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Zinc in PDB 5uag: Escherichia Coli Rna Polymerase Mutant - Rpob D516V

Enzymatic activity of Escherichia Coli Rna Polymerase Mutant - Rpob D516V

All present enzymatic activity of Escherichia Coli Rna Polymerase Mutant - Rpob D516V:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase Mutant - Rpob D516V, PDB code: 5uag was solved by V.Molodtsov, N.T.Scharf, M.A.Stefan, G.A.Garcia, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.826, 205.043, 307.347, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.1

Other elements in 5uag:

The structure of Escherichia Coli Rna Polymerase Mutant - Rpob D516V also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V (pdb code 5uag). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V, PDB code: 5uag:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5uag

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Zinc binding site 1 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:0.1
occ:1.00
 SG D:CYS70 2.1 0.7 1.0
SG D:CYS72 2.1 0.8 1.0
SG D:CYS85 2.3 0.6 1.0
SG D:CYS88 2.4 0.1 1.0
CB D:CYS72 2.7 1.0 1.0
CB D:CYS85 3.0 0.1 1.0
N D:CYS72 3.1 0.7 1.0
CA D:CYS72 3.4 0.4 1.0
O D:CYS88 3.7 0.3 1.0
N D:CYS88 3.7 0.9 1.0
CB D:CYS70 3.8 0.3 1.0
CB D:CYS88 4.0 0.0 1.0
N D:GLY73 4.0 0.7 1.0
C D:CYS72 4.2 0.1 1.0
CB D:LYS87 4.2 0.9 1.0
N D:LEU71 4.2 0.2 1.0
C D:LEU71 4.3 0.9 1.0
CA D:CYS88 4.3 0.2 1.0
N D:LYS74 4.5 0.1 1.0
C D:CYS88 4.5 0.4 1.0
CA D:CYS85 4.5 0.2 1.0
C D:CYS70 4.6 0.6 1.0
CB D:LYS74 4.7 0.8 1.0
CA D:LEU71 4.7 0.5 1.0
C D:LYS87 4.8 0.7 1.0
CA D:CYS70 4.8 0.2 1.0
CA D:LYS87 4.8 0.3 1.0
N D:LYS87 4.9 0.9 1.0
C D:CYS85 5.0 0.0 1.0

Zinc binding site 2 out of 4 in 5uag

Go back to Zinc Binding Sites List in 5uag
Zinc binding site 2 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:0.1
occ:1.00
 SG D:CYS888 2.2 0.4 1.0
SG D:CYS898 2.2 0.7 1.0
SG D:CYS814 2.3 0.6 1.0
CA D:CYS888 2.3 0.5 1.0
CB D:CYS888 2.3 0.5 1.0
SG D:CYS895 2.4 0.8 1.0
N D:ASP889 3.0 0.8 1.0
C D:CYS888 3.0 0.5 1.0
CB D:CYS898 3.0 0.5 1.0
CB D:CYS814 3.4 0.6 1.0
N D:CYS888 3.6 0.2 1.0
CB D:CYS895 3.7 1.0 1.0
NH2 D:ARG883 4.1 0.2 1.0
CG2 D:THR816 4.1 0.0 1.0
O D:CYS888 4.2 0.8 1.0
N D:THR890 4.3 0.7 1.0
CA D:ASP889 4.3 0.2 1.0
C D:SER887 4.4 0.9 1.0
CA D:CYS898 4.4 0.5 1.0
O D:SER887 4.4 0.4 1.0
N D:CYS895 4.4 0.2 1.0
CA D:CYS814 4.6 0.6 1.0
N D:CYS898 4.6 0.4 1.0
CA D:CYS895 4.6 0.7 1.0
N D:CYS814 4.7 0.4 1.0
O D:SER884 4.8 0.8 1.0
C D:ASP889 4.9 0.4 1.0
CB D:ASP889 4.9 0.0 1.0
O D:CYS895 4.9 0.7 1.0
CZ D:ARG883 5.0 0.8 1.0
NE D:ARG883 5.0 0.5 1.0

