Atomistry » Magnesium » PDB 2zjp-2zvj » 2zuv
Atomistry »
  Magnesium »
    PDB 2zjp-2zvj »
      2zuv »

Magnesium in PDB 2zuv: Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate

Enzymatic activity of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate

All present enzymatic activity of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate:
2.4.1.211;

Protein crystallography data

The structure of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate, PDB code: 2zuv was solved by M.Hidaka, M.Nishimoto, M.Kitaoka, T.Wakagi, H.Shoun, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.14 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.043, 68.020, 116.047, 90.00, 108.79, 90.00
R / Rfree (%) 14.9 / 19.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate (pdb code 2zuv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate, PDB code: 2zuv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 1 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


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 Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2017

b:24.4
occ:1.00
 O B:HOH1649 2.0 21.6 1.0
O A:HOH1658 2.1 26.2 1.0
O A:HOH1525 2.1 20.5 1.0
O A:HOH985 2.1 19.8 1.0
O A:HOH1639 2.2 21.9 1.0
O A:HOH1621 2.3 20.5 1.0
O B:HOH1234 4.0 23.4 1.0
O A:HOH771 4.0 13.4 1.0
O B:HOH1230 4.2 27.4 1.0
OD2 A:ASP79 4.2 18.0 1.0
OE2 A:GLU224 4.3 21.5 1.0
OE1 A:GLU224 4.3 18.6 1.0
CB A:SER95 4.3 14.9 1.0
O A:HOH931 4.3 37.7 1.0
OD1 A:ASP79 4.3 17.4 1.0
NZ A:LYS229 4.4 19.1 1.0
OE2 B:GLU640 4.5 27.0 1.0
O A:HOH1035 4.5 17.5 1.0
CG A:ASP79 4.7 16.3 1.0
CD A:GLU224 4.7 20.5 1.0
O A:HOH1477 4.9 36.3 1.0
CA A:SER95 4.9 14.0 1.0

Magnesium binding site 2 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 2 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


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 Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2021

b:34.1
occ:1.00
 O A:HOH1757 2.0 33.6 1.0
O A:HOH1466 2.1 34.2 1.0
O A:HOH1529 2.1 29.9 1.0
O A:HOH1343 2.2 30.1 1.0
O A:HOH1464 2.2 31.7 1.0
NH1 A:ARG272 3.9 14.2 1.0
O A:HOH1423 4.0 46.5 1.0
OD2 A:ASP511 4.2 30.8 1.0
O B:HOH1461 4.2 27.3 1.0
O B:HOH971 4.2 16.3 1.0
O A:HOH1221 4.4 17.4 1.0
O A:HOH1486 4.7 38.8 1.0
CZ A:ARG272 4.8 14.8 1.0
NH2 A:ARG272 4.8 16.3 1.0
NE B:ARG550 4.9 25.9 1.0
CG B:ARG550 5.0 21.4 1.0

Magnesium binding site 3 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 3 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


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 Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2023

b:34.7
occ:1.00
 O A:HOH1318 2.1 26.5 1.0
O A:HOH1642 2.2 39.7 1.0
O A:HOH1489 4.1 39.9 1.0
OD2 A:ASP207 4.2 21.0 1.0
OD1 A:ASP207 4.2 22.6 1.0
O A:HOH1784 4.3 45.7 1.0
NE2 A:GLN205 4.4 36.2 1.0
O A:GLN205 4.5 24.2 1.0
CG A:ASP207 4.6 21.4 1.0
O A:LYS48 4.6 29.9 1.0

Magnesium binding site 4 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 4 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


