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Magnesium in PDB 5uag: Escherichia Coli Rna Polymerase Mutant - Rpob D516V

Enzymatic activity of Escherichia Coli Rna Polymerase Mutant - Rpob D516V

All present enzymatic activity of Escherichia Coli Rna Polymerase Mutant - Rpob D516V:
2.7.7.6;

Protein crystallography data

The structure of Escherichia Coli Rna Polymerase Mutant - Rpob D516V, PDB code: 5uag 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) 29.99 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.826, 205.043, 307.347, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.1

Other elements in 5uag:

The structure of Escherichia Coli Rna Polymerase Mutant - Rpob D516V 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 Mutant - Rpob D516V (pdb code 5uag). 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 Mutant - Rpob D516V, PDB code: 5uag:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5uag

Go back to Magnesium Binding Sites List in 5uag
Magnesium binding site 1 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


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

b:0.1
occ:1.00
 OD2 D:ASP462 2.0 0.9 1.0
OD1 D:ASP464 2.1 0.8 1.0
OD2 D:ASP464 2.1 0.2 1.0
OD1 D:ASP462 2.2 0.5 1.0
CG D:ASP464 2.4 0.4 1.0
CG D:ASP462 2.4 0.9 1.0
CB D:ASP464 3.9 0.1 1.0
CB D:ASP462 4.0 0.9 1.0
NH1 D:ARG425 4.1 0.7 1.0
N D:ASP464 4.4 86.6 1.0
N D:ASP462 4.5 0.9 1.0
NH2 D:ARG425 4.5 0.6 1.0
CB D:ASP460 4.6 89.2 1.0
CA D:ASP464 4.6 89.9 1.0
CA D:ASP462 4.7 0.2 1.0
CZ D:ARG425 4.8 0.2 1.0
C D:ASP462 4.9 0.9 1.0
O D:ASP460 4.9 85.0 1.0
N D:ASP460 5.0 94.4 1.0

Magnesium binding site 2 out of 4 in 5uag

Go back to Magnesium Binding Sites List in 5uag
Magnesium binding site 2 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


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 Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:0.1
occ:1.00
 OD2 D:ASP460 2.0 87.3 1.0
OD1 D:ASP460 2.3 0.7 1.0
CG D:ASP460 2.4 90.0 1.0
OD1 D:ASN458 3.8 0.7 1.0
CB D:ASP460 3.9 89.2 1.0
OE1 C:GLU813 4.0 0.9 1.0
N D:ASP460 4.3 94.4 1.0
CA D:ASP460 4.3 90.3 1.0
CD C:GLU813 4.5 0.8 1.0
C D:ALA459 4.5 99.3 1.0
O D:ALA459 4.6 0.4 1.0
C D:ASN458 4.7 89.4 1.0
OE2 C:GLU813 4.7 0.9 1.0
O D:ASN458 4.8 90.8 1.0
N D:ALA459 4.9 98.4 1.0
CG D:ASN458 4.9 0.9 1.0
CA D:ASN458 4.9 86.4 1.0

Magnesium binding site 3 out of 4 in 5uag

Go back to Magnesium Binding Sites List in 5uag
Magnesium binding site 3 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


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 Mutant - Rpob D516V within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1401

b:0.1
occ:1.00
 OD2 J:ASP460 2.1 0.0 1.0
OE1 I:GLU813 2.2 0.5 1.0
OE2 I:GLU813 2.3 0.8 1.0
CD I:GLU813 2.3 0.8 1.0
CG J:ASP460 3.3 0.3 1.0
CG I:GLU813 3.5 0.0 1.0
OD1 J:ASP460 4.0 1.0 1.0
O J:ALA459 4.2 0.8 1.0
CA J:ASP460 4.3 0.3 1.0
CB J:ASP460 4.3 0.7 1.0
OE1 J:GLN504 4.5 0.5 1.0
CB I:GLU813 4.5 0.7 1.0
N J:ASP460 4.6 0.1 1.0
C J:ALA459 4.6 0.0 1.0
O J:CYS454 5.0 0.3 1.0

Magnesium binding site 4 out of 4 in 5uag

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Magnesium binding site 4 out of 4 in the Escherichia Coli Rna Polymerase Mutant - Rpob D516V


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

b:0.1
occ:1.00
 OD1 J:ASP464 1.8 0.7 1.0
NH2 J:ARG425 1.9 0.4 1.0
OD2 J:ASP464 2.1 0.5 1.0
CG J:ASP464 2.1 0.7 1.0
OD1 J:ASP462 2.7 0.1 1.0
OD2 J:ASP462 2.7 0.4 1.0
CZ J:ARG425 2.9 0.2 1.0
NH1 J:ARG425 3.0 0.2 1.0
CG J:ASP462 3.1 0.2 1.0
CB J:ASP464 3.6 0.8 1.0
NE J:ARG425 4.2 0.2 1.0
N J:ASP460 4.4 0.1 1.0
CB J:ASP460 4.4 0.7 1.0
CA J:ASP464 4.6 0.7 1.0
CB J:ASP462 4.7 0.2 1.0
N J:ASP464 4.7 0.4 1.0
O J:ASN458 4.7 0.5 1.0
O J:ASP460 4.8 0.3 1.0
CA J:ASP460 4.8 0.3 1.0
C J:ASP460 5.0 0.9 1.0
OD1 J:ASP460 5.0 1.0 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 Sep 30 05:15:22 2024

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