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Magnesium in PDB 2gyi: Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex

Enzymatic activity of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex

All present enzymatic activity of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex:
5.3.1.5;

Protein crystallography data

The structure of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex, PDB code: 2gyi was solved by K.N.Allen, A.Lavie, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.900, 99.050, 93.650, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex (pdb code 2gyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex, PDB code: 2gyi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2gyi

Go back to Magnesium Binding Sites List in 2gyi
Magnesium binding site 1 out of 4 in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:13.8
occ:1.00
 OE1 A:GLU216 2.3 11.3 1.0
O3 A:HYA960 2.4 4.7 1.0
OD2 A:ASP244 2.4 20.8 1.0
OD2 A:ASP286 2.4 11.1 1.0
O1 A:HYA960 2.4 2.0 1.0
OE2 A:GLU180 2.4 9.2 1.0
CG A:ASP286 3.1 8.8 1.0
CG A:ASP244 3.2 16.0 1.0
C2 A:HYA960 3.3 7.5 1.0
CD A:GLU180 3.3 12.4 1.0
C1 A:HYA960 3.3 5.7 1.0
C3 A:HYA960 3.4 8.0 1.0
O A:HOH1166 3.4 15.8 1.0
CB A:ASP286 3.5 8.9 1.0
CD A:GLU216 3.5 14.0 1.0
CB A:ASP244 3.5 13.6 1.0
OE1 A:GLU180 3.6 11.7 1.0
O A:HOH1604 3.9 45.5 1.0
MG A:MG401 4.1 3.4 1.0
O A:HOH1700 4.1 6.3 1.0
OD1 A:ASP286 4.1 8.9 1.0
OD1 A:ASP244 4.2 21.5 1.0
OE2 A:GLU216 4.2 14.0 1.0
O2 A:HYA960 4.4 16.0 1.0
CB A:GLU216 4.4 11.4 1.0
CG A:GLU216 4.5 13.0 1.0
CE1 A:HIS219 4.5 10.5 1.0
N A:HYA960 4.6 5.2 1.0
C4 A:HYA960 4.6 4.6 1.0
CG A:GLU180 4.6 8.3 1.0
NE2 A:HIS219 4.8 12.5 1.0
OD1 A:ASN214 4.8 14.2 1.0
CA A:ASP244 5.0 11.4 1.0
O A:HYA960 5.0 9.6 1.0

Magnesium binding site 2 out of 4 in 2gyi

Go back to Magnesium Binding Sites List in 2gyi
Magnesium binding site 2 out of 4 in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:3.4
occ:1.00
 O A:HOH1701 2.3 9.6 1.0
O A:HYA960 2.4 9.6 1.0
O1 A:HYA960 2.4 2.0 1.0
OE2 A:GLU216 2.4 14.0 1.0
O A:HOH1700 2.4 6.3 1.0
NE2 A:HIS219 2.6 12.5 1.0
C1 A:HYA960 3.0 5.7 1.0
N A:HYA960 3.1 5.2 1.0
CD A:GLU216 3.1 14.0 1.0
OE1 A:GLU216 3.1 11.3 1.0
CE1 A:HIS219 3.5 10.5 1.0
CD2 A:HIS219 3.5 11.4 1.0
OD1 A:ASP256 3.6 13.1 1.0
OD2 A:ASP256 4.0 15.1 1.0
MG A:MG400 4.1 13.8 1.0
CG A:ASP256 4.2 13.0 1.0
NZ A:LYS182 4.2 6.0 1.0
OD2 A:ASP254 4.2 16.4 1.0
C2 A:HYA960 4.3 7.5 1.0
CE A:LYS182 4.5 8.0 1.0
CG A:GLU216 4.5 13.0 1.0
ND1 A:HIS219 4.6 11.5 1.0
CG A:HIS219 4.6 7.6 1.0
OE2 A:GLU180 4.6 9.2 1.0
ND2 A:ASN246 4.7 6.9 1.0
OD2 A:ASP286 4.7 11.1 1.0
CG A:ASP286 4.7 8.8 1.0
OD1 A:ASP286 4.7 8.9 1.0
CZ B:PHE25 4.8 10.6 1.0
O A:HOH1338 5.0 34.5 1.0

