Atomistry » Magnesium » PDB 8gwk-8h5m » 8h18
Atomistry »
  Magnesium »
    PDB 8gwk-8h5m »
      8h18 »

Magnesium in PDB 8h18: Crystal Structure of Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710

Protein crystallography data

The structure of Crystal Structure of Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710, PDB code: 8h18 was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.51 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 96.298, 96.298, 61.455, 90, 90, 120
R / Rfree (%) 17.6 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710 (pdb code 8h18). 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 Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710, PDB code: 8h18:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8h18

Go back to Magnesium Binding Sites List in 8h18
Magnesium binding site 1 out of 2 in the Crystal Structure of Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710


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 Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.4
occ:1.00
OD2 A:ASP135 2.3 12.4 1.0
OD2 A:ASP279 2.3 15.6 1.0
OE2 A:GLU137 2.5 22.1 1.0
MG A:MG403 2.7 50.0 1.0
HB2 A:ASP279 3.0 10.9 1.0
CG A:ASP135 3.1 15.6 1.0
CG A:ASP279 3.2 16.3 1.0
OD1 A:ASP135 3.2 18.3 1.0
O A:HOH541 3.3 31.1 1.0
HG2 A:GLU137 3.4 15.1 1.0
CB A:ASP279 3.4 9.1 1.0
HB3 A:ASP279 3.5 10.9 1.0
CD A:GLU137 3.5 12.3 1.0
O A:HOH569 3.5 24.1 1.0
O A:HOH514 3.5 28.4 1.0
HA A:HIS274 3.5 17.4 1.0
HA A:ALA276 3.5 10.0 1.0
O A:ILE136 3.6 8.2 1.0
CG A:GLU137 3.9 12.5 1.0
O A:ARG275 4.2 11.6 1.0
OD1 A:ASP279 4.3 15.8 1.0
O A:HOH653 4.3 35.0 1.0
O A:HOH522 4.3 22.3 1.0
CA A:HIS274 4.4 14.5 1.0
C A:ARG275 4.4 10.9 1.0
C A:ILE136 4.4 6.5 1.0
CA A:ALA276 4.4 8.3 1.0
HG3 A:GLU137 4.4 15.1 1.0
C A:HIS274 4.4 15.1 1.0
N A:ARG275 4.4 13.6 1.0
H A:ARG275 4.5 16.4 1.0
OE1 A:GLU137 4.5 18.4 1.0
CB A:ASP135 4.5 8.6 1.0
N A:ALA276 4.6 8.7 1.0
HB3 A:ASP135 4.7 10.3 1.0
HA A:GLU137 4.7 9.0 1.0
H A:ILE136 4.7 7.2 1.0
H A:ASP279 4.9 11.9 1.0
N A:ILE136 4.9 5.9 1.0
CA A:ASP279 4.9 8.1 1.0
CA A:ARG275 4.9 11.2 1.0
HB3 A:HIS274 4.9 23.3 1.0
N A:GLU137 5.0 6.3 1.0

Magnesium binding site 2 out of 2 in 8h18

Go back to Magnesium Binding Sites List in 8h18
Magnesium binding site 2 out of 2 in the Crystal Structure of Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710


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 Dnaq Domain of Streptococcus Thermophilus Strain Dgcc 7710 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:50.0
occ:1.00
O A:HOH522 2.1 22.3 1.0
O A:HOH653 2.3 35.0 1.0
O A:HOH541 2.5 31.1 1.0
MG A:MG402 2.7 17.4 1.0
O A:ILE136 3.2 8.2 1.0
OD1 A:ASP135 3.3 18.3 1.0
O A:HOH514 3.3 28.4 1.0
O A:HOH576 3.5 22.7 1.0
O A:HOH569 3.6 24.1 1.0
OD2 A:ASP135 3.6 12.4 1.0
OE2 A:GLU137 3.8 22.1 1.0
CG A:ASP135 3.8 15.6 1.0
O A:HOH657 4.0 36.0 1.0
H A:ILE136 4.1 7.2 1.0
O A:HOH590 4.3 13.9 1.0
C A:ILE136 4.4 6.5 1.0
OD2 A:ASP279 4.4 15.6 1.0
CD A:GLU137 4.5 12.3 1.0
HE2 A:PHE219 4.6 12.4 1.0
OD1 A:ASP220 4.6 9.6 1.0
HD2 A:PHE219 4.7 11.4 1.0
HA A:GLU137 4.7 9.0 1.0
N A:ILE136 4.7 5.9 1.0
O A:HOH551 4.9 20.3 1.0
OE1 A:GLU137 5.0 18.4 1.0
HG13 A:ILE136 5.0 7.2 1.0
HG2 A:GLU137 5.0 15.1 1.0

Reference:

D.Tang, T.Jia, Y.Luo, B.Mou, J.Cheng, S.Qi, S.Yao, Z.Su, Y.Yu, Q.Chen. Dnaq Mediates Directional Spacer Acquisition in the Crispr-Cas System By A Time-Dependent Mechanism Innovation (N Y) V. 4 2023.
ISSN: ESSN 2666-6758
DOI: 10.1016/J.XINN.2023.100495
Page generated: Fri Oct 4 04:17:21 2024

Last articles

Cl in 2WPQ
Cl in 2WPN
Cl in 2WP6
Cl in 2WP5
Cl in 2WOI
Cl in 2WP8
Cl in 2WP0
Cl in 2WO6
Cl in 2WOC
Cl in 2WOD
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy