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Zinc in PDB 4xsz: Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme

Enzymatic activity of Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme

All present enzymatic activity of Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme, PDB code: 4xsz 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) 39.93 / 3.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.444, 206.331, 309.607, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28.6

Other elements in 4xsz:

The structure of Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme (pdb code 4xsz). 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 Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme, PDB code: 4xsz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xsz

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Zinc binding site 1 out of 4 in the Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme


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 Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.3
occ:1.00
 SG D:CYS70 2.3 87.1 1.0
SG D:CYS85 2.4 93.9 1.0
SG D:CYS72 2.4 0.2 1.0
CB D:CYS72 2.9 52.7 1.0
CB D:CYS85 3.4 89.0 1.0
SG D:CYS88 3.6 0.3 1.0
N D:CYS72 3.8 0.1 1.0
CB D:LYS87 3.8 0.2 1.0
O D:CYS88 3.8 0.5 1.0
CA D:CYS72 3.9 80.8 1.0
N D:CYS88 3.9 0.1 1.0
CB D:CYS70 4.0 0.4 1.0
N D:GLY73 4.6 0.9 1.0
C D:CYS72 4.6 92.6 1.0
CB D:LYS74 4.7 0.9 1.0
C D:CYS88 4.7 0.2 1.0
CA D:CYS88 4.7 0.7 1.0
CA D:LYS87 4.7 0.0 1.0
CB D:CYS88 4.8 0.6 1.0
N D:LEU71 4.8 0.8 1.0
CA D:CYS85 4.8 0.5 1.0
N D:LYS87 4.8 0.9 1.0
CG D:LYS87 4.8 0.7 1.0
N D:LYS74 4.8 0.6 1.0
C D:LYS87 4.8 0.7 1.0
C D:LEU71 5.0 0.9 1.0

Zinc binding site 2 out of 4 in 4xsz

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Zinc binding site 2 out of 4 in the Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme


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 Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:76.1
occ:1.00
 SG D:CYS888 2.2 0.9 1.0
SG D:CYS814 2.4 0.1 1.0
SG D:CYS898 2.5 0.9 1.0
CB D:CYS888 2.8 87.3 1.0
CB D:CYS898 2.9 87.5 1.0
SG D:CYS895 3.0 99.5 1.0
CA D:CYS888 3.2 97.6 1.0
CB D:CYS814 3.6 0.9 1.0
CB D:CYS895 3.9 1.0 1.0
N D:ASP889 3.9 0.1 1.0
C D:CYS888 4.0 0.8 1.0
N D:CYS895 4.2 0.9 1.0
CA D:CYS898 4.3 0.4 1.0
NH2 D:ARG883 4.4 0.0 1.0
N D:CYS888 4.4 0.8 1.0
N D:CYS898 4.5 0.7 1.0
N D:CYS814 4.6 0.0 1.0
CA D:CYS895 4.6 0.7 1.0
O D:CYS895 4.6 63.3 1.0
OG1 D:THR890 4.6 0.5 1.0
N D:THR890 4.7 0.6 1.0
CA D:CYS814 4.7 0.5 1.0
CG2 D:THR816 4.9 88.9 1.0
CB D:THR890 4.9 0.5 1.0
O D:SER884 5.0 0.3 1.0
C D:CYS895 5.0 79.0 1.0

Zinc binding site 3 out of 4 in 4xsz

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Zinc binding site 3 out of 4 in the Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme


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 Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:0.7
occ:1.00
 SG J:CYS85 2.4 54.1 1.0
SG J:CYS70 2.4 0.5 1.0
SG J:CYS72 2.4 91.5 1.0
CB J:CYS72 2.9 0.4 1.0
CB J:CYS85 3.4 64.3 1.0
SG J:CYS88 3.4 0.5 1.0
O J:CYS88 3.7 0.2 1.0
N J:CYS72 3.7 0.2 1.0
CB J:LYS87 3.8 0.4 1.0
N J:CYS88 3.8 0.1 1.0
CA J:CYS72 3.9 0.4 1.0
CB J:CYS70 4.1 0.1 1.0
CA J:CYS88 4.5 0.3 1.0
C J:CYS88 4.5 0.1 1.0
CB J:CYS88 4.6 0.2 1.0
CA J:LYS87 4.6 0.8 1.0
N J:GLY73 4.7 0.1 1.0
C J:CYS72 4.7 0.7 1.0
C J:LYS87 4.7 0.7 1.0
N J:LEU71 4.8 85.2 1.0
N J:LYS87 4.8 0.7 1.0
CG J:LYS87 4.8 0.2 1.0
CB J:LYS74 4.8 0.1 1.0
CA J:CYS85 4.8 73.5 1.0
C J:LEU71 4.9 0.8 1.0
N J:LYS74 4.9 0.2 1.0

Zinc binding site 4 out of 4 in 4xsz

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Zinc binding site 4 out of 4 in the Crystal Structure of Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme


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 Cbr 9393 Bound to Escherichia Coli Rna Polymerase Holoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1503

b:0.4
occ:1.00
 SG J:CYS888 2.3 0.0 1.0
SG J:CYS895 2.5 87.5 1.0
SG J:CYS898 2.6 72.3 1.0
SG J:CYS814 2.7 0.4 1.0
CB J:CYS898 2.7 62.5 1.0
CB J:CYS888 3.0 0.6 1.0
CB J:CYS895 3.5 1.0 1.0
CA J:CYS888 3.6 0.5 1.0
N J:CYS895 3.8 0.5 1.0
CB J:CYS814 3.8 0.1 1.0
CA J:CYS898 4.0 92.4 1.0
O J:CYS895 4.1 0.2 1.0
CA J:CYS895 4.1 93.3 1.0
N J:CYS898 4.2 66.7 1.0
N J:ASP889 4.3 0.8 1.0
C J:CYS888 4.4 0.5 1.0
NH2 J:ARG883 4.4 0.2 1.0
N J:CYS814 4.5 87.3 1.0
C J:CYS895 4.5 85.2 1.0
OG1 J:THR890 4.6 0.9 1.0
N J:CYS888 4.8 85.1 1.0
CA J:CYS814 4.8 94.7 1.0
N J:THR890 4.9 0.2 1.0
CG1 J:VAL894 4.9 88.2 1.0
CB J:THR890 4.9 0.6 1.0
C J:VAL894 5.0 89.6 1.0

Reference:

B.Bae, D.Nayak, A.Ray, A.Mustaev, R.Landick, S.A.Darst. Cbr Antimicrobials Inhibit Rna Polymerase Via at Least Two Bridge-Helix Cap-Mediated Effects on Nucleotide Addition. Proc.Natl.Acad.Sci.Usa V. 112 E4178 2015.
ISSN: ESSN 1091-6490
PubMed: 26195788
DOI: 10.1073/PNAS.1502368112
Page generated: Sun Oct 27 10:47:12 2024

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