Magnesium binding site 3 out of 4 in 2gyi

Go back to Magnesium Binding Sites List in 2gyi
Magnesium binding site 3 out of 4 in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg400

b:7.5
occ:1.00
 OD2 B:ASP286 2.4 8.9 1.0
OE1 B:GLU216 2.4 13.0 1.0
OD2 B:ASP244 2.4 6.1 1.0
OE2 B:GLU180 2.4 13.2 1.0
O1 B:HYA970 2.4 23.7 1.0
O3 B:HYA970 2.4 22.5 1.0
OE1 B:GLU180 2.8 12.3 1.0
CD B:GLU180 2.9 11.7 1.0
C1 B:HYA970 3.2 19.9 1.0
C3 B:HYA970 3.4 19.3 1.0
O2 B:HYA970 3.4 6.0 1.0
CD B:GLU216 3.4 14.5 1.0
C2 B:HYA970 3.5 16.9 1.0
CG B:ASP286 3.5 11.9 1.0
CG B:ASP244 3.5 10.6 1.0
MG B:MG401 3.6 2.0 1.0
OE2 B:GLU216 3.9 11.0 1.0
CB B:ASP286 4.1 12.6 1.0
O B:HOH1250 4.1 16.3 1.0
CB B:ASP244 4.2 9.8 1.0
O B:HOH1800 4.3 4.6 1.0
N B:HYA970 4.3 19.3 1.0
CG B:GLU180 4.4 13.2 1.0
CE1 B:HIS219 4.4 11.6 1.0
OD1 B:ASP286 4.4 9.9 1.0
OD1 B:ASP244 4.4 5.6 1.0
CB B:GLU216 4.5 8.7 1.0
CG B:GLU216 4.6 7.5 1.0
NE2 B:HIS219 4.6 9.2 1.0
C4 B:HYA970 4.7 17.4 1.0
ND2 B:ASN214 4.8 11.2 1.0
O B:HYA970 4.8 12.0 1.0

Magnesium binding site 4 out of 4 in 2gyi

Go back to Magnesium Binding Sites List in 2gyi
Magnesium binding site 4 out of 4 in the Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:2.0
occ:1.00
 NE2 B:HIS219 2.3 9.2 1.0
O B:HYA970 2.4 12.0 1.0
OE2 B:GLU216 2.4 11.0 1.0
O B:HOH1800 2.4 4.6 1.0
O B:HOH1801 2.4 22.7 1.0
O1 B:HYA970 2.6 23.7 1.0
N B:HYA970 2.9 19.3 1.0
C1 B:HYA970 3.0 19.9 1.0
CD B:GLU216 3.1 14.5 1.0
CE1 B:HIS219 3.2 11.6 1.0
CD2 B:HIS219 3.2 9.8 1.0
OE1 B:GLU216 3.3 13.0 1.0
MG B:MG400 3.6 7.5 1.0
O B:HOH1272 4.0 18.7 1.0
OD2 B:ASP286 4.0 8.9 1.0
NZ B:LYS182 4.2 11.2 1.0
OD1 B:ASP256 4.2 13.1 1.0
OE2 B:GLU180 4.3 13.2 1.0
ND1 B:HIS219 4.3 11.5 1.0
CG B:HIS219 4.3 8.1 1.0
CG B:GLU216 4.4 7.5 1.0
CE B:LYS182 4.4 10.6 1.0
C2 B:HYA970 4.4 16.9 1.0
OD2 B:ASP256 4.6 14.5 1.0
OD2 B:ASP254 4.6 13.8 1.0
CD B:LYS182 4.6 10.8 1.0
O2 B:HYA970 4.6 6.0 1.0
CB B:GLU216 4.8 8.7 1.0
CG B:ASP256 4.8 11.1 1.0
ND2 B:ASN246 5.0 6.6 1.0
CG B:ASP286 5.0 11.9 1.0

Reference:

K.N.Allen, A.Lavie, G.A.Petsko, D.Ringe. Design, Synthesis, and Characterization of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex Biochemistry V. 34 3742 1995.
ISSN: ISSN 0006-2960
PubMed: 7893671
DOI: 10.1021/BI00011A032
Page generated: Tue Aug 13 23:37:25 2024

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