Atomistry » Magnesium » PDB 5e7c-5egc » 5e9u
Atomistry »
  Magnesium »
    PDB 5e7c-5egc »
      5e9u »

Magnesium in PDB 5e9u: Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac

Protein crystallography data

The structure of Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac, PDB code: 5e9u was solved by Y.Chen, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.48 / 3.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 148.975, 196.005, 215.673, 90.00, 90.00, 90.00
R / Rfree (%) 26.9 / 33.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac (pdb code 5e9u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac, PDB code: 5e9u:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5e9u

Go back to Magnesium Binding Sites List in 5e9u
Magnesium binding site 1 out of 4 in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac


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 Gtfa/B Complex Bound to Udp and Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:40.2
occ:1.00
OD1 B:ASP83 3.5 83.8 1.0
OE2 C:GLU230 3.5 0.6 1.0
OD2 B:ASP83 3.7 77.0 1.0
CG B:ASP83 4.0 77.7 1.0
OE1 C:GLU230 4.1 95.2 1.0
NE1 B:TRP70 4.2 67.9 1.0
CD C:GLU230 4.2 0.0 1.0
CE B:MSE84 4.4 97.8 1.0
NH2 C:ARG202 4.7 0.8 1.0

Magnesium binding site 2 out of 4 in 5e9u

Go back to Magnesium Binding Sites List in 5e9u
Magnesium binding site 2 out of 4 in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac


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 Gtfa/B Complex Bound to Udp and Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:41.3
occ:1.00
NH2 A:ARG202 3.6 0.1 1.0
OD1 D:ASP83 3.6 79.5 1.0
NE1 D:TRP70 3.7 80.5 1.0
OE2 A:GLU230 3.8 0.5 1.0
OE1 A:GLU230 4.0 0.7 1.0
OD2 D:ASP83 4.2 85.9 1.0
CG D:ASP83 4.3 82.7 1.0
CZ2 D:TRP70 4.4 87.9 1.0
CE2 D:TRP70 4.4 81.4 1.0
CD A:GLU230 4.4 0.2 1.0
CZ A:ARG202 4.6 0.8 1.0
NH1 A:ARG202 4.7 0.2 1.0
CD1 D:TRP70 4.7 82.8 1.0

Magnesium binding site 3 out of 4 in 5e9u

Go back to Magnesium Binding Sites List in 5e9u
Magnesium binding site 3 out of 4 in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:40.3
occ:1.00
OE1 E:GLU230 3.0 0.8 1.0
OD1 H:ASP83 3.5 80.0 1.0
OE2 E:GLU230 3.7 85.4 1.0
NE2 E:GLN226 3.7 95.3 1.0
CD E:GLU230 3.7 93.0 1.0
NE1 H:TRP70 3.7 72.0 1.0
NH2 E:ARG202 4.3 0.7 1.0
CG H:ASP83 4.3 83.3 1.0
OD2 H:ASP83 4.4 81.6 1.0
NH1 E:ARG202 4.5 97.4 1.0
CD1 H:TRP70 4.6 72.5 1.0
CE2 H:TRP70 4.7 74.2 1.0
CZ E:ARG202 4.9 99.6 1.0
CG H:MSE84 4.9 0.2 1.0

Magnesium binding site 4 out of 4 in 5e9u

Go back to Magnesium Binding Sites List in 5e9u
Magnesium binding site 4 out of 4 in the Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Gtfa/B Complex Bound to Udp and Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:31.8
occ:1.00
OE2 G:GLU230 3.4 93.4 1.0
NH2 G:ARG202 3.6 0.0 1.0
NE1 F:TRP70 3.9 73.0 1.0
OD2 F:ASP83 4.0 72.2 1.0
CD G:GLU230 4.3 98.9 1.0
OD1 F:ASP83 4.4 85.6 1.0
OE1 G:GLU230 4.4 99.1 1.0
CG F:ASP83 4.6 78.4 1.0
CZ G:ARG202 4.6 1.0 1.0
NH1 G:ARG202 4.7 0.7 1.0
CD1 F:TRP70 4.8 80.1 1.0
CE2 F:TRP70 4.9 70.2 1.0

Reference:

Y.Chen, R.Seepersaud, B.A.Bensing, P.M.Sullam, T.A.Rapoport. Mechanism of A Cytosolic O-Glycosyltransferase Essential For the Synthesis of A Bacterial Adhesion Protein. Proc.Natl.Acad.Sci.Usa V. 113 E1190 2016.
ISSN: ESSN 1091-6490
PubMed: 26884191
DOI: 10.1073/PNAS.1600494113
Page generated: Sun Sep 29 03:33:04 2024

Last articles

Cl in 3TK5
Cl in 3TJY
Cl in 3TK1
Cl in 3TJE
Cl in 3TJA
Cl in 3TI2
Cl in 3TIX
Cl in 3TJ2
Cl in 3TJ4
Cl in 3TIK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy