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Magnesium in PDB 1xyc: 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: 1xyc 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 / 2.19
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.700, 99.300, 94.300, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 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 1xyc). 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: 1xyc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1xyc

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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:7.0
occ:1.00
 OE1 A:GLU216 2.3 10.6 1.0
OD2 A:ASP286 2.4 22.8 1.0
OE2 A:GLU180 2.5 23.6 1.0
O2 A:3MF950 2.5 49.0 1.0
OD2 A:ASP244 2.5 19.1 1.0
O4 A:3MF950 2.7 51.5 1.0
OE1 A:GLU180 3.0 20.2 1.0
CD A:GLU180 3.0 17.4 1.0
CG A:ASP286 3.5 18.6 1.0
CD A:GLU216 3.5 15.2 1.0
C2 A:3MF950 3.5 46.5 1.0
CG A:ASP244 3.6 15.1 1.0
C4 A:3MF950 3.6 50.1 1.0
O A:HOH1362 3.6 29.4 1.0
MG A:MG401 3.7 2.0 0.4
CB A:ASP286 3.9 12.8 1.0
CB A:ASP244 4.1 12.9 1.0
C3 A:3MF950 4.1 48.6 1.0
CE1 A:HIS219 4.2 10.7 1.0
OE2 A:GLU216 4.3 20.7 1.0
CG A:GLU180 4.3 14.8 1.0
CB A:GLU216 4.3 6.6 1.0
CG A:GLU216 4.4 9.7 1.0
OD1 A:ASP286 4.5 17.3 1.0
O3 A:3MF950 4.5 47.7 1.0
O6 A:3MF950 4.5 55.6 1.0
O A:HOH1700 4.5 50.8 1.0
OD1 A:ASP244 4.6 19.7 1.0
NE2 A:HIS219 4.6 10.3 1.0
C1 A:3MF950 4.8 40.7 1.0
ND2 A:ASN214 4.9 12.3 1.0
C5 A:3MF950 4.9 48.6 1.0

Magnesium binding site 2 out of 6 in 1xyc

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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 1.7 2.0 0.4
OD1 A:ASP254 2.4 28.9 1.0
OD2 A:ASP254 2.5 26.3 1.0
OD1 A:ASP256 2.6 20.3 1.0
OE2 A:GLU216 2.6 20.7 1.0
CG A:ASP254 2.7 25.6 1.0
NE2 A:HIS219 2.8 10.3 1.0
O A:HOH1700 3.1 50.8 1.0
O1 A:3MF950 3.2 36.6 1.0
CD2 A:HIS219 3.3 9.2 1.0
CG A:ASP256 3.4 15.1 1.0
OD2 A:ASP256 3.5 19.9 1.0
CD A:GLU216 3.6 15.2 1.0
OE1 A:GLU216 4.0 10.6 1.0
CE1 A:HIS219 4.0 10.7 1.0
O2 A:3MF950 4.2 49.0 1.0
ND2 A:ASN246 4.2 8.6 1.0
O A:HOH1225 4.2 11.8 1.0
CB A:ASP254 4.2 20.1 1.0
O A:HOH1141 4.2 44.0 1.0
C1 A:3MF950 4.4 40.7 1.0
NZ A:LYS182 4.4 10.8 1.0
CE A:LYS182 4.5 8.4 1.0
CG A:HIS219 4.6 9.2 1.0
C2 A:3MF950 4.6 46.5 1.0
CB A:ASP256 4.8 8.7 1.0
CG A:GLU216 4.9 9.7 1.0
ND1 A:HIS219 4.9 13.0 1.0

Magnesium binding site 3 out of 6 in 1xyc

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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:2.0
occ:0.40
 MG A:MG401 0.0 2.0 0.4
MG A:MG401 1.7 2.0 0.6
NE2 A:HIS219 2.4 10.3 1.0
O A:HOH1700 2.4 50.8 1.0
O1 A:3MF950 2.5 36.6 1.0
O2 A:3MF950 2.5 49.0 1.0
OE2 A:GLU216 2.5 20.7 1.0
OE1 A:GLU216 2.9 10.6 1.0
CD A:GLU216 3.1 15.2 1.0
C2 A:3MF950 3.1 46.5 1.0
CE1 A:HIS219 3.2 10.7 1.0
C1 A:3MF950 3.3 40.7 1.0
CD2 A:HIS219 3.4 9.2 1.0
OD1 A:ASP256 3.6 20.3 1.0
OD2 A:ASP254 3.6 26.3 1.0
MG A:MG400 3.7 7.0 1.0
OD1 A:ASP254 4.0 28.9 1.0
OD2 A:ASP256 4.1 19.9 1.0
OD2 A:ASP286 4.1 22.8 1.0
CG A:ASP254 4.2 25.6 1.0
CG A:ASP256 4.2 15.1 1.0
ND1 A:HIS219 4.3 13.0 1.0
CG A:HIS219 4.4 9.2 1.0
CG A:GLU216 4.5 9.7 1.0
C3 A:3MF950 4.5 48.6 1.0
OE2 A:GLU180 4.5 23.6 1.0
ND2 A:ASN246 4.6 8.6 1.0
O3 A:3MF950 4.6 47.7 1.0
CG A:ASP286 4.7 18.6 1.0
NZ A:LYS182 4.7 10.8 1.0
CE A:LYS182 4.9 8.4 1.0
OD1 A:ASP286 5.0 17.3 1.0

