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Magnesium in PDB 1xya: X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis

Enzymatic activity of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis

All present enzymatic activity of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis, PDB code: 1xya was solved by A.Lavie, K.N.Allen, 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 / 1.81
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.600, 99.340, 94.180, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis (pdb code 1xya). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis, PDB code: 1xya:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1xya

Go back to Magnesium Binding Sites List in 1xya
Magnesium binding site 1 out of 4 in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:38.6
occ:1.00
 OD2 A:ASP286 2.2 25.9 1.0
OE1 A:GLU216 2.2 24.9 1.0
OD2 A:ASP244 2.4 23.0 1.0
OE2 A:GLU180 2.7 29.6 1.0
CD A:GLU180 3.1 23.3 1.0
OE1 A:GLU180 3.2 24.2 1.0
CG A:ASP286 3.3 17.7 1.0
CD A:GLU216 3.3 21.5 1.0
CG A:ASP244 3.5 19.3 1.0
O A:HOH1454 3.8 43.5 1.0
CB A:ASP286 3.9 17.1 1.0
OE2 A:GLU216 4.0 21.8 1.0
CB A:ASP244 4.1 15.7 1.0
CG A:GLU180 4.3 17.0 1.0
O A:OH1700 4.3 33.6 1.0
OD1 A:ASP286 4.3 16.2 1.0
CE1 A:HIS219 4.4 9.8 1.0
CG A:GLU216 4.4 17.6 1.0
CB A:GLU216 4.4 15.4 1.0
OD1 A:ASP244 4.5 20.0 1.0
O A:HOH1423 4.5 64.6 1.0
NE2 A:HIS219 4.8 13.8 1.0
ND2 A:ASN214 5.0 17.7 1.0

Magnesium binding site 2 out of 4 in 1xya

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Magnesium binding site 2 out of 4 in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.6
occ:1.00
 O A:OH1700 1.9 33.6 1.0
OD1 A:ASP256 2.5 19.3 1.0
OD1 A:ASP254 2.5 25.3 1.0
OD2 A:ASP254 2.6 25.1 1.0
OE2 A:GLU216 2.6 21.8 1.0
NE2 A:HIS219 2.6 13.8 1.0
CG A:ASP254 2.9 23.0 1.0
CD2 A:HIS219 3.2 11.3 1.0
O A:HOH1415 3.3 27.6 1.0
CG A:ASP256 3.3 16.8 1.0
OD2 A:ASP256 3.4 22.9 1.0
CD A:GLU216 3.7 21.5 1.0
CE1 A:HIS219 3.7 9.8 1.0
ND2 A:ASN246 4.0 11.6 1.0
OE1 A:GLU216 4.2 24.9 1.0
CB A:ASP254 4.3 16.5 1.0
O A:HOH1174 4.4 18.2 1.0
CG A:HIS219 4.5 12.5 1.0
O A:HOH1307 4.6 60.4 1.0
NZ A:LYS182 4.6 14.1 1.0
CE A:LYS182 4.6 12.8 1.0
ND1 A:HIS219 4.7 14.4 1.0
CB A:ASP256 4.7 11.7 1.0
CG A:GLU216 4.8 17.6 1.0
O A:HOH1454 4.9 43.5 1.0

Magnesium binding site 3 out of 4 in 1xya

Go back to Magnesium Binding Sites List in 1xya
Magnesium binding site 3 out of 4 in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg900

b:34.9
occ:1.00
 OE2 B:GLU680 2.1 26.6 1.0
OD2 B:ASP744 2.5 24.2 1.0
OD2 B:ASP786 2.6 28.0 1.0
OE1 B:GLU716 2.6 19.2 1.0
CD B:GLU680 3.1 22.2 1.0
OE1 B:GLU680 3.5 22.4 1.0
CG B:ASP786 3.5 18.5 1.0
CG B:ASP744 3.6 19.3 1.0
CD B:GLU716 3.7 17.9 1.0
O B:HOH1452 3.8 37.0 1.0
CB B:ASP786 3.8 18.3 1.0
O B:OH1800 4.0 29.4 1.0
CB B:ASP744 4.1 16.3 1.0
CG B:GLU716 4.2 15.9 1.0
CB B:GLU716 4.3 12.2 1.0
CG B:GLU680 4.3 18.8 1.0
O B:HOH1363 4.4 53.1 1.0
CE1 B:HIS719 4.4 13.9 1.0
OD1 B:ASP744 4.6 20.3 1.0
OD1 B:ASP786 4.6 22.2 1.0
OE2 B:GLU716 4.7 25.2 1.0
NE2 B:HIS719 4.8 13.8 1.0
O B:HOH1435 4.8 43.8 1.0
ND2 B:ASN714 4.9 14.7 1.0

Magnesium binding site 4 out of 4 in 1xya

Go back to Magnesium Binding Sites List in 1xya
Magnesium binding site 4 out of 4 in the X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:24.3
occ:1.00
 O B:OH1800 1.9 29.4 1.0
OD1 B:ASP756 2.5 17.5 1.0
OD2 B:ASP754 2.6 26.4 1.0
OD1 B:ASP754 2.6 24.5 1.0
OE2 B:GLU716 2.7 25.2 1.0
NE2 B:HIS719 2.9 13.8 1.0
CG B:ASP754 2.9 24.2 1.0
OE1 B:GLU716 3.3 19.2 1.0
O B:HOH1354 3.3 28.1 1.0
CG B:ASP756 3.3 17.2 1.0
CD B:GLU716 3.3 17.9 1.0
CD2 B:HIS719 3.4 12.5 1.0
OD2 B:ASP756 3.5 21.4 1.0
CE1 B:HIS719 4.0 13.9 1.0
ND2 B:ASN746 4.2 14.7 1.0
CB B:ASP754 4.4 16.8 1.0
NZ B:LYS682 4.5 15.8 1.0
O B:HOH1076 4.6 24.4 1.0
CE B:LYS682 4.7 14.1 1.0
CG B:HIS719 4.7 11.3 1.0
CB B:ASP756 4.7 11.9 1.0
CG B:GLU716 4.8 15.9 1.0
O B:HOH1421 4.8 69.1 1.0
ND1 B:HIS719 4.9 16.1 1.0

Reference:

A.Lavie, K.N.Allen, G.A.Petsko, D.Ringe. X-Ray Crystallographic Structures of D-Xylose Isomerase-Substrate Complexes Position the Substrate and Provide Evidence For Metal Movement During Catalysis. Biochemistry V. 33 5469 1994.
ISSN: ISSN 0006-2960
PubMed: 8180169
DOI: 10.1021/BI00184A016
Page generated: Tue Aug 13 18:25:37 2024

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