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 Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2018

b:30.0
occ:1.00
 O B:HOH986 2.1 24.8 1.0
O B:HOH1641 2.1 24.0 1.0
O A:HOH1661 2.2 26.6 1.0
O B:HOH1331 2.2 29.0 1.0
O B:HOH797 2.2 30.2 1.0
O B:HOH1358 2.2 26.4 1.0
O A:HOH908 4.0 38.8 1.0
O B:HOH921 4.0 16.9 1.0
NZ B:LYS229 4.1 20.7 1.0
OE1 B:GLU224 4.2 20.6 1.0
OE2 B:GLU224 4.2 24.9 1.0
CB B:SER95 4.2 16.5 1.0
OD1 B:ASP79 4.3 21.9 1.0
OD2 B:ASP79 4.3 22.0 1.0
O A:HOH1132 4.3 29.4 1.0
O B:HOH1227 4.5 19.9 1.0
O B:HOH1512 4.5 35.1 1.0
O B:HOH1497 4.6 39.5 1.0
CD B:GLU224 4.7 22.4 1.0
CG B:ASP79 4.8 18.9 1.0
CA B:SER95 4.8 15.9 1.0
O A:HOH1762 4.9 52.2 0.0
O A:HOH1553 4.9 44.3 1.0

Magnesium binding site 5 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 5 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2019

b:30.6
occ:1.00
 O B:HOH1650 2.1 27.6 1.0
O B:HOH1609 2.1 29.3 1.0
O B:HOH1640 2.2 25.8 1.0
OD2 B:ASP595 2.2 24.3 1.0
CG B:ASP595 3.1 21.3 1.0
OD1 B:ASP595 3.5 22.9 1.0
O B:HOH1696 3.9 35.5 1.0
CB B:ASP595 4.3 19.2 1.0
O B:HOH1589 5.0 48.2 1.0

Magnesium binding site 6 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 6 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2020

b:34.1
occ:1.00
 O B:HOH1526 2.0 34.1 1.0
OE2 B:GLU135 4.2 33.4 1.0
OE1 B:GLU135 4.3 37.9 1.0
O B:HOH1553 4.6 38.9 1.0
CD B:GLU135 4.7 35.7 1.0

Magnesium binding site 7 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 7 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2022

b:25.3
occ:0.50
 O B:HOH1660 1.9 31.0 1.0
O B:HOH1135 1.9 32.7 1.0
OD1 B:ASP247 2.2 28.4 1.0
CG B:ASP247 3.3 28.3 1.0
OD2 B:ASP247 3.7 28.3 1.0
O B:ARG243 4.5 23.2 1.0
O B:HOH1056 4.5 22.1 0.5
CB B:ASP247 4.5 27.0 1.0
N B:ASP247 4.6 27.1 1.0
CA B:ASP247 4.7 27.1 1.0
CG B:ARG243 4.8 29.1 1.0
CB B:ASP246 4.9 27.9 1.0

Magnesium binding site 8 out of 8 in 2zuv

Go back to Magnesium Binding Sites List in 2zuv
Magnesium binding site 8 out of 8 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Glcnac, Ethylene Glycol, and Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2024

b:37.1
occ:1.00
 O B:HOH1705 2.1 32.9 1.0
O B:HOH1694 2.1 32.3 1.0
O B:HOH1688 2.2 33.0 1.0
O A:HOH1687 2.3 29.7 1.0
NH1 B:ARG272 3.7 16.0 1.0
OD2 B:ASP511 4.1 31.8 1.0
O A:HOH866 4.1 15.1 1.0
O A:HOH1177 4.2 25.3 1.0
O B:HOH1064 4.2 36.8 1.0
O B:HOH973 4.2 47.4 1.0
O B:HOH1306 4.3 26.4 1.0
CD A:ARG550 4.4 30.2 1.0
NH2 B:ARG272 4.5 18.3 1.0
CZ B:ARG272 4.6 17.2 1.0
O B:HOH799 4.6 39.3 1.0
O B:HOH1588 4.9 42.9 1.0

Reference:

M.Hidaka, M.Nishimoto, M.Kitaoka, T.Wakagi, H.Shoun, S.Fushinobu. The Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase: A Large Deformation of A Tim Barrel Scaffold J.Biol.Chem. V. 284 7273 2009.
ISSN: ISSN 0021-9258
PubMed: 19124470
DOI: 10.1074/JBC.M808525200
Page generated: Wed Aug 14 08:03:03 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy