Magnesium in PDB 5uac: Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type

Enzymatic activity of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type

All present enzymatic activity of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type, PDB code: 5uac 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) 29.98 / 3.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 188.958, 204.430, 313.619, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 29.6

Other elements in 5uac:

The structure of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type (pdb code 5uac). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type, PDB code: 5uac:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5uac

Go back to Magnesium Binding Sites List in 5uac
Magnesium binding site 1 out of 2 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1501

b:0.4
occ:1.00
OD2 D:ASP462 1.8 0.4 1.0
OD1 D:ASP462 2.0 1.0 1.0
CG D:ASP462 2.1 0.4 1.0
OD2 D:ASP464 2.4 0.0 1.0
OD1 D:ASP460 2.5 0.7 1.0
CB D:ASP460 2.8 0.0 1.0
OD1 D:ASP464 2.9 0.4 1.0
CG D:ASP464 3.0 0.3 1.0
CG D:ASP460 3.1 0.7 1.0
CB D:ASP462 3.6 0.9 1.0
CA D:ASP460 4.0 0.6 1.0
N D:ASP462 4.1 0.8 1.0
N D:ASP460 4.3 0.2 1.0
CA D:ASP462 4.3 0.4 1.0
OD2 D:ASP460 4.3 0.5 1.0
C D:ASP460 4.4 0.6 1.0
CB D:ASP464 4.6 0.8 1.0
C D:ASP462 4.7 0.8 1.0
N D:ASP464 4.8 100.0 1.0
O D:ASP462 4.8 0.5 1.0
O D:ASP460 4.9 99.8 1.0
N D:PHE461 4.9 0.6 1.0

Magnesium binding site 2 out of 2 in 5uac

Go back to Magnesium Binding Sites List in 5uac
Magnesium binding site 2 out of 2 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Rna Polymerase and Rifampin Complex, Wild-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1501

b:0.6
occ:1.00
OD2 J:ASP462 1.8 0.6 1.0
OD2 J:ASP464 1.9 0.3 1.0
OD1 J:ASP462 2.1 0.5 1.0
CG J:ASP462 2.2 0.5 1.0
CB J:ASP460 2.6 0.9 1.0
OD1 J:ASP460 2.7 0.1 1.0
CG J:ASP464 2.7 0.8 1.0
OD1 J:ASP464 2.8 1.0 1.0
CG J:ASP460 3.1 0.6 1.0
CA J:ASP460 3.7 0.5 1.0
CB J:ASP462 3.7 0.0 1.0
N J:ASP460 3.9 0.2 1.0
N J:ASP462 4.0 0.7 1.0
C J:ASP460 4.0 0.2 1.0
CB J:ASP464 4.3 0.0 1.0
CA J:ASP462 4.3 0.6 1.0
OD2 J:ASP460 4.4 0.3 1.0
O J:ASP460 4.5 0.3 1.0
N J:PHE461 4.6 0.3 1.0
N J:ASP464 4.7 0.2 1.0
C J:ASP462 4.7 0.4 1.0
NH1 J:ARG425 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: Mon Dec 14 21:14:24 2020

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