Atomistry » Magnesium » PDB 1q24-1qbk » 1q6q
Atomistry »
  Magnesium »
    PDB 1q24-1qbk »
      1q6q »

Magnesium in PDB 1q6q: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate

Protein crystallography data

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate, PDB code: 1q6q was solved by E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.29 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.182, 41.727, 92.125, 90.00, 95.87, 90.00
R / Rfree (%) 17.2 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate (pdb code 1q6q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate, PDB code: 1q6q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1q6q

Go back to Magnesium Binding Sites List in 1q6q
Magnesium binding site 1 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7300

b:14.9
occ:1.00
OD2 A:ASP62 2.0 12.5 1.0
OE2 A:GLU33 2.0 14.9 1.0
O A:HOH7376 2.1 14.9 1.0
O A:HOH7513 2.1 16.4 1.0
O3 A:LXP7301 2.2 13.7 1.0
O2 A:LXP7301 2.2 18.1 1.0
CG A:ASP62 3.1 15.0 1.0
CD A:GLU33 3.1 16.1 1.0
C2 A:LXP7301 3.1 14.8 1.0
C3 A:LXP7301 3.2 17.1 1.0
OE1 A:GLU33 3.5 15.1 1.0
CB A:ASP62 3.7 14.7 1.0
O4 A:LXP7301 3.8 15.6 1.0
C1 A:LXP7301 3.9 21.5 1.0
C4 A:LXP7301 4.0 14.6 1.0
O A:HOH7377 4.1 18.0 1.0
OD1 A:ASP11 4.1 21.0 1.0
OD1 A:ASP62 4.1 12.5 1.0
NZ A:LYS64 4.1 20.1 1.0
OD2 A:ASP11 4.2 17.2 1.0
CG A:GLU33 4.4 14.9 1.0
OG1 A:THR36 4.4 16.3 1.0
O1 A:LXP7301 4.4 25.2 1.0
NE2 A:HIS136 4.4 23.8 1.0
CA A:GLY35 4.5 15.3 1.0
N A:THR36 4.6 15.0 1.0
CG A:ASP11 4.6 20.0 1.0
CB A:ALA9 4.7 17.1 1.0
C5 A:LXP7301 4.7 17.4 1.0
O A:HOH7387 4.9 22.1 1.0
O A:HOH7385 5.0 28.3 1.0

Magnesium binding site 2 out of 2 in 1q6q

Go back to Magnesium Binding Sites List in 1q6q
Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound Xylitol 5-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg9300

b:14.0
occ:1.00
OE2 B:GLU33 2.0 13.9 1.0
O3 B:LXP9301 2.1 14.3 1.0
O B:HOH9499 2.1 14.8 1.0
OD2 B:ASP62 2.1 13.0 1.0
O B:HOH9390 2.1 13.8 1.0
O2 B:LXP9301 2.2 14.9 1.0
CD B:GLU33 3.0 11.9 1.0
C3 B:LXP9301 3.1 13.5 1.0
C2 B:LXP9301 3.1 18.0 1.0
CG B:ASP62 3.2 14.3 1.0
OE1 B:GLU33 3.4 13.8 1.0
O4 B:LXP9301 3.7 14.4 1.0
CB B:ASP62 3.8 12.2 1.0
C1 B:LXP9301 3.8 16.1 1.0
C4 B:LXP9301 3.9 14.1 1.0
NZ B:LYS64 4.1 19.2 1.0
OD2 B:ASP11 4.2 15.0 1.0
O B:HOH9392 4.2 17.6 1.0
OD1 B:ASP11 4.2 17.4 1.0
OD1 B:ASP62 4.2 14.2 1.0
OG1 B:THR36 4.3 15.7 1.0
NE2 B:HIS136 4.4 23.4 1.0
O1 B:LXP9301 4.4 20.4 1.0
CG B:GLU33 4.4 14.4 1.0
CB B:ALA9 4.6 14.2 1.0
C5 B:LXP9301 4.6 15.3 1.0
CA B:GLY35 4.6 12.8 1.0
CG B:ASP11 4.6 14.7 1.0
N B:THR36 4.7 12.6 1.0

Reference:

E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment. Structural Evidence For A 1,2-Enediolate Intermediate in the Reaction Catalyzed By 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, A Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Biochemistry V. 42 12133 2003.
ISSN: ISSN 0006-2960
PubMed: 14567674
DOI: 10.1021/BI0348819
Page generated: Mon Dec 14 06:37:05 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy