Magnesium in PDB 5w1t: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex

Enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex:
2.7.7.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex, PDB code: 5w1t was solved by K.S.Murakami, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.08 / 4.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.000, 204.894, 314.312, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.6

Other elements in 5w1t:

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex (pdb code 5w1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex, PDB code: 5w1t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5w1t

Go back to Magnesium Binding Sites List in 5w1t
Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:0.5
occ:1.00
OD1 D:ASP462 2.2 0.5 1.0
OD1 D:ASP464 2.2 0.8 1.0
OD2 D:ASP464 2.4 0.7 1.0
OD1 D:ASP460 2.4 0.8 1.0
OD2 D:ASP462 2.5 0.9 1.0
CG D:ASP464 2.6 0.7 1.0
CG D:ASP462 2.7 1.0 1.0
CG D:ASP460 3.5 0.4 1.0
NH2 D:ARG425 3.7 0.9 1.0
OD2 D:ASP460 4.0 0.1 1.0
CB D:ASP464 4.1 0.7 1.0
CB D:ASP462 4.2 0.8 1.0
NH1 D:ARG425 4.4 0.7 1.0
CZ D:ARG425 4.6 0.1 1.0
O D:ASP460 4.7 0.8 1.0
N D:ASP462 4.8 0.5 1.0
N D:ASP460 4.8 0.7 1.0
CB D:ASP460 4.9 0.3 1.0
N D:ASP464 4.9 0.4 1.0
CA D:ASP464 4.9 0.7 1.0
C D:ASP460 4.9 0.4 1.0
CA D:ASP462 4.9 0.4 1.0

Magnesium binding site 2 out of 2 in 5w1t

Go back to Magnesium Binding Sites List in 5w1t
Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2001

b:0.9
occ:1.00
OD1 J:ASP462 2.1 0.7 1.0
OD2 J:ASP464 2.3 0.6 1.0
OD1 J:ASP464 2.3 0.2 1.0
OD2 J:ASP462 2.4 0.7 1.0
OD1 J:ASP460 2.4 0.2 1.0
CG J:ASP462 2.6 0.4 1.0
CG J:ASP464 2.6 0.2 1.0
CG J:ASP460 3.4 0.6 1.0
OD2 J:ASP460 3.7 0.1 1.0
CB J:ASP462 4.1 0.3 1.0
CB J:ASP464 4.2 0.7 1.0
NH2 J:ARG425 4.5 0.9 1.0
N J:ASP462 4.7 0.9 1.0
CB J:ASP460 4.8 0.6 1.0
N J:ASP464 4.9 0.0 1.0
CA J:ASP462 4.9 0.1 1.0
N J:ASP460 5.0 0.2 1.0
CA J:ASP464 5.0 1.0 1.0
O J:ASP460 5.0 0.4 1.0

Reference:

V.Molodtsov, E.Sineva, L.Zhang, X.Huang, M.Cashel, S.E.Ades, K.S.Murakami. Allosteric Effector Ppgpp Potentiates the Inhibition of Transcript Initiation By Dksa. Mol. Cell V. 69 828 2018.
ISSN: ISSN 1097-4164
PubMed: 29478808
DOI: 10.1016/J.MOLCEL.2018.01.035
Page generated: Mon Dec 14 21:20:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy