Atomistry » Magnesium » PDB 1xoq-1xyc » 1xyb
Atomistry »
  Magnesium »
    PDB 1xoq-1xyc »
      1xyb »

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

Go back to Magnesium Binding Sites List in 1xyb
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

Go back to Magnesium Binding Sites List in 1xyb
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

Go back to Magnesium Binding Sites List in 1xyb
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

Go back to Magnesium Binding Sites List in 1xyb
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

Go back to Magnesium Binding Sites List in 1xyb
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

Go back to Magnesium Binding Sites List in 1xyb
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: Tue Aug 13 18:25:44 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy