Zinc in PDB 5uaq: Escherichia Coli Rna Polymerase Rpob H526Y Mutant

Enzymatic activity of Escherichia Coli Rna Polymerase Rpob H526Y Mutant

All present enzymatic activity of Escherichia Coli Rna Polymerase Rpob H526Y Mutant:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase Rpob H526Y Mutant, PDB code: 5uaq 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) 29.90 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 185.361, 206.280, 308.685, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 30.5

Other elements in 5uaq:

The structure of Escherichia Coli Rna Polymerase Rpob H526Y Mutant also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase Rpob H526Y Mutant (pdb code 5uaq). 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 Rpob H526Y Mutant, PDB code: 5uaq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5uaq

Go back to Zinc Binding Sites List in 5uaq
Zinc binding site 1 out of 4 in the Escherichia Coli Rna Polymerase Rpob H526Y Mutant


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 Rpob H526Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.0
occ:1.00
 SG D:CYS85 1.9 0.2 1.0
SG D:CYS70 2.0 0.5 1.0
SG D:CYS72 2.2 0.9 1.0
SG D:CYS88 2.6 0.1 1.0
CB D:CYS85 2.7 0.1 1.0
CB D:CYS72 3.4 0.9 1.0
CB D:CYS70 3.6 0.7 1.0
N D:CYS88 3.7 0.8 1.0
CB D:LYS87 3.8 0.6 1.0
O D:CYS88 3.8 0.2 1.0
N D:CYS72 4.0 0.8 1.0
CA D:CYS85 4.2 0.8 1.0
CA D:CYS72 4.2 1.0 1.0
CB D:LYS74 4.2 0.1 1.0
N D:LYS74 4.3 0.8 1.0
N D:GLY73 4.3 0.6 1.0
CB D:CYS88 4.3 0.7 1.0
CA D:CYS88 4.4 0.6 1.0
N D:LYS87 4.5 0.9 1.0
CA D:LYS87 4.5 0.6 1.0
C D:CYS88 4.5 0.7 1.0
C D:CYS72 4.6 0.8 1.0
C D:CYS85 4.6 0.1 1.0
C D:LYS87 4.6 0.6 1.0
N D:LEU71 4.7 0.7 1.0
CD1 D:TYR75 4.7 0.4 1.0
CA D:CYS70 4.8 0.2 1.0
CA D:LYS74 4.8 0.8 1.0
CG D:LYS87 4.9 0.6 1.0
N D:TYR75 5.0 0.7 1.0
C D:CYS70 5.0 0.4 1.0

Zinc binding site 2 out of 4 in 5uaq

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Zinc binding site 2 out of 4 in the Escherichia Coli Rna Polymerase Rpob H526Y Mutant


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 Rpob H526Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:52.0
occ:1.00
 SG D:CYS888 2.0 0.5 1.0
SG D:CYS895 2.2 91.9 1.0
SG D:CYS814 2.3 0.4 1.0
SG D:CYS898 2.3 0.5 1.0
CB D:CYS888 2.6 99.7 1.0
CB D:CYS898 3.0 0.5 1.0
CA D:CYS888 3.0 99.0 1.0
CB D:CYS814 3.3 1.0 1.0
CB D:CYS895 3.4 99.9 1.0
N D:ASP889 3.5 0.3 1.0
C D:CYS888 3.7 98.9 1.0
N D:CYS895 4.0 94.4 1.0
N D:CYS814 4.1 100.0 1.0
CA D:CYS895 4.2 95.0 1.0
CA D:CYS898 4.2 0.9 1.0
NH2 D:ARG883 4.2 0.0 1.0
O D:CYS895 4.2 97.2 1.0
N D:CYS888 4.3 99.0 1.0
CA D:CYS814 4.3 0.0 1.0
N D:CYS898 4.3 0.9 1.0
N D:THR890 4.6 0.6 1.0
O D:CYS888 4.7 98.3 1.0
C D:CYS895 4.7 95.1 1.0
CA D:ASP889 4.7 0.2 1.0
CG2 D:THR816 4.9 0.8 1.0

Zinc binding site 3 out of 4 in 5uaq

Go back to Zinc Binding Sites List in 5uaq
Zinc binding site 3 out of 4 in the Escherichia Coli Rna Polymerase Rpob H526Y Mutant


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 Rpob H526Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:0.5
occ:1.00
 SG J:CYS72 2.0 0.7 1.0
SG J:CYS85 2.0 0.8 1.0
SG J:CYS70 2.1 0.7 1.0
SG J:CYS88 2.7 0.2 1.0
CB J:CYS72 2.9 0.2 1.0
CB J:CYS85 3.1 0.8 1.0
N J:CYS72 3.6 0.4 1.0
CB J:LYS87 3.7 0.5 1.0
N J:CYS88 3.7 0.2 1.0
O J:CYS88 3.7 0.4 1.0
CA J:CYS72 3.8 0.9 1.0
CB J:CYS70 3.9 1.0 1.0
CB J:CYS88 4.2 0.4 1.0
N J:GLY73 4.4 0.0 1.0
CA J:CYS88 4.4 0.6 1.0
C J:CYS72 4.5 0.0 1.0
CA J:CYS85 4.5 0.8 1.0
C J:CYS88 4.5 0.0 1.0
CA J:LYS87 4.5 0.4 1.0
N J:LYS87 4.5 0.3 1.0
N J:LEU71 4.6 0.1 1.0
C J:LYS87 4.6 1.0 1.0
CB J:LYS74 4.7 0.2 1.0
N J:LYS74 4.7 0.3 1.0
CG J:LYS87 4.7 0.5 1.0
C J:LEU71 4.8 0.8 1.0
C J:CYS85 4.9 0.7 1.0
CA J:CYS70 5.0 0.3 1.0
C J:CYS70 5.0 0.5 1.0

Zinc binding site 4 out of 4 in 5uaq

Go back to Zinc Binding Sites List in 5uaq
Zinc binding site 4 out of 4 in the Escherichia Coli Rna Polymerase Rpob H526Y Mutant


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 Rpob H526Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1503

b:97.3
occ:1.00
 SG J:CYS895 1.9 0.3 1.0
SG J:CYS898 2.0 0.6 1.0
SG J:CYS814 2.0 0.8 1.0
SG J:CYS888 2.3 0.9 1.0
CB J:CYS898 2.9 0.6 1.0
CB J:CYS895 3.2 0.7 1.0
CB J:CYS814 3.2 0.5 1.0
CB J:CYS888 3.3 0.3 1.0
NH2 J:ARG883 3.7 0.5 1.0
CA J:CYS888 3.9 0.8 1.0
N J:CYS895 4.0 0.1 1.0
N J:CYS814 4.0 0.2 1.0
CA J:CYS898 4.0 0.7 1.0
N J:CYS898 4.1 0.7 1.0
O J:CYS895 4.1 0.8 1.0
CA J:CYS895 4.1 0.9 1.0
N J:ASP889 4.2 0.1 1.0
CA J:CYS814 4.2 0.5 1.0
OG1 J:THR890 4.4 0.2 1.0
C J:CYS888 4.4 0.1 1.0
CZ J:ARG883 4.5 0.8 1.0
C J:CYS895 4.5 0.7 1.0
N J:THR890 4.6 0.0 1.0
CG2 J:THR816 4.7 1.0 1.0
OD1 J:ASP813 4.7 0.0 1.0
NE J:ARG883 4.8 0.2 1.0
N J:GLY815 4.9 0.4 1.0
CB J:THR890 4.9 0.2 1.0
C J:CYS814 4.9 0.6 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: Wed Dec 16 11:01:30 2020

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