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Magnesium in PDB 5uah: Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant

Enzymatic activity of Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant

All present enzymatic activity of Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant, PDB code: 5uah 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) 29.74 / 4.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.814, 206.668, 310.286, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 28.7

Other elements in 5uah:

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

Magnesium binding site 1 out of 4 in 5uah

Go back to Magnesium Binding Sites List in 5uah
Magnesium binding site 1 out of 4 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant


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, Rpob D516V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:0.5
occ:1.00
 OE1 C:GLU813 2.2 0.7 1.0
OD2 D:ASP460 2.3 0.9 1.0
CD C:GLU813 2.3 0.6 1.0
OE2 C:GLU813 2.3 0.7 1.0
CG C:GLU813 3.4 0.3 1.0
CG D:ASP460 3.5 0.2 1.0
O D:ALA459 3.9 0.3 1.0
CA D:ASP460 4.1 0.8 1.0
CB D:ASP460 4.3 0.8 1.0
OD1 D:ASP460 4.3 0.0 1.0
C D:ALA459 4.4 0.9 1.0
CB C:GLU813 4.4 0.5 1.0
N D:ASP460 4.4 0.1 1.0
O D:CYS454 4.9 0.5 1.0

Magnesium binding site 2 out of 4 in 5uah

Go back to Magnesium Binding Sites List in 5uah
Magnesium binding site 2 out of 4 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant


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, Rpob D516V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:0.5
occ:1.00
 OD2 D:ASP462 2.0 0.1 1.0
OD2 D:ASP464 2.2 0.2 1.0
OD1 D:ASP464 2.2 0.1 1.0
OD1 D:ASP462 2.3 0.1 1.0
CG D:ASP462 2.4 0.5 1.0
CG D:ASP464 2.5 0.5 1.0
CB D:ASP462 3.9 0.7 1.0
CB D:ASP464 4.0 0.3 1.0
CB D:ASP460 4.3 0.8 1.0
N D:ASP462 4.4 0.7 1.0
N D:ASP464 4.5 0.3 1.0
CA D:ASP462 4.6 0.2 1.0
NH1 D:ARG425 4.6 0.3 1.0
CA D:ASP464 4.7 0.1 1.0
C D:ASP462 4.8 0.1 1.0
O D:ASP460 4.8 0.0 1.0
C D:ASP460 4.9 0.2 1.0
CA D:ASP460 4.9 0.8 1.0
N D:ASP460 4.9 0.1 1.0

Magnesium binding site 3 out of 4 in 5uah

Go back to Magnesium Binding Sites List in 5uah
Magnesium binding site 3 out of 4 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1401

b:0.5
occ:1.00
 OD2 J:ASP460 2.3 0.6 1.0
CD I:GLU813 2.3 0.4 1.0
OE1 I:GLU813 2.3 0.7 1.0
OE2 I:GLU813 2.3 0.4 1.0
CG I:GLU813 3.3 0.4 1.0
CG J:ASP460 3.5 0.2 1.0
O J:ALA459 4.0 0.5 1.0
CA J:ASP460 4.2 0.7 1.0
OD1 J:ASP460 4.3 0.8 1.0
CB J:ASP460 4.4 0.5 1.0
CB I:GLU813 4.4 0.8 1.0
C J:ALA459 4.5 0.4 1.0
N J:ASP460 4.5 0.4 1.0
OE1 J:GLN504 4.6 0.3 1.0
CD J:GLN504 4.9 0.6 1.0
O J:CYS454 4.9 0.6 1.0
NE2 J:GLN504 5.0 0.8 1.0

Magnesium binding site 4 out of 4 in 5uah

Go back to Magnesium Binding Sites List in 5uah
Magnesium binding site 4 out of 4 in the Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli Rna Polymerase and Rifampin Complex, Rpob D516V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2001

b:0.5
occ:1.00
 NH2 J:ARG425 1.9 0.5 1.0
OD1 J:ASP464 1.9 0.1 1.0
OD2 J:ASP464 2.1 0.3 1.0
CG J:ASP464 2.1 0.9 1.0
OD1 J:ASP462 2.6 0.3 1.0
OD2 J:ASP462 2.7 0.0 1.0
CZ J:ARG425 2.9 0.1 1.0
NH1 J:ARG425 3.0 0.1 1.0
CG J:ASP462 3.1 0.6 1.0
CB J:ASP464 3.5 0.5 1.0
NE J:ARG425 4.2 0.6 1.0
N J:ASP460 4.2 0.4 1.0
CB J:ASP460 4.3 0.5 1.0
O J:ASP460 4.6 0.7 1.0
CA J:ASP460 4.6 0.7 1.0
CA J:ASP464 4.6 0.3 1.0
CB J:ASP462 4.7 0.0 1.0
C J:ASP460 4.7 0.2 1.0
N J:ASP464 4.8 0.2 1.0
O J:ASN458 4.9 0.2 1.0
OD1 J:ASP460 4.9 0.8 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: Tue Aug 12 20:46:57 2025

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