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Zinc in PDB 4ylp: E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna

Enzymatic activity of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna

All present enzymatic activity of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna, PDB code: 4ylp was solved by Y.Zuo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.98 / 5.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 237.674, 204.988, 248.838, 90.00, 116.86, 90.00
R / Rfree (%) 23.1 / 31.3

Other elements in 4ylp:

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna (pdb code 4ylp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna, PDB code: 4ylp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ylp

Go back to Zinc Binding Sites List in 4ylp
Zinc binding site 1 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:0.1
occ:1.00
 SG D:CYS88 2.0 0.8 1.0
SG D:CYS72 2.0 0.0 1.0
SG D:CYS85 2.3 0.7 1.0
SG D:CYS70 2.8 0.5 1.0
N D:CYS72 3.2 0.2 1.0
CB D:CYS85 3.2 0.4 1.0
CB D:CYS72 3.3 0.6 1.0
CB D:CYS88 3.4 0.7 1.0
CA D:CYS72 3.8 0.9 1.0
N D:LEU71 4.0 0.1 1.0
N D:CYS88 4.0 0.5 1.0
CB D:LEU71 4.2 0.6 1.0
CB D:CYS70 4.2 0.8 1.0
C D:LEU71 4.3 0.0 1.0
N D:GLY73 4.3 0.1 1.0
CA D:CYS88 4.3 1.0 1.0
CA D:LEU71 4.4 0.5 1.0
C D:CYS72 4.4 0.9 1.0
CA D:CYS85 4.7 0.2 1.0
C D:CYS70 4.7 0.8 1.0
CB D:LYS87 4.8 0.2 1.0
N D:LYS74 4.9 0.7 1.0

Zinc binding site 2 out of 6 in 4ylp

Go back to Zinc Binding Sites List in 4ylp
Zinc binding site 2 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.4
occ:1.00
 SG D:CYS888 1.9 0.1 1.0
SG D:CYS814 2.0 0.2 1.0
SG D:CYS898 2.4 0.1 1.0
SG D:CYS895 2.5 0.8 1.0
NH2 D:ARG883 2.9 0.2 1.0
CB D:CYS895 3.0 0.5 1.0
CB D:CYS888 3.1 1.0 1.0
CB D:CYS898 3.3 0.3 1.0
N D:CYS895 3.3 0.5 1.0
OG1 D:THR890 3.5 0.8 1.0
CB D:CYS814 3.6 0.8 1.0
CA D:CYS888 3.7 0.7 1.0
CA D:CYS895 3.7 0.9 1.0
OG1 D:THR816 3.8 0.4 1.0
CZ D:ARG883 4.0 0.8 1.0
N D:ASP889 4.0 0.9 1.0
NE D:ARG883 4.2 0.5 1.0
N D:CYS898 4.3 0.2 1.0
C D:CYS888 4.4 0.4 1.0
N D:CYS814 4.4 0.9 1.0
O D:CYS895 4.4 0.9 1.0
C D:VAL894 4.4 0.4 1.0
C D:CYS895 4.4 0.4 1.0
CA D:CYS898 4.5 0.9 1.0
N D:THR890 4.5 0.8 1.0
CA D:CYS814 4.6 0.7 1.0
CB D:VAL894 4.7 1.0 1.0
CA D:VAL894 4.7 0.2 1.0
CB D:THR890 4.7 0.6 1.0
N D:CYS888 4.9 0.7 1.0

Zinc binding site 3 out of 6 in 4ylp

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Zinc binding site 3 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1501

b:0.9
occ:1.00
 SG J:CYS88 2.0 0.3 1.0
SG J:CYS85 2.6 0.0 1.0
SG J:CYS72 2.6 0.6 1.0
N J:CYS72 2.7 0.5 1.0
SG J:CYS70 2.7 0.8 1.0
CB J:CYS88 3.2 0.3 1.0
CB J:CYS72 3.2 0.3 1.0
CA J:CYS72 3.3 0.3 1.0
N J:GLY73 3.5 1.0 1.0
CB J:CYS85 3.5 0.4 1.0
C J:CYS72 3.8 0.1 1.0
C J:LEU71 3.8 0.1 1.0
N J:LEU71 3.8 0.2 1.0
CB J:CYS70 3.9 0.5 1.0
CA J:LEU71 4.2 0.4 1.0
N J:CYS88 4.2 0.7 1.0
C J:CYS70 4.3 0.3 1.0
CB J:LEU71 4.3 0.9 1.0
CA J:CYS88 4.3 0.5 1.0
N J:LYS74 4.4 0.3 1.0
CA J:GLY73 4.6 1.0 1.0
CB J:VAL90 4.7 0.6 1.0
CA J:CYS70 4.7 0.3 1.0
O J:CYS70 4.8 0.7 1.0
O J:LEU71 4.9 0.4 1.0
O J:CYS72 4.9 0.8 1.0
CA J:CYS85 5.0 0.9 1.0

Zinc binding site 4 out of 6 in 4ylp

Go back to Zinc Binding Sites List in 4ylp
Zinc binding site 4 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:0.5
occ:1.00
 SG J:CYS814 1.5 0.3 1.0
SG J:CYS898 2.3 0.5 1.0
NH2 J:ARG883 2.6 0.8 1.0
SG J:CYS895 2.7 0.5 1.0
SG J:CYS888 2.7 0.9 1.0
OG1 J:THR816 2.8 0.6 1.0
CB J:CYS895 3.0 0.0 1.0
CB J:CYS814 3.3 0.5 1.0
CZ J:ARG883 3.5 0.8 1.0
NE J:ARG883 3.6 0.4 1.0
CB J:CYS888 3.6 0.2 1.0
CB J:CYS898 3.7 0.4 1.0
CA J:CYS888 3.8 0.9 1.0
N J:ASP889 3.9 0.9 1.0
CB J:THR816 4.0 0.1 1.0
N J:CYS814 4.0 0.9 1.0
CA J:CYS814 4.2 0.5 1.0
CA J:CYS895 4.2 0.5 1.0
OG1 J:THR890 4.3 0.4 1.0
N J:CYS895 4.4 0.1 1.0
C J:CYS888 4.5 0.8 1.0
N J:CYS898 4.5 0.2 1.0
NH1 J:ARG883 4.6 0.6 1.0
CA J:CYS898 4.7 0.9 1.0
N J:THR816 4.8 0.5 1.0
CG2 J:THR816 4.9 0.4 1.0
C J:CYS814 4.9 0.8 1.0
N J:GLY815 4.9 0.7 1.0
CD J:ARG883 4.9 0.7 1.0
C J:CYS895 4.9 0.2 1.0
CB J:ASP889 4.9 0.4 1.0
N J:THR890 5.0 0.7 1.0
CA J:ASP889 5.0 0.1 1.0

Zinc binding site 5 out of 6 in 4ylp

Go back to Zinc Binding Sites List in 4ylp
Zinc binding site 5 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1501

b:0.5
occ:1.00
 SG P:CYS88 1.4 0.1 1.0
SG P:CYS70 1.5 0.3 1.0
SG P:CYS85 2.7 0.8 1.0
CB P:CYS88 2.8 0.6 1.0
SG P:CYS72 3.1 0.5 1.0
CB P:CYS70 3.1 0.7 1.0
CB P:CYS85 3.3 0.8 1.0
CB P:LYS74 3.5 0.0 1.0
N P:CYS72 3.9 0.8 1.0
N P:LEU71 3.9 0.6 1.0
CA P:CYS88 4.0 0.2 1.0
N P:CYS88 4.0 0.1 1.0
N P:LYS74 4.2 0.9 1.0
CD P:LYS74 4.2 0.2 1.0
C P:CYS70 4.2 0.9 1.0
CA P:CYS70 4.2 0.8 1.0
CB P:CYS72 4.4 0.8 1.0
CG P:LYS74 4.5 0.3 1.0
CA P:LYS74 4.5 0.1 1.0
N P:GLY73 4.5 0.4 1.0
CA P:CYS72 4.6 0.6 1.0
CA P:LEU71 4.7 0.9 1.0
C P:LEU71 4.7 0.7 1.0
CA P:CYS85 4.8 0.9 1.0
N P:TYR75 4.8 0.2 1.0
C P:CYS88 4.9 0.8 1.0
CB P:LEU71 4.9 0.1 1.0
C P:CYS72 5.0 0.1 1.0
O P:CYS70 5.0 0.3 1.0

Zinc binding site 6 out of 6 in 4ylp

Go back to Zinc Binding Sites List in 4ylp
Zinc binding site 6 out of 6 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 5-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1502

b:0.9
occ:1.00
 SG P:CYS898 1.9 0.8 1.0
SG P:CYS814 1.9 0.3 1.0
SG P:CYS888 2.4 0.7 1.0
SG P:CYS895 2.8 0.1 1.0
NH2 P:ARG883 2.9 0.6 1.0
CB P:CYS898 3.3 0.8 1.0
CB P:CYS888 3.4 0.2 1.0
CB P:CYS895 3.5 1.0 1.0
NE P:ARG883 3.6 0.5 1.0
CA P:CYS888 3.7 0.7 1.0
CZ P:ARG883 3.7 0.4 1.0
CB P:CYS814 3.7 0.5 1.0
N P:ASP889 4.1 0.0 1.0
N P:CYS898 4.3 0.7 1.0
CA P:CYS898 4.3 1.0 1.0
N P:CYS895 4.4 0.4 1.0
N P:CYS814 4.4 1.0 1.0
OG1 P:THR890 4.5 0.7 1.0
C P:CYS888 4.5 0.3 1.0
CA P:CYS895 4.5 0.2 1.0
CA P:CYS814 4.6 0.2 1.0
N P:CYS888 4.8 0.1 1.0
CD P:ARG883 5.0 0.6 1.0

Reference:

Y.Zuo, T.A.Steitz. Crystal Structures of the E. Coli Transcription Initiation Complexes with A Complete Bubble. Mol.Cell V. 58 534 2015.
ISSN: ISSN 1097-2765
PubMed: 25866247
DOI: 10.1016/J.MOLCEL.2015.03.010
Page generated: Sun Oct 27 11:20:15 2024

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