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Zinc in PDB 5tjg: Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp

Enzymatic activity of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp

All present enzymatic activity of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp:
2.7.7.6;

Protein crystallography data

The structure of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp, PDB code: 5tjg was solved by S.A.Darst, B.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.63 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 104.098, 111.423, 143.177, 104.12, 99.66, 109.43
R / Rfree (%) 22.4 / 26.2

Other elements in 5tjg:

The structure of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp (pdb code 5tjg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp, PDB code: 5tjg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5tjg

Go back to Zinc Binding Sites List in 5tjg
Zinc binding site 1 out of 2 in the Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.8
occ:1.00
SG D:CYS1204 2.3 82.3 1.0
SG D:CYS1194 2.3 78.7 1.0
SG D:CYS1112 2.4 89.2 1.0
SG D:CYS1201 2.6 69.9 1.0
CB D:CYS1204 3.0 81.4 1.0
CB D:CYS1112 3.3 61.5 1.0
CB D:CYS1194 3.3 57.3 1.0
CB D:CYS1201 3.4 82.7 1.0
CA D:CYS1194 3.6 66.0 1.0
OG1 D:THR1196 3.8 56.2 1.0
N D:CYS1201 3.9 58.5 1.0
N D:GLN1195 3.9 56.7 1.0
NH2 D:ARG1189 4.2 66.2 1.0
N D:CYS1112 4.2 63.1 1.0
CA D:CYS1201 4.2 57.5 1.0
CA D:CYS1204 4.2 55.6 1.0
C D:CYS1194 4.2 66.6 1.0
N D:CYS1204 4.3 52.7 1.0
CA D:CYS1112 4.3 61.1 1.0
N D:THR1196 4.4 73.6 1.0
CG2 D:THR1114 4.7 87.7 1.0
CB D:THR1196 4.7 75.4 1.0
C D:CYS1201 4.9 47.0 1.0
C D:VAL1200 4.9 64.9 1.0
N D:CYS1194 4.9 57.9 1.0
O D:CYS1201 4.9 51.1 1.0
CA D:GLN1195 5.0 78.0 1.0

Zinc binding site 2 out of 2 in 5tjg

Go back to Zinc Binding Sites List in 5tjg
Zinc binding site 2 out of 2 in the Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Aquaticus DELTA1.1-Sigmaa Holoenzyme/Downstream-Fork Promoter Complex with An Open Clamp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.5
occ:1.00
SG D:CYS76 2.3 95.9 1.0
SG D:CYS73 2.3 77.1 1.0
SG D:CYS58 2.3 0.9 1.0
SG D:CYS60 2.4 0.9 1.0
CB D:CYS76 3.0 95.2 1.0
CB D:CYS73 3.1 92.2 1.0
CB D:CYS58 3.1 74.5 1.0
CB D:CYS60 3.4 66.3 1.0
N D:CYS60 3.5 88.6 1.0
CA D:CYS60 3.9 87.9 1.0
N D:ALA59 4.0 72.9 1.0
N D:GLY61 4.0 82.9 1.0
N D:CYS76 4.1 90.2 1.0
CA D:CYS76 4.1 74.3 1.0
CA D:CYS58 4.3 79.4 1.0
N D:LYS62 4.3 62.8 1.0
C D:CYS58 4.4 80.5 1.0
C D:CYS60 4.5 89.3 1.0
CA D:CYS73 4.5 80.0 1.0
C D:ALA59 4.6 74.2 1.0
CB D:LYS62 4.6 76.1 1.0
CA D:ALA59 4.8 69.2 1.0

Reference:

A.Feklistov, B.Bae, J.Hauver, A.Lass-Napiorkowska, M.Kalesse, F.Glaus, K.H.Altmann, T.Heyduk, R.Landick, S.A.Darst. Rna Polymerase Motions During Promoter Melting. Science V. 356 863 2017.
ISSN: ESSN 1095-9203
PubMed: 28546214
DOI: 10.1126/SCIENCE.AAM7858
Page generated: Wed Dec 16 10:56:06 2020

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