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Zinc in PDB 4xlp: Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork Promoter

Enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork Promoter

All present enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork Promoter:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork Promoter, PDB code: 4xlp 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) 50.03 / 4.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 289.870, 289.870, 537.360, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 29.7

Other elements in 4xlp:

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork 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 Promoter (pdb code 4xlp). 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 Promoter, PDB code: 4xlp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xlp

Go back to Zinc Binding Sites List in 4xlp
Zinc binding site 1 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork 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 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.5
occ:1.00
 SG D:CYS1194 2.2 86.8 1.0
SG D:CYS1204 2.2 86.8 1.0
SG D:CYS1201 2.2 94.6 1.0
SG D:CYS1112 2.3 86.8 1.0
CB D:CYS1204 2.7 98.3 1.0
CB D:CYS1112 3.2 0.4 1.0
CB D:CYS1194 3.4 0.1 1.0
OG1 D:THR1196 3.6 0.2 1.0
CB D:CYS1201 3.7 1.0 1.0
CA D:CYS1194 3.8 86.8 1.0
CA D:CYS1204 4.0 0.1 1.0
NZ D:LYS1203 4.1 0.3 1.0
N D:CYS1204 4.2 0.1 1.0
N D:CYS1201 4.3 0.4 1.0
N D:CYS1112 4.3 0.8 1.0
CE D:LYS1203 4.3 0.7 1.0
CA D:CYS1112 4.3 93.1 1.0
N D:GLN1195 4.4 87.5 1.0
CA D:CYS1201 4.5 0.9 1.0
CG2 D:THR1114 4.5 0.3 1.0
C D:CYS1194 4.6 86.8 1.0
NH2 D:ARG1189 4.6 0.8 1.0
C D:CYS1201 4.8 0.3 1.0
N D:THR1196 4.9 0.3 1.0
O D:CYS1201 4.9 0.9 1.0
CB D:THR1196 5.0 0.1 1.0

Zinc binding site 2 out of 4 in 4xlp

Go back to Zinc Binding Sites List in 4xlp
Zinc binding site 2 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork 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 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.9
occ:1.00
 SG D:CYS60 2.3 86.8 1.0
SG D:CYS73 2.3 0.6 1.0
SG D:CYS76 2.5 0.7 1.0
SG D:CYS58 2.5 0.6 1.0
CB D:CYS73 2.7 0.9 1.0
CG D:LYS62 3.2 0.8 1.0
CB D:CYS58 3.4 0.5 1.0
CD D:LYS62 3.7 0.4 1.0
CG D:ARG75 3.8 0.1 1.0
CB D:CYS60 3.9 86.8 1.0
CA D:CYS73 4.1 0.5 1.0
CB D:CYS76 4.2 0.0 1.0
CB D:LYS62 4.2 0.3 1.0
N D:CYS60 4.3 1.0 1.0
N D:CYS76 4.3 0.2 1.0
CD D:ARG75 4.4 0.9 1.0
N D:LYS62 4.4 0.7 1.0
C D:CYS73 4.6 1.0 1.0
CA D:CYS60 4.6 0.3 1.0
N D:GLY61 4.6 0.6 1.0
N D:ALA59 4.7 0.6 1.0
N D:ARG75 4.8 0.5 1.0
N D:GLU74 4.8 0.4 1.0
CA D:CYS58 4.8 0.4 1.0
CA D:CYS76 4.8 0.1 1.0
CB D:ARG75 4.9 0.2 1.0
CA D:LYS62 4.9 0.9 1.0
N D:TYR63 5.0 0.8 1.0

Zinc binding site 3 out of 4 in 4xlp

Go back to Zinc Binding Sites List in 4xlp
Zinc binding site 3 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork 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 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:0.6
occ:1.00
 SG J:CYS1194 2.2 0.0 1.0
SG J:CYS1204 2.2 98.5 1.0
SG J:CYS1112 2.3 86.8 1.0
SG J:CYS1201 2.3 0.0 1.0
CB J:CYS1204 2.7 87.0 1.0
CB J:CYS1112 3.2 0.2 1.0
CB J:CYS1194 3.4 0.6 1.0
OG1 J:THR1196 3.6 0.4 1.0
CB J:CYS1201 3.7 0.7 1.0
CA J:CYS1194 3.8 0.8 1.0
CA J:CYS1204 4.0 98.4 1.0
NZ J:LYS1203 4.1 1.0 1.0
N J:CYS1204 4.2 98.1 1.0
N J:CYS1201 4.3 0.0 1.0
N J:CYS1112 4.3 0.4 1.0
CE J:LYS1203 4.3 0.5 1.0
CA J:CYS1112 4.3 0.8 1.0
N J:GLN1195 4.4 0.7 1.0
CG2 J:THR1114 4.5 0.9 1.0
CA J:CYS1201 4.5 0.5 1.0
NH2 J:ARG1189 4.6 0.3 1.0
C J:CYS1194 4.6 0.9 1.0
C J:CYS1201 4.8 0.8 1.0
N J:THR1196 4.9 0.4 1.0
O J:CYS1201 4.9 0.5 1.0
CB J:THR1196 5.0 0.5 1.0

Zinc binding site 4 out of 4 in 4xlp

Go back to Zinc Binding Sites List in 4xlp
Zinc binding site 4 out of 4 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork 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 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.3
occ:1.00
 SG J:CYS60 2.3 0.9 1.0
SG J:CYS73 2.3 0.9 1.0
SG J:CYS58 2.5 0.3 1.0
SG J:CYS76 2.5 0.7 1.0
CB J:CYS73 2.7 1.0 1.0
CG J:LYS62 3.1 1.0 1.0
CB J:CYS58 3.4 0.4 1.0
CD J:LYS62 3.7 0.5 1.0
CG J:ARG75 3.9 0.5 1.0
CB J:CYS60 3.9 0.8 1.0
CA J:CYS73 4.1 0.7 1.0
CB J:LYS62 4.2 0.6 1.0
CB J:CYS76 4.3 0.3 1.0
N J:CYS60 4.3 0.6 1.0
N J:CYS76 4.3 0.2 1.0
N J:LYS62 4.4 0.7 1.0
CD J:ARG75 4.4 0.2 1.0
C J:CYS73 4.6 0.7 1.0
CA J:CYS60 4.6 0.3 1.0
N J:GLY61 4.7 0.3 1.0
N J:ALA59 4.8 0.0 1.0
N J:GLU74 4.8 0.2 1.0
N J:ARG75 4.8 0.5 1.0
CA J:CYS58 4.8 0.5 1.0
CA J:LYS62 4.9 0.8 1.0
CB J:ARG75 4.9 0.0 1.0
CA J:CYS76 4.9 0.9 1.0
N J:TYR63 4.9 0.1 1.0
CD2 J:TYR63 5.0 0.7 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 10:34:56 2024

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