Zinc binding site 3 out of 4 in 5uag

Go back to Zinc Binding Sites List in 5uag
Zinc binding site 3 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Rna Polymerase Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2002

b:0.0
occ:1.00
 SG J:CYS70 2.1 0.4 1.0
SG J:CYS85 2.2 0.3 1.0
SG J:CYS72 2.3 0.5 1.0
CB J:CYS85 2.4 0.5 1.0
SG J:CYS88 2.5 0.2 1.0
CB J:CYS72 3.1 0.6 1.0
O J:CYS88 3.4 1.0 1.0
N J:CYS72 3.7 0.4 1.0
N J:CYS88 3.7 0.4 1.0
CB J:CYS70 3.8 0.7 1.0
CA J:CYS85 3.9 0.2 1.0
CA J:CYS72 4.0 0.5 1.0
CB J:CYS88 4.0 0.3 1.0
CA J:CYS88 4.2 0.4 1.0
C J:CYS88 4.2 0.5 1.0
CB J:LYS87 4.3 0.3 1.0
C J:CYS85 4.5 0.5 1.0
N J:LEU71 4.5 0.6 1.0
N J:GLY73 4.6 0.9 1.0
C J:CYS72 4.7 0.8 1.0
C J:LYS87 4.7 0.2 1.0
N J:CYS85 4.7 0.3 1.0
N J:LYS87 4.8 0.0 1.0
CA J:LYS87 4.8 0.1 1.0
C J:LEU71 4.8 0.6 1.0
CA J:CYS70 4.9 0.3 1.0
O J:CYS85 4.9 0.2 1.0
N J:LYS74 4.9 0.6 1.0
CB J:LYS74 4.9 0.2 1.0
C J:CYS70 4.9 0.6 1.0
CB J:VAL90 5.0 0.0 1.0

Zinc binding site 4 out of 4 in 5uag

Go back to Zinc Binding Sites List in 5uag
Zinc binding site 4 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Escherichia Coli Rna Polymerase Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2003

b:0.1
occ:1.00
 SG J:CYS895 2.0 0.8 1.0
SG J:CYS898 2.1 0.6 1.0
SG J:CYS814 2.1 0.9 1.0
SG J:CYS888 2.2 0.8 1.0
CB J:CYS898 2.8 0.4 1.0
CB J:CYS888 3.0 0.0 1.0
CB J:CYS814 3.2 0.3 1.0
CB J:CYS895 3.3 0.3 1.0
CA J:CYS888 3.5 0.5 1.0
NH2 J:ARG883 3.8 0.4 1.0
N J:ASP889 3.9 0.9 1.0
CA J:CYS898 3.9 0.9 1.0
N J:CYS898 4.0 0.9 1.0
N J:CYS814 4.1 0.3 1.0
C J:CYS888 4.1 0.0 1.0
CA J:CYS814 4.3 0.2 1.0
N J:CYS895 4.3 0.8 1.0
CA J:CYS895 4.3 0.9 1.0
CG2 J:THR816 4.3 0.9 1.0
OG1 J:THR890 4.4 0.6 1.0
N J:THR890 4.5 0.3 1.0
O J:CYS895 4.6 0.5 1.0
CZ J:ARG883 4.7 0.8 1.0
N J:CYS888 4.7 0.6 1.0
C J:CYS895 4.8 0.5 1.0
CB J:THR890 4.8 0.5 1.0
NE J:ARG883 4.9 0.4 1.0

Reference:

V.Molodtsov, N.T.Scharf, M.A.Stefan, G.A.Garcia, K.S.Murakami. Structural Basis For Rifamycin Resistance of Bacterial Rna Polymerase By the Three Most Clinically Important Rpob Mutations Found in Mycobacterium Tuberculosis. Mol. Microbiol. V. 103 1034 2017.
ISSN: ESSN 1365-2958
PubMed: 28009073
DOI: 10.1111/MMI.13606
Page generated: Mon Oct 28 09:15:06 2024

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