Magnesium in PDB 5z87: Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus

Protein crystallography data

The structure of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus, PDB code: 5z87 was solved by J.X.Li, X.J.Hu, Y.Zhao, L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.32 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.640, 132.150, 194.560, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 21.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus (pdb code 5z87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus, PDB code: 5z87:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5z87

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Magnesium binding site 1 out of 5 in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:13.2
occ:1.00
 OG1 A:THR538 3.1 17.8 1.0
NH1 A:ARG583 3.2 19.5 1.0
O A:HOH1213 3.4 24.4 1.0
NH1 A:ARG552 3.4 15.2 1.0
O A:HOH1098 3.4 18.4 1.0
CD A:ARG552 3.7 17.6 1.0
CB A:THR538 3.7 17.9 1.0
CD2 A:LEU585 3.8 22.9 1.0
CA A:GLY534 4.0 19.6 1.0
CG A:ARG583 4.1 19.9 1.0
C A:THR538 4.1 22.5 1.0
O A:THR538 4.1 20.8 1.0
CD A:ARG583 4.2 20.0 1.0
N A:ALA539 4.3 20.2 1.0
CZ A:ARG552 4.3 21.4 1.0
CZ A:ARG583 4.4 24.6 1.0
NE A:ARG552 4.4 19.6 1.0
CD1 A:LEU585 4.5 20.2 1.0
CB A:ALA539 4.5 13.8 1.0
CA A:THR538 4.5 24.9 1.0
CG A:LEU585 4.6 19.0 1.0
NE A:ARG583 4.8 20.5 1.0
N A:GLY534 4.8 23.5 1.0
CG A:ARG552 4.9 20.4 1.0
CA A:ALA539 4.9 19.1 1.0
CG2 A:THR538 4.9 20.6 1.0
C A:GLY534 4.9 21.3 1.0
N A:ASN535 5.0 22.8 1.0

Magnesium binding site 2 out of 5 in 5z87

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Magnesium binding site 2 out of 5 in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:23.7
occ:1.00
 OD1 A:ASP713 2.0 21.1 1.0
O A:ILE715 2.1 24.6 1.0
O A:HOH971 2.1 20.4 1.0
O A:HOH967 2.1 22.2 1.0
O A:HOH925 2.1 17.1 1.0
O A:HOH999 2.2 24.1 1.0
CG A:ASP713 3.0 22.6 1.0
C A:ILE715 3.3 18.0 1.0
OD2 A:ASP713 3.3 22.8 1.0
N A:ILE715 3.9 21.2 1.0
O A:HOH1179 4.0 26.8 1.0
CA A:ILE715 4.1 19.2 1.0
O A:GLU765 4.1 23.1 1.0
O A:PRO763 4.2 26.1 1.0
N A:ALA716 4.3 19.0 1.0
O A:HOH1107 4.3 26.5 1.0
O A:GLU762 4.3 23.1 1.0
CB A:ASP713 4.3 19.5 1.0
O A:HOH1066 4.4 22.7 1.0
CA A:ALA716 4.4 20.3 1.0
CB A:ILE715 4.5 23.6 1.0
C A:ASP713 4.5 20.1 1.0
N A:SER714 4.6 19.2 1.0
C A:GLY764 4.6 27.1 1.0
CA A:GLY764 4.6 20.8 1.0
CB A:ALA716 4.6 16.9 1.0
CA A:ASP713 4.6 17.6 1.0
CD1 A:ILE766 4.7 18.3 1.0
CB A:GLU762 4.7 23.3 1.0
N A:GLU765 4.7 21.5 1.0
OE2 A:GLU762 4.7 23.7 1.0
C A:PRO763 4.8 22.8 1.0
C A:GLU762 4.9 23.6 1.0
O A:GLY764 5.0 27.6 1.0
O A:ASP713 5.0 20.3 1.0
C A:SER714 5.0 24.3 1.0

Magnesium binding site 3 out of 5 in 5z87

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Magnesium binding site 3 out of 5 in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:43.9
occ:1.00
 OD2 A:ASP292 2.8 28.1 1.0
O A:HOH1248 3.0 27.5 1.0
CG A:ASP292 3.7 26.0 1.0
OD1 A:ASP292 3.7 30.8 1.0
CD2 A:HIS294 3.9 24.0 1.0
O A:HOH1237 4.2 20.1 1.0
CD2 A:LEU295 4.3 23.4 1.0
O A:HOH1041 4.5 20.6 1.0
O A:HOH1378 4.5 22.0 1.0
CD1 A:ILE284 4.7 15.6 1.0
CG A:HIS294 4.8 26.0 1.0
CD1 A:LEU295 4.8 24.5 1.0
NE2 A:HIS294 4.8 29.7 1.0
O A:HOH1297 4.8 36.1 1.0
CB A:ILE284 4.9 20.3 1.0
CB A:LEU295 4.9 27.5 1.0
CG A:LEU295 4.9 38.9 1.0
CG2 A:ILE284 4.9 14.7 1.0
CB A:HIS294 5.0 25.5 1.0

Magnesium binding site 4 out of 5 in 5z87

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Magnesium binding site 4 out of 5 in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:7.5
occ:1.00
 OG1 B:THR538 3.1 19.2 1.0
NH1 B:ARG583 3.3 17.5 1.0
O B:HOH1166 3.3 18.6 1.0
NH1 B:ARG552 3.5 14.7 1.0
O B:HOH969 3.5 20.5 1.0
CD B:ARG552 3.7 20.2 1.0
CD2 B:LEU585 3.8 18.3 1.0
CB B:THR538 3.8 18.6 1.0
O B:THR538 3.9 13.6 1.0
CG B:ARG583 4.0 15.7 1.0
CA B:GLY534 4.0 16.4 1.0
CD B:ARG583 4.1 17.9 1.0
C B:THR538 4.1 18.5 1.0
CZ B:ARG552 4.3 20.2 1.0
N B:ALA539 4.4 16.1 1.0
CZ B:ARG583 4.4 19.1 1.0
NE B:ARG552 4.4 15.9 1.0
CB B:ALA539 4.4 16.9 1.0
CG B:LEU585 4.5 15.8 1.0
CD1 B:LEU585 4.5 17.6 1.0
CA B:THR538 4.6 18.5 1.0
NE B:ARG583 4.7 22.8 1.0
N B:GLY534 4.8 17.4 1.0
CG B:ARG552 4.9 17.6 1.0
CA B:ALA539 4.9 18.2 1.0
O B:GLY533 4.9 16.5 1.0
C B:GLY534 5.0 17.8 1.0
N B:ASN535 5.0 15.6 1.0

Magnesium binding site 5 out of 5 in 5z87

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Magnesium binding site 5 out of 5 in the Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural of A Novel B-Glucosidase EMGH1 at 2.3 Angstrom From Erythrobacter Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:24.5
occ:1.00
 O B:ILE715 2.0 23.4 1.0
O B:HOH1015 2.0 21.7 1.0
O B:HOH1054 2.1 28.6 1.0
OD1 B:ASP713 2.1 21.7 1.0
O B:HOH948 2.2 18.3 1.0
O B:HOH1022 2.2 22.1 1.0
CG B:ASP713 3.1 19.3 1.0
C B:ILE715 3.2 20.7 1.0
OD2 B:ASP713 3.4 20.4 1.0
N B:ILE715 3.7 22.9 1.0
CA B:ILE715 4.0 20.4 1.0
O B:GLU765 4.1 27.7 1.0
N B:ALA716 4.2 19.7 1.0
O B:PRO763 4.2 28.5 1.0
O B:HOH1278 4.3 22.3 1.0
O B:HOH1067 4.3 23.6 1.0
CA B:ALA716 4.3 21.0 1.0
O B:GLU762 4.4 26.7 1.0
CB B:ILE715 4.4 21.3 1.0
CB B:ASP713 4.4 20.5 1.0
N B:SER714 4.5 18.9 1.0
C B:ASP713 4.5 20.8 1.0
O B:HOH1079 4.6 21.7 1.0
CA B:GLY764 4.6 21.0 1.0
OE2 B:GLU762 4.6 23.2 1.0
CB B:ALA716 4.6 18.2 1.0
C B:GLY764 4.7 22.9 1.0
CA B:ASP713 4.7 19.2 1.0
N B:GLU765 4.8 25.1 1.0
C B:PRO763 4.8 26.9 1.0
CB B:GLU762 4.9 21.4 1.0
O B:ASP713 4.9 22.0 1.0
C B:SER714 4.9 23.2 1.0
CD1 B:ILE766 4.9 24.0 1.0

Reference:

L.Li, Y.Zhao, X.J.Hu, J.X.Li. Structural and Biochemical Analysis of A Novel B-Glucosidase EMGH1 From Erythrobacter Marinus To Be Published.
Page generated: Mon Dec 14 22:16:39 2020

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