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Zinc in PDB 5d4e: Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp

Enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp, PDB code: 5d4e 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) 39.68 / 3.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.811, 103.948, 297.143, 90.00, 98.47, 90.00
R / Rfree (%) 21 / 24.6

Other elements in 5d4e:

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa and Ctp (pdb code 5d4e). 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 3'-Dephosphate-Coa and Ctp, PDB code: 5d4e:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5d4e

Go back to Zinc Binding Sites List in 5d4e
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa 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 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:20.5
occ:1.00
 SG D:CYS1204 2.2 12.7 1.0
SG D:CYS1201 2.3 17.0 1.0
SG D:CYS1194 2.3 13.9 1.0
SG D:CYS1112 2.3 19.1 1.0
CB D:CYS1204 3.2 16.1 1.0
CB D:CYS1194 3.2 19.0 1.0
CB D:CYS1201 3.4 15.5 1.0
CB D:CYS1112 3.5 22.2 1.0
CA D:CYS1194 3.6 16.0 1.0
OG1 D:THR1196 3.8 19.7 1.0
N D:GLN1195 3.9 20.6 1.0
N D:CYS1201 4.0 17.8 1.0
NH2 D:ARG1189 4.2 21.1 1.0
C D:CYS1194 4.2 17.1 1.0
CG2 D:THR1114 4.2 22.7 1.0
CA D:CYS1201 4.2 15.9 1.0
N D:CYS1112 4.3 24.5 1.0
CA D:CYS1204 4.4 15.8 1.0
CA D:CYS1112 4.5 22.2 1.0
N D:CYS1204 4.5 17.4 1.0
N D:THR1196 4.6 18.8 1.0
N D:CYS1194 4.8 11.4 1.0
CB D:THR1196 4.9 19.2 1.0
C D:CYS1201 4.9 14.6 1.0

Zinc binding site 2 out of 4 in 5d4e

Go back to Zinc Binding Sites List in 5d4e
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa 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 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:92.5
occ:1.00
 SG D:CYS60 2.3 90.0 1.0
SG D:CYS76 2.3 87.3 1.0
SG D:CYS58 2.3 0.2 1.0
SG D:CYS73 2.3 85.2 1.0
CB D:CYS73 2.9 82.1 1.0
CB D:CYS58 3.1 98.6 1.0
CB D:LYS62 3.6 0.8 1.0
N D:LYS62 3.8 98.9 1.0
CB D:CYS60 3.9 91.9 1.0
CB D:CYS76 3.9 88.2 1.0
N D:CYS76 4.1 92.4 1.0
N D:CYS60 4.1 94.9 1.0
N D:GLY61 4.2 95.7 1.0
CA D:LYS62 4.3 0.6 1.0
CA D:CYS73 4.4 81.3 1.0
CA D:CYS60 4.4 96.9 1.0
CA D:CYS58 4.5 89.7 1.0
CA D:CYS76 4.6 90.5 1.0
CD2 D:TYR63 4.6 0.4 1.0
N D:ALA59 4.6 75.2 1.0
N D:TYR63 4.6 0.8 1.0
C D:CYS60 4.7 94.3 1.0
CG D:LYS62 4.8 0.4 1.0
CB D:ARG75 4.8 79.6 1.0
C D:CYS58 4.8 80.7 1.0
CD D:LYS62 4.8 97.9 1.0
C D:GLY61 4.9 96.0 1.0
CE2 D:TYR63 5.0 98.4 1.0

Zinc binding site 3 out of 4 in 5d4e

Go back to Zinc Binding Sites List in 5d4e
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa 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 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1602

b:16.0
occ:1.00
 SG N:CYS1204 2.2 11.3 1.0
SG N:CYS1112 2.3 18.7 1.0
SG N:CYS1201 2.3 14.4 1.0
SG N:CYS1194 2.3 19.9 1.0
CB N:CYS1194 3.3 19.5 1.0
CB N:CYS1204 3.3 14.7 1.0
CB N:CYS1201 3.4 15.1 1.0
CB N:CYS1112 3.5 20.7 1.0
CA N:CYS1194 3.7 17.1 1.0
OG1 N:THR1196 3.9 19.3 1.0
NH2 N:ARG1189 3.9 18.9 1.0
N N:CYS1112 4.1 20.9 1.0
N N:GLN1195 4.1 18.2 1.0
CG2 N:THR1114 4.2 27.5 1.0
N N:CYS1201 4.2 15.2 1.0
CA N:CYS1112 4.4 21.8 1.0
N N:CYS1204 4.4 20.0 1.0
C N:CYS1194 4.4 19.6 1.0
CA N:CYS1204 4.4 17.7 1.0
CA N:CYS1201 4.4 14.6 1.0
O N:HOH2178 4.8 24.1 1.0
N N:THR1196 4.8 16.8 1.0
OD1 N:ASP1111 4.8 26.6 1.0
N N:CYS1194 4.9 13.4 1.0
CZ N:ARG1189 4.9 25.5 1.0

Zinc binding site 4 out of 4 in 5d4e

Go back to Zinc Binding Sites List in 5d4e
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with 3'-Dephosphate-Coa 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 3'-Dephosphate-Coa and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1603

b:50.4
occ:1.00
 SG N:CYS60 2.3 45.8 1.0
SG N:CYS76 2.3 43.3 1.0
SG N:CYS58 2.3 55.6 1.0
SG N:CYS73 2.3 43.0 1.0
CB N:CYS58 3.1 44.1 1.0
CB N:CYS73 3.2 41.9 1.0
CB N:CYS76 3.7 37.2 1.0
N N:CYS60 3.7 50.4 1.0
CB N:CYS60 3.8 47.6 1.0
CB N:LYS62 4.0 57.3 1.0
N N:CYS76 4.0 57.8 1.0
N N:LYS62 4.1 56.4 1.0
N N:ALA59 4.2 36.9 1.0
N N:GLY61 4.2 62.8 1.0
CA N:CYS60 4.2 50.0 1.0
CA N:CYS58 4.4 44.6 1.0
CA N:CYS76 4.4 43.7 1.0
C N:CYS58 4.5 37.4 1.0
C N:CYS60 4.6 57.4 1.0
CD2 N:TYR63 4.6 53.5 1.0
CA N:CYS73 4.6 43.8 1.0
CA N:LYS62 4.7 56.0 1.0
CB N:ARG75 4.7 55.7 1.0
CE2 N:TYR63 4.7 58.5 1.0
C N:ALA59 4.8 53.2 1.0
CA N:ALA59 4.9 40.5 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: Sun Oct 27 14:38:15 2024

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