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Zinc in PDB 4xlq: Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter

Enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter

All present enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter, PDB code: 4xlq was solved by B.Bae, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 4.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 288.230, 288.230, 535.250, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 28.1

Other elements in 4xlq:

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter (pdb code 4xlq). 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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter, PDB code: 4xlq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xlq

Go back to Zinc Binding Sites List in 4xlq
Zinc binding site 1 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.9
occ:1.00
 CB D:CYS1112 1.7 0.3 1.0
SG D:CYS1201 2.3 0.9 1.0
SG D:CYS1194 2.3 0.9 1.0
SG D:CYS1204 2.4 0.3 1.0
SG D:CYS1112 2.4 0.5 1.0
CB D:CYS1201 3.0 1.0 1.0
NH2 D:ARG1189 3.0 0.1 1.0
CA D:CYS1112 3.2 0.5 1.0
CB D:CYS1194 3.5 0.2 1.0
CB D:CYS1204 3.6 0.4 1.0
N D:CYS1112 3.6 0.5 1.0
CA D:CYS1194 3.7 0.3 1.0
OG1 D:THR1196 4.0 0.3 1.0
N D:GLN1195 4.1 0.9 1.0
CZ D:ARG1189 4.1 0.2 1.0
CA D:CYS1201 4.1 0.2 1.0
C D:CYS1112 4.1 0.5 1.0
N D:CYS1201 4.2 0.5 1.0
C D:CYS1194 4.4 0.8 1.0
N D:CYS1204 4.5 0.2 1.0
N D:GLY1113 4.5 0.3 1.0
CA D:CYS1204 4.6 0.1 1.0
NE D:ARG1189 4.7 0.0 1.0
C D:CYS1201 4.7 0.2 1.0
N D:THR1196 4.8 0.5 1.0
NH1 D:ARG1189 4.9 0.1 1.0
N D:CYS1194 4.9 1.0 1.0
O D:CYS1112 4.9 0.8 1.0
C D:ASP1111 4.9 0.8 1.0
CG2 D:THR1114 4.9 0.3 1.0

Zinc binding site 2 out of 4 in 4xlq

Go back to Zinc Binding Sites List in 4xlq
Zinc binding site 2 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.6
occ:1.00
 SG D:CYS73 2.2 0.2 1.0
SG D:CYS76 2.3 0.3 1.0
SG D:CYS60 2.4 0.1 1.0
SG D:CYS58 2.5 0.2 1.0
CG D:LYS62 3.2 0.4 1.0
CB D:CYS73 3.4 0.5 1.0
CB D:LYS62 3.5 0.9 1.0
CB D:CYS58 3.7 0.5 1.0
N D:LYS62 3.7 0.6 1.0
CB D:CYS76 3.8 0.8 1.0
N D:CYS76 3.8 0.2 1.0
CD D:LYS62 3.9 0.9 1.0
CB D:CYS60 4.1 0.7 1.0
CA D:LYS62 4.2 0.8 1.0
N D:GLY61 4.2 0.7 1.0
N D:CYS60 4.3 0.6 1.0
CA D:CYS76 4.3 1.0 1.0
CB D:ARG75 4.4 0.5 1.0
N D:TYR63 4.6 0.1 1.0
CA D:CYS60 4.6 0.9 1.0
CA D:CYS73 4.7 1.0 1.0
N D:ALA59 4.7 0.5 1.0
C D:GLY61 4.8 1.0 1.0
N D:ARG75 4.8 0.8 1.0
C D:ARG75 4.8 0.1 1.0
N D:GLY77 4.8 0.2 1.0
C D:CYS60 4.8 0.1 1.0
C D:LYS62 4.9 0.2 1.0
CA D:ARG75 4.9 0.1 1.0
CA D:CYS58 4.9 0.2 1.0
C D:CYS76 5.0 0.1 1.0
C D:CYS58 5.0 0.7 1.0
CA D:GLY61 5.0 0.6 1.0

Zinc binding site 3 out of 4 in 4xlq

Go back to Zinc Binding Sites List in 4xlq
Zinc binding site 3 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:0.7
occ:1.00
 CB J:CYS1112 1.8 0.6 1.0
SG J:CYS1201 2.3 0.5 1.0
SG J:CYS1194 2.3 0.9 1.0
SG J:CYS1204 2.4 84.7 1.0
SG J:CYS1112 2.4 0.8 1.0
CB J:CYS1201 3.0 0.0 1.0
CA J:CYS1112 3.2 0.2 1.0
CB J:CYS1194 3.5 0.8 1.0
CB J:CYS1204 3.6 0.3 1.0
NH2 J:ARG1189 3.6 0.3 1.0
N J:CYS1112 3.7 0.5 1.0
CA J:CYS1194 3.7 0.7 1.0
OG1 J:THR1196 4.1 0.0 1.0
N J:GLN1195 4.1 0.3 1.0
CA J:CYS1201 4.1 0.5 1.0
N J:CYS1201 4.1 0.1 1.0
C J:CYS1112 4.2 0.3 1.0
C J:CYS1194 4.4 0.6 1.0
N J:CYS1204 4.4 0.5 1.0
N J:GLY1113 4.5 0.2 1.0
CA J:CYS1204 4.6 0.5 1.0
CZ J:ARG1189 4.6 0.2 1.0
C J:CYS1201 4.7 0.3 1.0
N J:THR1196 4.8 0.8 1.0
NE J:ARG1189 4.8 0.6 1.0
N J:CYS1194 4.9 0.2 1.0
CG2 J:THR1114 4.9 0.5 1.0
C J:ASP1111 4.9 0.7 1.0
O J:CYS1112 5.0 0.7 1.0

Zinc binding site 4 out of 4 in 4xlq

Go back to Zinc Binding Sites List in 4xlq
Zinc binding site 4 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.6
occ:1.00
 SG J:CYS73 2.2 0.9 1.0
SG J:CYS60 2.3 0.9 1.0
SG J:CYS76 2.3 0.2 1.0
SG J:CYS58 2.4 0.5 1.0
CG J:LYS62 3.2 0.6 1.0
CB J:LYS62 3.4 0.6 1.0
CB J:CYS73 3.5 0.4 1.0
N J:LYS62 3.6 0.7 1.0
CB J:CYS58 3.6 0.9 1.0
CB J:CYS76 3.8 0.6 1.0
N J:CYS76 3.9 0.9 1.0
CD J:LYS62 3.9 0.9 1.0
CB J:CYS60 4.0 0.8 1.0
CA J:LYS62 4.1 0.5 1.0
N J:GLY61 4.1 0.2 1.0
N J:CYS60 4.2 0.4 1.0
CA J:CYS76 4.4 0.8 1.0
CB J:ARG75 4.5 0.2 1.0
N J:TYR63 4.5 0.1 1.0
CA J:CYS60 4.6 0.5 1.0
C J:GLY61 4.7 0.5 1.0
N J:ALA59 4.7 0.8 1.0
CA J:CYS73 4.8 0.8 1.0
C J:CYS60 4.8 0.3 1.0
C J:LYS62 4.8 0.2 1.0
CA J:GLY61 4.8 0.1 1.0
CA J:CYS58 4.9 0.9 1.0
C J:CYS58 4.9 0.4 1.0
N J:ARG75 4.9 0.5 1.0
C J:ARG75 4.9 0.5 1.0
N J:GLY77 5.0 0.1 1.0

Reference:

B.Bae, A.Feklistov, A.Lass-Napiorkowska, R.Landick, S.A.Darst. Structure of A Bacterial Rna Polymerase Holoenzyme Open Promoter Complex. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26349032
DOI: 10.7554/ELIFE.08504
Page generated: Sun Oct 27 10:35:00 2024

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