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

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

Go back to Magnesium Binding Sites List in 1xyc
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

Go back to Magnesium Binding Sites List in 1xyc
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

Go back to Magnesium Binding Sites List in 1xyc
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

Go back to Magnesium Binding Sites List in 1xyc
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

Go back to Magnesium Binding Sites List in 1xyc
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: Tue Aug 13 18:25:50 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy