Go back to Zinc Binding Sites List in 5d4c
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp


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 Product Complex For Transcription Initiation with Atp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:92.2
occ:1.00
SG D:CYS76 2.3 72.4 1.0
SG D:CYS60 2.4 75.0 1.0
SG D:CYS73 2.6 82.8 1.0
SG D:CYS58 2.8 84.8 1.0
CB D:CYS76 3.3 63.5 1.0
CB D:CYS73 3.5 71.5 1.0
CB D:CYS58 3.6 68.6 1.0
N D:CYS60 3.7 81.2 1.0
N D:CYS76 3.7 80.6 1.0
CB D:CYS60 3.8 74.4 1.0
CB D:LYS62 4.0 88.9 1.0
CA D:CYS76 4.1 76.0 1.0
N D:LYS62 4.1 92.8 1.0
N D:GLY61 4.1 92.3 1.0
CA D:CYS60 4.1 81.9 1.0
N D:ALA59 4.3 61.2 1.0
C D:CYS60 4.5 86.3 1.0
CB D:ARG75 4.5 78.0 1.0
CA D:LYS62 4.7 92.9 1.0
C D:CYS58 4.7 60.3 1.0
C D:ALA59 4.7 74.8 1.0
CA D:CYS58 4.8 66.7 1.0
C D:ARG75 4.8 83.2 1.0
CA D:ALA59 4.9 60.9 1.0
C D:CYS76 4.9 71.4 1.0
CA D:CYS73 5.0 73.8 1.0

Zinc binding site 3 out of 4 in 5d4c

Go back to Zinc Binding Sites List in 5d4c
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp


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 Product Complex For Transcription Initiation with Atp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1602

b:8.2
occ:1.00
SG N:CYS1204 2.1 10.3 1.0
SG N:CYS1201 2.2 15.5 1.0
SG N:CYS1112 2.5 20.2 1.0
SG N:CYS1194 2.5 5.8 1.0
CB N:CYS1201 3.1 8.5 1.0
CB N:CYS1112 3.3 17.5 1.0
CB N:CYS1194 3.4 9.1 1.0
CA N:CYS1194 3.6 8.5 1.0
CB N:CYS1204 3.7 10.9 1.0
N N:GLN1195 3.8 11.5 1.0
OG1 N:THR1196 3.9 13.2 1.0
CG2 N:THR1114 4.0 17.9 1.0
N N:CYS1201 4.1 13.3 1.0
N N:CYS1112 4.2 18.4 1.0
NH2 N:ARG1189 4.2 16.3 1.0
C N:CYS1194 4.2 10.5 1.0
CA N:CYS1201 4.2 9.3 1.0
CA N:CYS1112 4.3 17.7 1.0
N N:THR1196 4.5 11.3 1.0
CB N:THR1114 4.8 19.8 1.0
N N:CYS1194 4.8 6.3 1.0
CA N:CYS1204 4.8 8.8 1.0
N N:CYS1204 4.8 9.3 1.0
C N:CYS1112 4.9 16.1 1.0
CA N:GLN1195 4.9 12.4 1.0
OD1 N:ASP1111 4.9 26.5 1.0
CB N:THR1196 5.0 11.8 1.0

Zinc binding site 4 out of 4 in 5d4c

Go back to Zinc Binding Sites List in 5d4c
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Atp and Ctp


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 Product Complex For Transcription Initiation with Atp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1603

b:0.1
occ:1.00
SG N:CYS60 2.4 0.9 1.0
SG N:CYS58 2.5 0.2 1.0
SG N:CYS73 2.5 0.7 1.0
SG N:CYS76 2.6 0.7 1.0
CB N:CYS73 3.2 0.5 1.0
CB N:CYS58 3.2 0.8 1.0
CB N:LYS62 3.8 0.5 1.0
N N:LYS62 3.8 0.9 1.0
CB N:CYS60 3.9 1.0 1.0
N N:CYS60 3.9 0.5 1.0
N N:GLY61 4.0 0.9 1.0
CB N:CYS76 4.1 0.7 1.0
N N:CYS76 4.3 0.9 1.0
CA N:CYS60 4.3 0.4 1.0
CA N:LYS62 4.4 0.9 1.0
N N:ALA59 4.4 95.1 1.0
C N:CYS60 4.6 0.8 1.0
CA N:CYS58 4.6 95.4 1.0
CA N:CYS73 4.7 0.3 1.0
C N:CYS58 4.8 84.9 1.0
CA N:CYS76 4.8 0.8 1.0
N N:TYR63 4.8 0.3 1.0
C N:GLY61 4.8 0.4 1.0
CB N:ARG75 4.9 0.9 1.0
CD2 N:TYR63 4.9 0.8 1.0
CA N:GLY61 4.9 0.9 1.0

Reference:

J.G.Bird, Y.Zhang, Y.Tian, N.Panova, I.Barvik, L.Greene, M.Liu, B.Buckley, L.Krasny, J.K.Lee, C.D.Kaplan, R.H.Ebright, B.E.Nickels. The Mechanism of Rna 5' Capping with Nad(+), Nadh and Desphospho-Coa. Nature V. 535 444 2016.
ISSN: ESSN 1476-4687
PubMed: 27383794
DOI: 10.1038/NATURE18622
Page generated: Wed Dec 16 06:07:58 2020

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