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Zinc in PDB 4kn7: X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C

Enzymatic activity of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C

All present enzymatic activity of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C, PDB code: 4kn7 was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 3.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 185.830, 204.579, 308.701, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 30.9

Other elements in 4kn7:

The structure of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C (pdb code 4kn7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C, PDB code: 4kn7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4kn7

Go back to Zinc Binding Sites List in 4kn7
Zinc binding site 1 out of 4 in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:54.5
occ:1.00
SG D:CYS72 2.3 37.9 1.0
SG D:CYS85 2.3 0.3 1.0
SG D:CYS70 2.4 64.0 1.0
SG D:CYS88 2.8 96.9 1.0
CB D:CYS85 3.0 0.2 1.0
CB D:CYS70 3.3 41.2 1.0
N D:CYS72 3.7 62.2 1.0
CB D:CYS72 3.8 19.7 1.0
N D:GLY73 4.1 84.0 1.0
O D:CYS88 4.1 92.7 1.0
N D:LEU71 4.1 54.1 1.0
CA D:CYS72 4.3 65.5 1.0
N D:LYS74 4.3 46.1 1.0
CB D:CYS88 4.4 82.7 1.0
N D:CYS88 4.4 0.9 1.0
CA D:CYS85 4.5 2.5 1.0
CB D:LYS74 4.5 55.8 1.0
CA D:CYS70 4.6 5.4 1.0
C D:CYS70 4.6 1.5 1.0
CG D:LYS74 4.6 84.3 1.0
C D:LEU71 4.7 64.8 1.0
C D:CYS72 4.7 72.1 1.0
CD1 D:TYR75 4.8 45.0 1.0
CA D:CYS88 4.8 1.0 1.0
CA D:LEU71 4.8 56.4 1.0
C D:CYS88 4.9 99.1 1.0

Zinc binding site 2 out of 4 in 4kn7

Go back to Zinc Binding Sites List in 4kn7
Zinc binding site 2 out of 4 in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:8.6
occ:1.00
SG D:CYS898 2.3 9.1 1.0
SG D:CYS888 2.3 2.5 1.0
CB D:CYS895 2.3 26.6 1.0
SG D:CYS814 2.6 8.5 1.0
CB D:CYS888 3.1 2.2 1.0
SG D:CYS895 3.1 34.4 1.0
CB D:CYS898 3.3 0.0 1.0
CA D:CYS888 3.6 20.8 1.0
CA D:CYS895 3.7 42.6 1.0
N D:CYS895 3.9 42.8 1.0
CB D:CYS814 4.2 40.9 1.0
C D:CYS888 4.2 36.1 1.0
N D:ASP889 4.4 6.2 1.0
CA D:CYS898 4.5 0.9 1.0
O D:GLY815 4.5 11.2 1.0
C D:CYS895 4.6 51.6 1.0
N D:CYS898 4.6 0.2 1.0
O D:CYS895 4.8 68.6 1.0
N D:CYS814 4.8 34.6 1.0
N D:CYS888 4.8 48.0 1.0
N D:THR890 4.9 78.8 1.0
CA D:CYS814 4.9 28.6 1.0
CB D:THR890 4.9 1.4 1.0

Zinc binding site 3 out of 4 in 4kn7

Go back to Zinc Binding Sites List in 4kn7
Zinc binding site 3 out of 4 in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1501

b:60.2
occ:1.00
SG I:CYS72 2.4 61.3 1.0
SG I:CYS88 2.4 0.3 1.0
SG I:CYS85 2.5 0.2 1.0
SG I:CYS70 2.6 0.9 1.0
CB I:CYS85 3.1 20.9 1.0
CB I:CYS70 3.5 50.9 1.0
N I:CYS72 3.6 0.8 1.0
CB I:CYS72 3.7 63.5 1.0
O I:CYS88 4.0 0.3 1.0
CB I:CYS88 4.1 0.5 1.0
N I:LEU71 4.1 66.7 1.0
N I:CYS88 4.2 0.2 1.0
CA I:CYS72 4.2 0.6 1.0
N I:GLY73 4.3 38.2 1.0
CA I:CYS88 4.6 0.8 1.0
C I:LEU71 4.6 60.2 1.0
CA I:CYS85 4.6 54.6 1.0
C I:CYS70 4.7 76.7 1.0
CA I:CYS70 4.7 79.6 1.0
CA I:LEU71 4.7 29.1 1.0
N I:LYS74 4.7 97.3 1.0
C I:CYS88 4.8 0.4 1.0
CB I:LEU71 4.8 0.9 1.0
C I:CYS72 4.8 0.2 1.0
CD1 I:TYR75 4.9 5.2 1.0
CB I:LYS87 4.9 26.2 1.0
CB I:LYS74 4.9 69.5 1.0

Zinc binding site 4 out of 4 in 4kn7

Go back to Zinc Binding Sites List in 4kn7
Zinc binding site 4 out of 4 in the X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycin-2C within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1502

b:49.6
occ:1.00
CB I:CYS895 2.3 15.5 1.0
SG I:CYS898 2.3 4.2 1.0
SG I:CYS888 2.4 30.0 1.0
SG I:CYS814 2.4 80.3 1.0
SG I:CYS895 2.8 60.0 1.0
CB I:CYS888 3.4 15.3 1.0
CB I:CYS898 3.5 6.2 1.0
CA I:CYS895 3.7 91.4 1.0
CB I:CYS814 4.0 0.1 1.0
CA I:CYS888 4.0 53.3 1.0
O I:GLY815 4.2 0.4 1.0
N I:CYS895 4.2 0.2 1.0
NH2 I:ARG883 4.5 45.0 1.0
N I:CYS898 4.5 29.4 1.0
N I:CYS814 4.5 50.7 1.0
CA I:CYS898 4.6 22.9 1.0
C I:CYS895 4.6 85.0 1.0
C I:CYS888 4.6 59.0 1.0
CA I:CYS814 4.7 48.7 1.0
N I:ASP889 4.7 43.0 1.0
CG2 I:THR816 4.8 70.3 1.0
C I:CYS814 4.8 66.4 1.0
O I:CYS895 4.9 97.4 1.0
O I:CYS814 4.9 82.8 1.0
CB I:THR890 5.0 2.4 1.0

Reference:

V.Molodtsov, I.N.Nawarathne, N.T.Scharf, P.D.Kirchhoff, H.D.Showalter, G.A.Garcia, K.S.Murakami. X-Ray Crystal Structures of the Escherichia Coli Rna Polymerase in Complex with Benzoxazinorifamycins. J.Med.Chem. V. 56 4758 2013.
ISSN: ISSN 0022-2623
PubMed: 23679862
DOI: 10.1021/JM4004889
Page generated: Wed Dec 16 05:29:40 2020

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