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Magnesium in PDB 1xyb: 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: 1xyb 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 / 1.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.700, 99.400, 94.200, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 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 1xyb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 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: 1xyb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1xyb

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Magnesium binding site 1 out of 6 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:2.0
occ:0.60
 OE1 A:GLU216 2.4 16.9 1.0
OD2 A:ASP244 2.4 13.6 1.0
OD2 A:ASP286 2.4 17.4 1.0
OE2 A:GLU180 2.4 22.8 1.0
O4 A:GLO950 2.5 62.3 1.0
O2 A:GLO950 2.7 62.1 1.0
CD A:GLU180 3.0 19.0 1.0
OE1 A:GLU180 3.0 19.3 1.0
CG A:ASP244 3.4 13.3 1.0
CG A:ASP286 3.4 13.0 1.0
CD A:GLU216 3.5 18.4 1.0
C4 A:GLO950 3.7 62.3 1.0
CB A:ASP286 3.8 9.6 1.0
MG A:MG401 3.8 3.3 0.4
O A:HOH1282 3.8 30.5 1.0
CB A:ASP244 3.9 10.7 1.0
C2 A:GLO950 4.0 60.5 1.0
CB A:GLU216 4.2 9.2 1.0
CG A:GLU216 4.2 13.3 1.0
C3 A:GLO950 4.2 62.5 1.0
CG A:GLU180 4.3 15.4 1.0
CE1 A:HIS219 4.3 11.2 1.0
O A:HOH1700 4.3 33.1 1.0
OE2 A:GLU216 4.4 25.1 1.0
O3 A:GLO950 4.4 63.4 1.0
OD1 A:ASP244 4.4 16.7 1.0
OD1 A:ASP286 4.5 13.6 1.0
NE2 A:HIS219 4.8 12.4 1.0
ND2 A:ASN214 4.8 10.9 1.0
O6 A:GLO950 4.8 64.7 1.0
C5 A:GLO950 4.9 61.3 1.0
ND1 A:HIS219 5.0 14.0 1.0

Magnesium binding site 2 out of 6 in 1xyb

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Magnesium binding site 2 out of 6 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:2.0
occ:0.60
 MG A:MG401 0.0 2.0 0.6
MG A:MG401 1.8 3.3 0.4
OD1 A:ASP254 2.4 22.7 1.0
OD1 A:ASP256 2.4 13.4 1.0
OD2 A:ASP254 2.5 24.7 1.0
OE2 A:GLU216 2.5 25.1 1.0
CG A:ASP254 2.7 22.0 1.0
NE2 A:HIS219 2.9 12.4 1.0
O A:HOH1700 3.1 33.1 1.0
CG A:ASP256 3.2 12.7 1.0
O1 A:GLO950 3.3 53.9 1.0
CD2 A:HIS219 3.3 11.8 1.0
OD2 A:ASP256 3.4 15.2 1.0
CD A:GLU216 3.5 18.4 1.0
OE1 A:GLU216 3.8 16.9 1.0
O A:HOH1262 4.0 13.9 1.0
CE1 A:HIS219 4.0 11.2 1.0
ND2 A:ASN246 4.1 5.9 1.0
CB A:ASP254 4.2 15.8 1.0
O2 A:GLO950 4.2 62.1 1.0
C1 A:GLO950 4.3 58.1 1.0
O A:HOH1326 4.3 46.6 1.0
NZ A:LYS182 4.5 10.4 1.0
CE A:LYS182 4.6 9.7 1.0
CG A:HIS219 4.6 8.2 1.0
CB A:ASP256 4.6 8.1 1.0
CG A:GLU216 4.8 13.3 1.0
C2 A:GLO950 4.9 60.5 1.0
N A:ASP256 4.9 8.2 1.0
ND1 A:HIS219 4.9 14.0 1.0
CA A:ASP254 5.0 10.0 1.0
CA A:ASP256 5.0 7.6 1.0

Magnesium binding site 3 out of 6 in 1xyb

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Magnesium binding site 3 out of 6 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
A:Mg401

b:3.3
occ:0.40
 MG A:MG401 0.0 3.3 0.4
MG A:MG401 1.8 2.0 0.6
O1 A:GLO950 2.3 53.9 1.0
O A:HOH1700 2.4 33.1 1.0
NE2 A:HIS219 2.4 12.4 1.0
O2 A:GLO950 2.4 62.1 1.0
OE2 A:GLU216 2.7 25.1 1.0
OE1 A:GLU216 2.9 16.9 1.0
C1 A:GLO950 3.0 58.1 1.0
CE1 A:HIS219 3.0 11.2 1.0
CD A:GLU216 3.2 18.4 1.0
C2 A:GLO950 3.2 60.5 1.0
CD2 A:HIS219 3.4 11.8 1.0
OD2 A:ASP254 3.5 24.7 1.0
OD1 A:ASP256 3.7 13.4 1.0
MG A:MG400 3.8 2.0 0.6
OD2 A:ASP286 4.0 17.4 1.0
OD1 A:ASP254 4.1 22.7 1.0
OD2 A:ASP256 4.1 15.2 1.0
CG A:ASP254 4.2 22.0 1.0
ND1 A:HIS219 4.2 14.0 1.0
O3 A:GLO950 4.2 63.4 1.0
C3 A:GLO950 4.3 62.5 1.0
CG A:ASP256 4.3 12.7 1.0
CG A:HIS219 4.4 8.2 1.0
OE2 A:GLU180 4.4 22.8 1.0
NZ A:LYS182 4.6 10.4 1.0
CG A:GLU216 4.6 13.3 1.0
CE A:LYS182 4.7 9.7 1.0
O4 A:GLO950 4.8 62.3 1.0
CG A:ASP286 4.8 13.0 1.0
CD A:LYS182 4.8 7.1 1.0
ND2 A:ASN246 4.8 5.9 1.0

