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Zinc in PDB 5d4d: Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp

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

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

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp, PDB code: 5d4d 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) 42.17 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.000, 103.510, 296.300, 90.00, 98.27, 90.00
R / Rfree (%) 20.1 / 25.4

Other elements in 5d4d:

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

Magnesium (Mg) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad and Ctp (pdb code 5d4d). 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 Nad and Ctp, PDB code: 5d4d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5d4d

Go back to Zinc Binding Sites List in 5d4d
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:5.8
occ:1.00
 SG D:CYS1204 2.1 3.0 1.0
SG D:CYS1112 2.2 5.5 1.0
SG D:CYS1194 2.2 5.5 1.0
SG D:CYS1201 2.3 2.0 1.0
CB D:CYS1204 3.1 2.6 1.0
CB D:CYS1194 3.2 5.7 1.0
CB D:CYS1201 3.4 4.3 1.0
CB D:CYS1112 3.6 9.7 1.0
CA D:CYS1194 3.6 4.2 1.0
OG1 D:THR1196 4.0 10.1 1.0
NH2 D:ARG1189 4.0 5.4 1.0
N D:CYS1112 4.1 10.0 1.0
CG2 D:THR1114 4.1 11.1 1.0
N D:GLN1195 4.2 7.0 1.0
N D:CYS1201 4.3 2.4 1.0
CA D:CYS1204 4.3 2.8 1.0
N D:CYS1204 4.3 4.1 1.0
CA D:CYS1201 4.4 3.1 1.0
C D:CYS1194 4.4 6.1 1.0
CA D:CYS1112 4.4 10.4 1.0
N D:CYS1194 4.8 3.1 1.0
N D:THR1196 4.9 8.3 1.0
C D:CYS1201 5.0 2.6 1.0
OD1 D:ASP1111 5.0 14.2 1.0

Zinc binding site 2 out of 4 in 5d4d

Go back to Zinc Binding Sites List in 5d4d
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:40.1
occ:1.00
 SG D:CYS76 2.3 35.5 1.0
SG D:CYS73 2.3 45.9 1.0
SG D:CYS60 2.3 44.6 1.0
SG D:CYS58 2.3 38.4 1.0
CB D:CYS73 3.3 36.3 1.0
CB D:CYS58 3.3 38.2 1.0
CB D:CYS76 3.6 33.2 1.0
N D:CYS76 3.8 48.6 1.0
CB D:CYS60 3.8 40.0 1.0
N D:CYS60 3.9 41.8 1.0
CB D:LYS62 4.0 48.0 1.0
N D:LYS62 4.1 42.2 1.0
N D:GLY61 4.2 46.0 1.0
CA D:CYS76 4.3 41.2 1.0
CA D:CYS60 4.3 41.7 1.0
CD2 D:TYR63 4.4 45.9 1.0
N D:ALA59 4.4 26.6 1.0
CA D:CYS58 4.6 32.2 1.0
CB D:ARG75 4.6 44.9 1.0
CA D:LYS62 4.6 46.7 1.0
C D:CYS58 4.6 29.5 1.0
C D:CYS60 4.7 46.2 1.0
CA D:CYS73 4.7 37.9 1.0
CE2 D:TYR63 4.7 53.5 1.0
N D:TYR63 4.9 48.1 1.0
C D:ARG75 4.9 47.8 1.0
C D:ALA59 4.9 41.6 1.0

Zinc binding site 3 out of 4 in 5d4d

Go back to Zinc Binding Sites List in 5d4d
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2001

b:7.1
occ:1.00
 SG N:CYS1204 2.1 1.7 1.0
SG N:CYS1194 2.2 2.4 1.0
SG N:CYS1201 2.3 2.9 1.0
SG N:CYS1112 2.4 5.0 1.0
CB N:CYS1204 3.0 2.2 1.0
CB N:CYS1194 3.1 3.7 1.0
CB N:CYS1201 3.2 2.9 1.0
CA N:CYS1194 3.5 3.0 1.0
CB N:CYS1112 3.5 6.2 1.0
N N:CYS1201 3.8 3.5 1.0
N N:GLN1195 4.0 6.0 1.0
CA N:CYS1201 4.1 3.0 1.0
OG1 N:THR1196 4.1 7.2 1.0
NH2 N:ARG1189 4.1 9.3 1.0
CG2 N:THR1114 4.2 7.8 1.0
C N:CYS1194 4.2 4.4 1.0
CA N:CYS1204 4.3 2.5 1.0
N N:CYS1112 4.3 7.2 1.0
N N:CYS1204 4.4 3.1 1.0
CA N:CYS1112 4.6 6.2 1.0
N N:CYS1194 4.7 2.4 1.0
C N:CYS1201 4.7 2.6 1.0
N N:THR1196 4.7 6.0 1.0
O N:CYS1201 4.8 2.7 1.0
O N:HOH2147 4.9 3.2 1.0
C N:VAL1200 5.0 2.7 1.0

Zinc binding site 4 out of 4 in 5d4d

Go back to Zinc Binding Sites List in 5d4d
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Product Complex For Transcription Initiation with Nad 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 Nad and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2002

b:89.6
occ:1.00
 SG N:CYS58 2.3 94.2 1.0
SG N:CYS60 2.3 85.7 1.0
SG N:CYS76 2.3 79.9 1.0
SG N:CYS73 2.4 73.3 1.0
CB N:CYS73 2.9 76.4 1.0
CB N:CYS58 3.2 81.7 1.0
CB N:LYS62 3.9 83.9 1.0
N N:LYS62 4.0 78.9 1.0
CB N:CYS76 4.0 75.5 1.0
CB N:CYS60 4.0 80.1 1.0
N N:GLY61 4.3 90.9 1.0
N N:CYS76 4.3 82.3 1.0
N N:TYR63 4.4 87.2 1.0
CA N:CYS73 4.4 73.5 1.0
N N:CYS60 4.4 88.9 1.0
CA N:LYS62 4.4 82.2 1.0
CA N:CYS58 4.6 73.9 1.0
CA N:CYS76 4.7 77.6 1.0
CA N:CYS60 4.7 84.3 1.0
N N:ALA59 4.8 59.1 1.0
C N:CYS58 4.9 67.5 1.0
C N:CYS60 4.9 85.5 1.0
C N:LYS62 4.9 84.5 1.0
C N:CYS73 4.9 72.5 1.0
C N:GLY61 5.0 79.3 1.0
CB N:ARG75 5.0 78.1 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 14:37:29 2024

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