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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

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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

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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

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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

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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

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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

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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

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