Magnesium binding site 4 out of 6 in 1xyc

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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:10.5
occ:1.00
 OE1 B:GLU716 2.4 9.5 1.0
OE2 B:GLU680 2.4 22.8 1.0
OD2 B:ASP744 2.5 18.5 1.0
OD2 B:ASP786 2.5 19.6 1.0
O4 B:3MF960 2.5 52.9 1.0
O2 B:3MF960 2.5 50.9 1.0
CD B:GLU680 3.0 19.1 1.0
OE1 B:GLU680 3.1 18.7 1.0
C4 B:3MF960 3.5 53.2 1.0
CD B:GLU716 3.5 13.9 1.0
CG B:ASP744 3.5 13.8 1.0
C2 B:3MF960 3.5 49.5 1.0
CG B:ASP786 3.6 15.7 1.0
O B:HOH1380 3.7 46.8 1.0
MG B:MG901 3.8 2.0 0.4
CB B:ASP786 4.0 14.6 1.0
CB B:ASP744 4.0 11.7 1.0
C3 B:3MF960 4.0 52.3 1.0
CE1 B:HIS719 4.2 12.9 1.0
CB B:GLU716 4.2 7.0 1.0
CG B:GLU716 4.3 12.3 1.0
CG B:GLU680 4.3 16.9 1.0
O6 B:3MF960 4.3 55.0 1.0
OE2 B:GLU716 4.3 23.6 1.0
O3 B:3MF960 4.4 55.1 1.0
O B:HOH1800 4.4 51.2 1.0
OD1 B:ASP744 4.5 19.8 1.0
NE2 B:HIS719 4.5 11.8 1.0
OD1 B:ASP786 4.6 17.9 1.0
C5 B:3MF960 4.8 52.4 1.0
C1 B:3MF960 4.8 44.3 1.0
ND2 B:ASN714 4.8 12.6 1.0
O1 B:3MF960 4.9 40.0 1.0
ND1 B:HIS719 5.0 14.5 1.0

Magnesium binding site 5 out of 6 in 1xyc

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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 1.8 2.0 0.4
OD1 B:ASP754 2.4 26.9 1.0
OD2 B:ASP754 2.5 28.0 1.0
OD1 B:ASP756 2.5 17.0 1.0
CG B:ASP754 2.7 24.0 1.0
OE2 B:GLU716 2.7 23.6 1.0
NE2 B:HIS719 3.0 11.8 1.0
CD2 B:HIS719 3.3 8.7 1.0
CG B:ASP756 3.4 15.6 1.0
O1 B:3MF960 3.4 40.0 1.0
O B:HOH1800 3.4 51.2 1.0
OD2 B:ASP756 3.5 17.5 1.0
CD B:GLU716 3.7 13.9 1.0
OE1 B:GLU716 4.1 9.5 1.0
O B:HOH1094 4.1 16.1 1.0
CB B:ASP754 4.2 15.6 1.0
ND2 B:ASN746 4.2 7.2 1.0
CE1 B:HIS719 4.2 12.9 1.0
NZ B:LYS682 4.3 8.9 1.0
C1 B:3MF960 4.3 44.3 1.0
O2 B:3MF960 4.4 50.9 1.0
CE B:LYS682 4.5 2.7 1.0
CG B:HIS719 4.7 8.8 1.0
CB B:ASP756 4.8 6.5 1.0
C2 B:3MF960 4.9 49.5 1.0
CA B:ASP754 4.9 11.1 1.0
N B:ASP756 5.0 7.0 1.0
C B:ASP754 5.0 9.7 1.0

Magnesium binding site 6 out of 6 in 1xyc

Go back to Magnesium Binding Sites List in 1xyc
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:2.0
occ:0.40
 MG B:MG901 0.0 2.0 0.4
MG B:MG901 1.8 2.0 0.6
O B:HOH1800 2.5 51.2 1.0
O1 B:3MF960 2.5 40.0 1.0
NE2 B:HIS719 2.6 11.8 1.0
OE2 B:GLU716 2.7 23.6 1.0
O2 B:3MF960 2.7 50.9 1.0
OE1 B:GLU716 2.9 9.5 1.0
CD B:GLU716 3.1 13.9 1.0
C1 B:3MF960 3.2 44.3 1.0
C2 B:3MF960 3.3 49.5 1.0
OD1 B:ASP756 3.4 17.0 1.0
CE1 B:HIS719 3.4 12.9 1.0
CD2 B:HIS719 3.5 8.7 1.0
OD2 B:ASP754 3.7 28.0 1.0
MG B:MG900 3.8 10.5 1.0
OD2 B:ASP786 3.9 19.6 1.0
OD2 B:ASP756 4.0 17.5 1.0
CG B:ASP756 4.1 15.6 1.0
OD1 B:ASP754 4.1 26.9 1.0
CG B:ASP754 4.3 24.0 1.0
ND1 B:HIS719 4.5 14.5 1.0
ND2 B:ASN746 4.5 7.2 1.0
CG B:GLU716 4.6 12.3 1.0
CG B:HIS719 4.6 8.8 1.0
NZ B:LYS682 4.6 8.9 1.0
C3 B:3MF960 4.6 52.3 1.0
CG B:ASP786 4.7 15.7 1.0
OE2 B:GLU680 4.7 22.8 1.0
O3 B:3MF960 4.8 55.1 1.0
CE B:LYS682 4.9 2.7 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 07:38:17 2025

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