Magnesium binding site 4 out of 6 in 1xyb

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Magnesium binding site 4 out of 6 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:Mg900

b:4.6
occ:0.60
 OD2 B:ASP744 2.3 15.6 1.0
OE1 B:GLU716 2.3 13.8 1.0
OE2 B:GLU680 2.4 19.5 1.0
OD2 B:ASP786 2.4 17.6 1.0
O4 B:GLO960 2.5 64.0 1.0
O2 B:GLO960 2.6 64.6 1.0
CD B:GLU680 2.9 17.8 1.0
OE1 B:GLU680 3.0 18.1 1.0
CG B:ASP744 3.4 13.7 1.0
CD B:GLU716 3.4 16.3 1.0
CG B:ASP786 3.4 13.5 1.0
C4 B:GLO960 3.7 65.5 1.0
O B:HOH1149 3.7 40.5 1.0
C2 B:GLO960 3.7 63.1 1.0
CB B:ASP786 3.8 11.7 1.0
CB B:ASP744 3.8 11.2 1.0
MG B:MG901 3.9 2.5 0.4
CG B:GLU716 4.0 13.9 1.0
CB B:GLU716 4.1 11.6 1.0
CG B:GLU680 4.2 15.7 1.0
C3 B:GLO960 4.3 64.9 1.0
OE2 B:GLU716 4.3 22.4 1.0
CE1 B:HIS719 4.3 15.3 1.0
OD1 B:ASP744 4.3 17.9 1.0
O B:HOH1800 4.4 48.3 1.0
O6 B:GLO960 4.4 69.6 1.0
OD1 B:ASP786 4.5 18.6 1.0
NE2 B:HIS719 4.7 14.0 1.0
O3 B:GLO960 4.7 64.3 1.0
ND2 B:ASN714 4.8 12.1 1.0
C5 B:GLO960 5.0 65.6 1.0
C1 B:GLO960 5.0 60.2 1.0

Magnesium binding site 5 out of 6 in 1xyb

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Magnesium binding site 5 out of 6 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 5 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:2.0
occ:0.60
 MG B:MG901 0.0 2.0 0.6
MG B:MG901 1.7 2.5 0.4
OD1 B:ASP754 2.4 23.2 1.0
OD1 B:ASP756 2.4 13.3 1.0
OD2 B:ASP754 2.4 23.3 1.0
OE2 B:GLU716 2.5 22.4 1.0
CG B:ASP754 2.7 21.1 1.0
NE2 B:HIS719 2.7 14.0 1.0
O1 B:GLO960 3.2 56.4 1.0
CD2 B:HIS719 3.2 14.4 1.0
CG B:ASP756 3.3 14.5 1.0
O B:HOH1800 3.4 48.3 1.0
CD B:GLU716 3.4 16.3 1.0
OD2 B:ASP756 3.5 17.3 1.0
OE1 B:GLU716 3.7 13.8 1.0
CE1 B:HIS719 3.9 15.3 1.0
O B:HOH1314 4.1 16.7 1.0
O2 B:GLO960 4.1 64.6 1.0
ND2 B:ASN746 4.1 3.9 1.0
CB B:ASP754 4.2 13.7 1.0
C1 B:GLO960 4.2 60.2 1.0
NZ B:LYS682 4.5 12.5 1.0
CG B:HIS719 4.5 10.2 1.0
CE B:LYS682 4.6 10.5 1.0
CB B:ASP756 4.7 7.8 1.0
C2 B:GLO960 4.8 63.1 1.0
CG B:GLU716 4.8 13.9 1.0
ND1 B:HIS719 4.8 17.7 1.0
N B:ASP756 4.9 8.3 1.0
CA B:ASP754 4.9 9.5 1.0

Magnesium binding site 6 out of 6 in 1xyb

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Magnesium binding site 6 out of 6 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 6 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:2.5
occ:0.40
 MG B:MG901 0.0 2.5 0.4
MG B:MG901 1.7 2.0 0.6
O1 B:GLO960 2.3 56.4 1.0
O2 B:GLO960 2.4 64.6 1.0
O B:HOH1800 2.4 48.3 1.0
NE2 B:HIS719 2.4 14.0 1.0
OE2 B:GLU716 2.6 22.4 1.0
OE1 B:GLU716 2.7 13.8 1.0
CD B:GLU716 3.0 16.3 1.0
C1 B:GLO960 3.1 60.2 1.0
CE1 B:HIS719 3.2 15.3 1.0
C2 B:GLO960 3.3 63.1 1.0
OD1 B:ASP756 3.4 13.3 1.0
CD2 B:HIS719 3.4 14.4 1.0
OD2 B:ASP754 3.4 23.3 1.0
OD2 B:ASP756 3.9 17.3 1.0
MG B:MG900 3.9 4.6 0.6
OD2 B:ASP786 4.0 17.6 1.0
OD1 B:ASP754 4.0 23.2 1.0
CG B:ASP756 4.0 14.5 1.0
CG B:ASP754 4.1 21.1 1.0
ND1 B:HIS719 4.3 17.7 1.0
CG B:GLU716 4.5 13.9 1.0
CG B:HIS719 4.5 10.2 1.0
C3 B:GLO960 4.5 64.9 1.0
OE2 B:GLU680 4.5 19.5 1.0
ND2 B:ASN746 4.6 3.9 1.0
O3 B:GLO960 4.6 64.3 1.0
NZ B:LYS682 4.6 12.5 1.0
CG B:ASP786 4.7 13.5 1.0
CE B:LYS682 4.8 10.5 1.0
O4 B:GLO960 4.9 64.0 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: Sun Aug 10 07:37:46 2025

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