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

Magnesium in PDB 2zut: Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac

Enzymatic activity of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac

All present enzymatic activity of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac:
2.4.1.211;

Protein crystallography data

The structure of Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac, PDB code: 2zut 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) 44.81 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 67.861, 111.658, 118.660, 105.20, 90.48, 107.27
R / Rfree (%) 16.1 / 20.4

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

Magnesium binding site 1 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 1 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4016

b:48.3
occ:1.00
 O A:HOH2597 2.0 39.5 1.0
O A:HOH2324 2.0 29.7 1.0
O A:HOH2656 2.2 43.2 1.0
O A:HOH1740 4.0 39.1 1.0
O A:HOH1610 4.2 46.9 1.0
O A:HOH1022 4.2 37.9 1.0
O A:ASP500 4.3 20.5 1.0
OD1 A:ASP502 4.4 22.7 1.0
ND2 A:ASN440 4.7 24.6 1.0
CA A:ASP500 4.7 21.8 1.0
O A:HOH2953 4.8 43.1 1.0
OD2 A:ASP502 4.9 21.3 1.0
C A:ASP500 4.9 20.0 1.0
CB A:ASP500 5.0 21.9 1.0

Magnesium binding site 2 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 2 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4015

b:47.5
occ:1.00
 O A:HOH2391 2.2 40.8 1.0
O B:HOH2337 2.2 31.7 1.0
O B:HOH1397 2.3 29.3 1.0
O B:HOH2133 2.3 26.3 1.0
NZ B:LYS229 3.6 29.3 1.0
O A:HOH912 4.1 42.8 1.0
O B:HOH1907 4.1 19.5 1.0
OE1 B:GLU224 4.1 25.8 1.0
CB B:SER95 4.2 22.4 1.0
OE2 B:GLU224 4.2 27.1 1.0
OD1 B:ASP79 4.3 25.3 1.0
O B:HOH2424 4.3 41.9 1.0
OD2 B:ASP79 4.4 26.1 1.0
CD B:GLU224 4.6 27.0 1.0
O B:HOH2201 4.6 28.0 1.0
CA B:SER95 4.7 22.3 1.0
CG B:ASP79 4.8 21.7 1.0
O B:SER95 4.9 21.8 1.0

Magnesium binding site 3 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 3 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4019

b:31.6
occ:1.00
 O B:HOH1599 2.0 32.9 1.0
O B:HOH1798 2.0 30.8 1.0
O B:HOH1472 2.1 30.7 1.0
O B:HOH2026 2.1 24.2 1.0
O B:HOH2225 2.1 32.5 1.0
O B:HOH1743 2.2 26.3 1.0
OE2 B:GLU249 4.0 33.5 1.0
O B:HOH2202 4.2 28.7 1.0
O B:GLY253 4.3 27.8 1.0
C B:GLY253 4.7 28.1 1.0
CA B:TYR254 4.7 27.1 1.0
O B:HOH3009 5.0 42.2 1.0
CD B:GLU249 5.0 34.3 1.0
N B:TYR254 5.0 27.6 1.0

Magnesium binding site 4 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 4 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg4018

b:43.0
occ:1.00
 OD1 C:ASP174 2.1 36.4 1.0
O C:HOH1425 2.1 38.8 1.0
O C:HOH2803 2.1 39.1 1.0
O C:HOH1642 2.2 31.6 1.0
O C:HOH987 2.2 31.3 1.0
O C:HOH2307 2.3 34.3 1.0
CG C:ASP174 3.1 38.3 1.0
OD2 C:ASP174 3.5 37.8 1.0
O C:HOH1589 3.7 54.8 1.0
CB C:ASP174 4.4 37.6 1.0

Magnesium binding site 5 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 5 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4017

b:25.4
occ:1.00
 O D:HOH2264 2.0 23.1 1.0
O D:HOH914 2.0 24.1 1.0
O D:HOH1377 2.0 25.8 1.0
O D:HOH806 2.0 22.8 1.0
O D:HOH994 2.1 25.3 1.0
O D:HOH1162 2.1 25.0 1.0
O D:HOH1902 4.1 21.7 1.0
O D:GLY253 4.2 21.4 1.0
O D:HOH812 4.4 32.2 1.0
OE2 D:GLU249 4.4 23.4 1.0
O D:HOH1452 4.4 44.0 1.0
C D:GLY253 4.6 21.3 1.0
CA D:TYR254 4.8 21.0 1.0
N D:TYR254 4.9 21.2 1.0

Magnesium binding site 6 out of 6 in 2zut

Go back to Magnesium Binding Sites List in 2zut
Magnesium binding site 6 out of 6 in the Crystal Structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase in Complex with Galnac


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 Galnac within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4020

b:43.4
occ:1.00
 O D:HOH2245 2.0 37.3 1.0
O D:HOH2329 2.1 37.0 1.0
O D:HOH2113 2.2 26.1 1.0
O C:HOH1571 2.3 38.2 1.0
O D:HOH1301 2.4 31.1 1.0
O D:HOH3047 2.4 45.9 1.0
O C:HOH1622 3.7 38.0 1.0
NZ D:LYS229 3.8 29.6 1.0
O D:HOH1957 4.0 19.5 1.0
OE1 D:GLU224 4.0 24.8 1.0
OE2 D:GLU224 4.1 32.5 1.0
O D:HOH876 4.1 43.1 1.0
CB D:SER95 4.2 21.7 1.0
O D:HOH2976 4.2 45.3 1.0
O C:HOH2890 4.2 46.7 1.0
OD1 D:ASP79 4.4 28.4 1.0
OD2 D:ASP79 4.4 28.5 1.0
CD D:GLU224 4.5 27.4 1.0
O D:HOH2128 4.7 30.7 1.0
CA D:SER95 4.7 21.7 1.0
CG D:ASP79 4.8 23.8 1.0
O D:SER95 4.9 22.0 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 08:02:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy