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Zinc in PDB 6cux: Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A

Enzymatic activity of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A

All present enzymatic activity of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A, PDB code: 6cux was solved by V.Molodtsov, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.03 / 4.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 188.167, 204.685, 311.577, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.5

Other elements in 6cux:

The structure of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A (pdb code 6cux). 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 Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A, PDB code: 6cux:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6cux

Go back to Zinc Binding Sites List in 6cux
Zinc binding site 1 out of 4 in the Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.2
occ:1.00
 SG D:CYS70 2.0 0.1 1.0
SG D:CYS72 2.1 0.1 1.0
SG D:CYS85 2.3 1.0 1.0
CB D:CYS85 2.9 0.2 1.0
CB D:CYS72 3.2 0.2 1.0
SG D:CYS88 3.3 0.8 1.0
N D:CYS72 3.6 0.8 1.0
O D:CYS88 3.8 0.5 1.0
CB D:CYS70 3.8 0.3 1.0
CA D:CYS72 3.9 0.9 1.0
N D:CYS88 4.1 0.7 1.0
N D:GLY73 4.3 0.3 1.0
CB D:LYS87 4.4 0.2 1.0
CB D:LYS74 4.4 0.5 1.0
CA D:CYS85 4.4 0.1 1.0
N D:LYS74 4.4 0.2 1.0
N D:LEU71 4.4 0.5 1.0
C D:CYS72 4.5 0.9 1.0
C D:CYS88 4.6 0.2 1.0
CB D:CYS88 4.7 0.0 1.0
CA D:CYS88 4.8 0.7 1.0
CA D:CYS70 4.8 0.3 1.0
C D:LEU71 4.8 0.7 1.0
C D:CYS70 4.8 0.5 1.0
N D:LYS87 5.0 0.7 1.0
C D:CYS85 5.0 0.1 1.0
CD1 D:TYR75 5.0 0.4 1.0

Zinc binding site 2 out of 4 in 6cux

Go back to Zinc Binding Sites List in 6cux
Zinc binding site 2 out of 4 in the Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:0.9
occ:1.00
 SG D:CYS814 1.9 0.7 1.0
SG D:CYS888 1.9 0.4 1.0
SG D:CYS898 2.0 1.0 1.0
SG D:CYS895 2.1 0.9 1.0
CB D:CYS888 2.6 0.5 1.0
CB D:CYS898 2.9 0.5 1.0
CA D:CYS888 3.3 0.1 1.0
CB D:CYS814 3.3 0.3 1.0
CB D:CYS895 3.6 0.1 1.0
N D:ASP889 3.9 0.4 1.0
C D:CYS888 4.0 0.1 1.0
NH2 D:ARG883 4.1 0.5 1.0
N D:CYS895 4.2 0.4 1.0
CA D:CYS898 4.2 0.5 1.0
N D:CYS814 4.3 0.3 1.0
CA D:CYS814 4.4 0.9 1.0
N D:CYS898 4.4 0.0 1.0
O D:CYS895 4.4 0.7 1.0
CA D:CYS895 4.5 0.2 1.0
N D:CYS888 4.5 0.8 1.0
N D:THR890 4.6 0.3 1.0
OG1 D:THR890 4.7 0.3 1.0
CG2 D:THR816 4.9 0.0 1.0
C D:CYS895 4.9 0.2 1.0
O D:CYS888 5.0 0.5 1.0

Zinc binding site 3 out of 4 in 6cux

Go back to Zinc Binding Sites List in 6cux
Zinc binding site 3 out of 4 in the Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:0.0
occ:1.00
 SG J:CYS72 1.9 0.5 1.0
SG J:CYS70 2.2 0.2 1.0
CB J:CYS72 2.7 0.4 1.0
SG J:CYS85 2.8 0.2 1.0
N J:CYS72 3.3 0.6 1.0
SG J:CYS88 3.3 0.5 1.0
CA J:CYS72 3.5 0.5 1.0
CB J:CYS85 3.5 0.5 1.0
CB J:CYS70 3.7 0.6 1.0
N J:GLY73 3.9 0.4 1.0
O J:CYS88 3.9 0.4 1.0
C J:CYS72 4.1 0.8 1.0
N J:CYS88 4.2 0.7 1.0
CB J:LYS87 4.3 1.0 1.0
N J:LYS74 4.4 0.4 1.0
N J:LEU71 4.4 0.9 1.0
C J:LEU71 4.5 0.8 1.0
CB J:LYS74 4.7 0.4 1.0
C J:CYS70 4.7 0.4 1.0
CB J:CYS88 4.8 0.1 1.0
C J:CYS88 4.8 0.0 1.0
CA J:CYS88 4.8 0.2 1.0
CA J:CYS70 4.8 1.0 1.0
CA J:CYS85 5.0 0.5 1.0
CA J:LEU71 5.0 0.5 1.0

Zinc binding site 4 out of 4 in 6cux

Go back to Zinc Binding Sites List in 6cux
Zinc binding site 4 out of 4 in the Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Escherichia Coli Rpob S531L Mutant Rna Polymerase Holoenzyme in Complex with Kanglemycin A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1503

b:0.4
occ:1.00
 SG J:CYS895 2.2 0.0 1.0
SG J:CYS898 2.4 0.7 1.0
SG J:CYS888 2.5 0.4 1.0
SG J:CYS814 2.6 0.5 1.0
CB J:CYS898 2.9 0.1 1.0
CB J:CYS888 3.3 0.5 1.0
CB J:CYS895 3.7 0.3 1.0
CA J:CYS888 3.8 0.8 1.0
CB J:CYS814 3.9 0.4 1.0
CA J:CYS898 3.9 0.8 1.0
N J:CYS898 3.9 0.5 1.0
NH2 J:ARG883 4.1 0.9 1.0
N J:CYS814 4.1 0.8 1.0
N J:ASP889 4.2 0.4 1.0
OD1 J:ASP813 4.4 0.1 1.0
C J:CYS888 4.4 0.7 1.0
O J:CYS895 4.5 0.9 1.0
OG1 J:THR890 4.5 0.4 1.0
CA J:CYS814 4.6 0.9 1.0
N J:CYS895 4.6 0.2 1.0
CA J:CYS895 4.6 0.3 1.0
CG2 J:THR816 4.7 0.0 1.0
N J:THR890 4.7 0.9 1.0
C J:CYS895 4.9 0.3 1.0
C J:HIS897 5.0 0.9 1.0
N J:CYS888 5.0 0.4 1.0

Reference:

H.Mosaei, V.Molodtsov, B.Kepplinger, J.Harbottle, C.W.Moon, R.E.Jeeves, L.Ceccaroni, Y.Shin, S.Morton-Laing, E.C.L.Marrs, C.Wills, W.Clegg, Y.Yuzenkova, J.D.Perry, J.Bacon, J.Errington, N.E.E.Allenby, M.J.Hall, K.S.Murakami, N.Zenkin. Mode of Action of Kanglemycin A, An Ansamycin Natural Product That Is Active Against Rifampicin-Resistant Mycobacterium Tuberculosis. Mol. Cell V. 72 263 2018.
ISSN: ISSN 1097-4164
PubMed: 30244835
DOI: 10.1016/J.MOLCEL.2018.08.028
Page generated: Mon Oct 28 19:09:52 2024

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