Atomistry » Magnesium » PDB 5wu3-5x86 » 5ww6
Atomistry »
  Magnesium »
    PDB 5wu3-5x86 »
      5ww6 »

Magnesium in PDB 5ww6: Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer

Protein crystallography data

The structure of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer, PDB code: 5ww6 was solved by S.M.Williams, D.Chatterji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.04
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 90.170, 90.170, 420.712, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.4

Other elements in 5ww6:

The structure of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer also contains other interesting chemical elements:

Iron (Fe) 9 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer (pdb code 5ww6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer, PDB code: 5ww6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5ww6

Go back to Magnesium Binding Sites List in 5ww6
Magnesium binding site 1 out of 2 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:3.1
occ:0.33
OD1 A:ASN48 2.1 6.7 1.0
OD2 A:ASP51 2.1 7.3 1.0
CG A:ASN48 3.1 7.3 1.0
CG A:ASP51 3.1 7.8 1.0
ND2 A:ASN48 3.6 7.1 1.0
CB A:ASP51 3.8 7.9 1.0
OD1 A:ASP51 4.0 8.0 1.0
CB A:ASN48 4.4 7.4 1.0
N A:ASP51 4.6 7.8 1.0
CA A:ASN48 4.7 7.7 1.0
CA A:ASP51 4.8 8.0 1.0
O A:HOH307 4.8 12.7 0.3

Magnesium binding site 2 out of 2 in 5ww6

Go back to Magnesium Binding Sites List in 5ww6
Magnesium binding site 2 out of 2 in the Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis Soaked with Iron in the Ratio of 240 Iron Atoms Per Dodecamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:7.0
occ:1.00
OD1 D:ASN48 2.0 11.3 1.0
OD2 D:ASP51 2.0 10.1 1.0
CG D:ASP51 3.0 10.2 1.0
CG D:ASN48 3.0 11.2 1.0
ND2 D:ASN48 3.6 10.6 1.0
CB D:ASP51 3.7 10.1 1.0
OD1 D:ASP51 3.9 10.2 1.0
CB D:ASN48 4.3 11.4 1.0
N D:ASP51 4.5 9.9 1.0
CA D:ASN48 4.6 11.3 1.0
CA D:ASP51 4.7 10.3 1.0

Reference:

S.M.Williams, D.Chatterji. Flexible Aspartates Propel Iron to the Ferroxidation Sites Along Pathways Stabilized By A Conserved Arginine in Dps Proteins From Mycobacterium Smegmatis Metallomics V. 9 685 2017.
ISSN: ESSN 1756-591X
PubMed: 28418062
DOI: 10.1039/C7MT00008A
Page generated: Mon Sep 30 08:57:17 2024

Last articles

Cl in 3LFS
Cl in 3LF1
Cl in 3LFA
Cl in 3LDV
Cl in 3LEZ
Cl in 3LEP
Cl in 3LCE
Cl in 3LE6
Cl in 3LD6
Cl in 3LDA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy