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Magnesium in PDB 5m6g: Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea

Enzymatic activity of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea

All present enzymatic activity of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea:
3.2.1.74;

Protein crystallography data

The structure of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea, PDB code: 5m6g was solved by A.Gabdulkhakov, S.Tishchenko, A.Lisov, A.Leontievsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.51 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.292, 75.717, 113.893, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea (pdb code 5m6g). 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 Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea, PDB code: 5m6g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5m6g

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Magnesium binding site 1 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:14.0
occ:1.00
 O A:HOH843 2.3 23.7 1.0
O A:ASP315 2.3 20.8 1.0
OD1 A:ASP318 2.4 29.2 1.0
O A:ASP322 2.4 23.9 1.0
O A:GLN320 2.4 26.1 1.0
OE2 A:GLU327 2.5 19.5 1.0
OE1 A:GLU327 2.6 23.0 1.0
CD A:GLU327 2.9 21.9 1.0
CG A:ASP318 3.0 27.1 1.0
OD2 A:ASP318 3.1 26.4 1.0
C A:ASP315 3.3 17.4 1.0
C A:GLN320 3.5 28.2 1.0
C A:ASP322 3.7 22.9 1.0
O A:GLU321 3.7 27.6 1.0
CA A:ASP315 3.8 18.0 1.0
N A:GLN320 4.1 27.6 1.0
C A:GLU321 4.1 25.1 1.0
CA A:GLN320 4.2 31.0 1.0
CA A:PHE323 4.3 22.6 1.0
CG A:GLU327 4.4 23.4 1.0
CB A:ASP318 4.4 23.5 1.0
N A:ASP318 4.4 24.3 1.0
N A:PHE323 4.4 26.9 1.0
N A:LYS316 4.5 18.6 1.0
CB A:GLN320 4.5 30.7 1.0
N A:ASP322 4.5 23.5 1.0
N A:GLU321 4.5 23.4 1.0
O A:ILE314 4.5 17.9 1.0
CB A:ASP315 4.5 17.5 1.0
O A:HOH1028 4.5 26.3 1.0
CA A:ASP322 4.7 26.1 1.0
CA A:GLU321 4.8 29.0 1.0
N A:THR324 4.8 20.9 1.0
CA A:ASP318 4.8 26.0 1.0
CG2 A:THR324 4.8 19.4 1.0
N A:LEU317 4.9 21.9 1.0
CA A:LYS316 4.9 17.8 1.0
N A:GLY319 4.9 29.4 1.0
C A:PHE323 4.9 21.3 1.0
C A:ASP318 5.0 30.1 1.0

Magnesium binding site 2 out of 6 in 5m6g

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Magnesium binding site 2 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:19.4
occ:1.00
 O A:HOH962 2.0 20.6 1.0
OD1 A:ASP243 2.1 19.2 1.0
O A:HOH1032 2.1 16.6 1.0
O A:HOH919 2.1 19.7 1.0
OD2 A:ASP509 2.1 14.9 1.0
O A:HOH1054 2.1 22.7 1.0
CG A:ASP509 3.2 15.8 1.0
CG A:ASP243 3.3 22.1 1.0
CB A:ASP509 3.5 14.6 1.0
N A:ASP244 3.9 15.5 1.0
OD2 A:ASP243 4.0 24.7 1.0
CA A:ASP243 4.3 17.8 1.0
OD1 A:ASP509 4.3 11.9 1.0
CB A:ASP243 4.3 16.3 1.0
O A:ASP244 4.4 16.2 1.0
O A:PHE506 4.4 15.9 1.0
CB A:PHE506 4.5 15.1 1.0
C A:ASP243 4.5 17.0 1.0
CB A:ASP244 4.6 11.9 1.0
CA A:ASP244 4.7 14.6 1.0
CA A:PHE506 4.8 17.4 1.0

Magnesium binding site 3 out of 6 in 5m6g

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Magnesium binding site 3 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:21.5
occ:1.00
 OE1 A:GLU199 2.2 12.9 1.0
O A:HOH831 2.2 19.0 1.0
O A:HOH916 2.3 12.7 1.0
O A:ILE596 2.3 14.5 1.0
OD1 A:ASN597 2.4 15.0 1.0
CG A:ASN597 3.2 16.2 1.0
CD A:GLU199 3.2 17.9 1.0
O A:HOH1020 3.4 12.8 1.0
C A:ILE596 3.5 14.7 1.0
CB A:GLU199 3.5 16.3 1.0
CA A:ASN597 3.9 15.0 1.0
ND2 A:ASN597 3.9 14.0 1.0
O A:ARG186 3.9 17.8 1.0
CG A:GLU199 4.0 13.5 1.0
CB A:ASN597 4.1 16.0 1.0
OE2 A:GLU199 4.1 15.8 1.0
N A:ASN597 4.2 13.9 1.0
O A:ALA185 4.2 14.2 1.0
N A:THR586 4.2 15.3 1.0
C A:ARG186 4.3 15.1 1.0
OD1 A:ASP188 4.3 24.1 1.0
CA A:ARG186 4.4 12.6 1.0
CG A:MET585 4.4 19.2 1.0
CB A:MET585 4.5 15.6 1.0
O A:THR586 4.6 14.8 1.0
N A:ILE596 4.6 14.8 1.0
CB A:THR586 4.6 14.1 1.0
CA A:ILE596 4.6 13.8 1.0
CG2 A:ILE596 4.8 12.3 1.0
CA A:MET585 4.8 13.7 1.0
CA A:THR586 4.9 14.9 1.0
CA A:GLU199 4.9 17.9 1.0
CG A:ASP188 5.0 19.9 1.0
C A:MET585 5.0 17.0 1.0

Magnesium binding site 4 out of 6 in 5m6g

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Magnesium binding site 4 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:27.5
occ:1.00
 O A:HOH1051 1.9 25.6 1.0
OE1 A:GLU167 1.9 28.0 1.0
O A:HOH1040 2.1 30.6 1.0
NE2 A:HIS401 2.2 18.1 1.0
O A:HOH937 2.2 33.3 1.0
O A:HOH1052 2.3 30.5 1.0
CD A:GLU167 3.0 31.1 1.0
CE1 A:HIS401 3.1 26.2 1.0
CD2 A:HIS401 3.2 15.6 1.0
OE2 A:GLU167 3.4 34.5 1.0
O A:HOH860 4.1 25.4 1.0
ND1 A:HIS401 4.3 18.6 1.0
CG A:GLU167 4.3 23.8 1.0
CG A:HIS401 4.3 18.1 1.0
CB A:GLU167 4.7 22.9 1.0
CA A:ALA164 4.8 13.9 1.0
CB A:THR395 4.9 20.3 1.0
CB A:ALA164 4.9 15.2 1.0
CG2 A:THR395 4.9 20.0 1.0

Magnesium binding site 5 out of 6 in 5m6g

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Magnesium binding site 5 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:21.2
occ:1.00
 O A:HOH999 2.0 20.5 1.0
O A:HOH1021 2.0 24.8 1.0
O A:GLY173 2.0 13.7 1.0
O A:HOH921 2.1 15.2 1.0
OD1 A:ASP175 2.2 16.2 1.0
O A:HOH866 2.2 20.7 1.0
C A:GLY173 3.1 15.6 1.0
CG A:ASP175 3.3 17.3 1.0
CA A:GLY173 3.7 14.9 1.0
OH A:TYR108 3.8 13.7 1.0
O A:ILE174 3.8 13.7 1.0
C A:ILE174 3.9 13.6 1.0
OD2 A:ASP175 4.0 14.0 1.0
CA A:ASP175 4.0 10.3 1.0
CB A:ASP175 4.1 14.9 1.0
N A:ASP175 4.1 12.1 1.0
N A:ILE174 4.2 13.2 1.0
CZ A:TYR108 4.2 16.5 1.0
OE1 A:GLN389 4.4 34.4 1.0
CA A:ILE174 4.5 13.8 1.0
CD2 A:LEU382 4.5 19.0 1.0
CE2 A:TYR108 4.6 15.4 1.0
CE1 A:TYR108 4.7 14.8 1.0
O A:HOH918 4.8 22.8 1.0
O A:PHE387 4.8 18.4 1.0
N A:GLY173 4.9 16.5 1.0

Magnesium binding site 6 out of 6 in 5m6g

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Magnesium binding site 6 out of 6 in the Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:27.9
occ:1.00
 O A:HOH1025 2.0 16.4 1.0
O A:HOH964 2.1 28.8 1.0
O A:HOH883 2.1 22.5 1.0
O A:GLY462 2.2 14.3 1.0
O A:HOH1030 2.2 19.4 1.0
O A:HOH805 2.3 21.2 1.0
C A:GLY462 3.3 13.8 1.0
N A:GLY462 3.6 13.0 1.0
CA A:GLY462 4.0 14.6 1.0
O A:HOH993 4.1 21.2 1.0
OD1 A:ASP458 4.2 23.3 1.0
N A:THR463 4.3 13.0 1.0
OE1 A:GLU467 4.3 15.8 1.0
OD2 A:ASP458 4.3 32.9 1.0
CD1 A:ILE441 4.5 13.6 1.0
CA A:THR463 4.5 13.7 1.0
CG1 A:ILE441 4.6 17.6 1.0
C A:GLU461 4.7 17.4 1.0
CG A:ASP458 4.7 23.3 1.0
O A:THR460 4.7 17.9 1.0
CA A:GLU461 4.8 17.1 1.0
OE2 A:GLU467 4.9 15.9 1.0

Reference:

A.Gabdulkhakov, S.Tishchenko. Crystal Structure Glucan 1,4-Beta-Glucosidase From Saccharopolyspora Erythraea To Be Published.
Page generated: Tue Aug 12 14:51:34 2025

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