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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

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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

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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

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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

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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

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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

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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

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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

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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

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