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Magnesium in PDB 5j78: Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius

Enzymatic activity of Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius

All present enzymatic activity of Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius:
1.2.1.10;

Protein crystallography data

The structure of Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius, PDB code: 5j78 was solved by S.J.Crennell, J.P.Extance, M.J.Danson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.579, 109.120, 196.243, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius (pdb code 5j78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius, PDB code: 5j78:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5j78

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Magnesium binding site 1 out of 4 in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius


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 An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:55.9
occ:1.00
 O A:HOH1225 2.1 32.7 1.0
O A:HOH1177 2.1 36.8 1.0
OD1 A:ASP215 2.2 25.1 1.0
O A:HOH1204 3.1 29.0 1.0
CG A:ASP215 3.3 19.7 1.0
O B:HOH1390 3.4 45.0 1.0
O B:HOH1129 3.5 43.0 1.0
OD2 A:ASP215 3.8 17.4 1.0
O A:LYS212 3.9 21.7 0.5
O A:LYS212 3.9 21.5 0.3
O A:LYS212 4.0 21.7 0.2
HA A:ASP215 4.0 15.3 1.0
HA B:ILE446 4.1 19.6 1.0
HA A:LEU213 4.1 17.4 1.0
O A:HOH1129 4.2 25.6 1.0
O A:LEU213 4.4 18.4 1.0
O B:HOH1102 4.4 33.8 1.0
CB A:ASP215 4.5 16.8 1.0
O A:THR214 4.5 15.6 1.0
HG13 B:ILE446 4.6 29.3 1.0
O B:ALA445 4.6 22.4 1.0
C A:LEU213 4.6 19.7 1.0
CA A:ASP215 4.7 12.8 1.0
HB3 A:ASP215 4.8 20.2 1.0
CA A:LEU213 4.8 14.5 1.0
C A:THR214 4.9 16.1 1.0
HZ1 A:LYS234 4.9 31.1 1.0
N A:ASP215 5.0 12.0 1.0

Magnesium binding site 2 out of 4 in 5j78

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Magnesium binding site 2 out of 4 in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius


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 An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:49.2
occ:1.00
 O B:HOH1200 2.1 29.9 1.0
O B:HOH1264 2.1 53.9 1.0
O B:HOH1148 2.2 43.4 1.0
O B:HOH1183 2.2 37.3 1.0
OD1 B:ASP215 2.2 27.9 1.0
CG B:ASP215 3.2 20.2 1.0
OD2 B:ASP215 3.5 16.6 1.0
HO3 B:GOL1009 3.8 88.7 1.0
HA B:LEU213 3.9 14.8 1.0
O A:HOH1125 4.0 41.6 1.0
O A:HOH1395 4.0 45.0 1.0
O B:LYS212 4.0 25.1 1.0
O B:LEU213 4.0 23.5 1.0
H32 B:GOL1009 4.1 59.0 1.0
HA B:ASP215 4.2 22.2 1.0
O B:HOH1238 4.4 24.8 1.0
HA A:ILE446 4.4 26.6 1.0
C B:LEU213 4.4 13.4 1.0
CB B:ASP215 4.5 16.0 1.0
O3 B:GOL1009 4.6 73.9 1.0
CA B:LEU213 4.6 12.4 1.0
O A:HOH1224 4.8 34.2 1.0
CA B:ASP215 4.8 18.5 1.0
O B:THR214 4.8 18.4 1.0
HG13 A:ILE446 4.8 32.7 1.0
HB3 B:ASP215 4.9 19.2 1.0
C3 B:GOL1009 4.9 49.2 1.0
O B:HOH1426 4.9 47.6 1.0
C B:THR214 5.0 20.3 1.0
HD23 B:LEU213 5.0 30.4 1.0
N B:ASP215 5.0 15.3 1.0

Magnesium binding site 3 out of 4 in 5j78

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Magnesium binding site 3 out of 4 in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius


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 An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1004

b:44.0
occ:1.00
 O C:HOH1110 2.1 31.4 1.0
O C:HOH1136 2.2 29.6 1.0
O C:HOH1217 2.2 41.4 1.0
O C:HOH1207 2.3 31.6 1.0
OD1 C:ASP215 2.3 26.8 1.0
CG C:ASP215 3.2 21.6 1.0
HO1 C:GOL1011 3.4 84.6 1.0
OD2 C:ASP215 3.5 18.9 1.0
HA C:LEU213 3.8 17.8 1.0
O C:LEU213 4.0 19.2 1.0
O C:LYS212 4.0 22.1 1.0
O D:HOH1387 4.1 45.7 1.0
HA C:ASP215 4.2 21.0 1.0
O1 C:GOL1011 4.2 70.5 1.0
C C:LEU213 4.3 17.0 1.0
HA D:ILE446 4.4 27.4 1.0
O C:HOH1131 4.4 25.8 1.0
CB C:ASP215 4.5 16.1 1.0
CA C:LEU213 4.6 14.8 1.0
O D:HOH1178 4.6 32.0 1.0
CA C:ASP215 4.7 17.5 1.0
HG13 D:ILE446 4.8 31.1 1.0
O C:THR214 4.8 23.4 1.0
HD23 C:LEU213 4.8 29.4 1.0
C C:THR214 4.9 15.1 1.0
HB3 C:ASP215 4.9 19.4 1.0
N C:ASP215 4.9 14.0 1.0
O D:ALA445 5.0 18.5 1.0

Magnesium binding site 4 out of 4 in 5j78

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Magnesium binding site 4 out of 4 in the Crystal Structure of An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius


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 An Acetylating Aldehyde Dehydrogenase From Geobacillus Thermoglucosidasius within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:49.7
occ:1.00
 O D:HOH1122 2.1 30.2 1.0
O D:HOH1129 2.1 35.8 1.0
O D:HOH1201 2.1 44.1 1.0
O D:HOH1208 2.2 33.7 1.0
OD1 D:ASP215 2.2 21.4 1.0
CG D:ASP215 3.1 21.5 1.0
OD2 D:ASP215 3.4 20.8 1.0
HO1 D:GOL1006 3.5 67.1 1.0
HA D:LEU213 3.7 21.0 1.0
O1 D:GOL1006 3.8 55.9 1.0
O D:LEU213 3.9 23.2 1.0
O D:LYS212 4.0 21.5 0.5
O D:LYS212 4.1 21.2 0.5
O D:HOH1216 4.1 47.5 1.0
O D:HOH1153 4.2 25.4 1.0
O C:HOH1373 4.2 43.2 1.0
O C:HOH1139 4.2 34.8 1.0
HA D:ASP215 4.3 20.1 1.0
C D:LEU213 4.3 16.2 1.0
CA D:LEU213 4.5 17.5 1.0
CB D:ASP215 4.5 14.7 1.0
HA C:ILE446 4.5 23.1 1.0
O D:THR214 4.7 18.2 1.0
O C:HOH1157 4.8 30.0 1.0
CA D:ASP215 4.8 16.7 1.0
HD23 D:LEU213 4.8 37.0 1.0
HB3 D:ASP215 4.9 17.6 1.0
C D:THR214 4.9 20.5 1.0
HG13 C:ILE446 4.9 22.3 1.0
N D:ASP215 4.9 15.2 1.0

Reference:

J.Extance, M.J.Danson, S.J.Crennell. Structure of An Acetylating Aldehyde Dehydrogenase From the Thermophilic Ethanologen Geobacillus Thermoglucosidasius. Protein Sci. V. 25 2045 2016.
ISSN: ESSN 1469-896X
PubMed: 27571338
DOI: 10.1002/PRO.3027
Page generated: Mon Dec 14 20:32:52 2020

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