Atomistry » Magnesium » PDB 1xyl-1ydf » 1xym
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1xym »

Magnesium in PDB 1xym: The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid

Enzymatic activity of The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid

All present enzymatic activity of The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid:
5.3.1.5;

Protein crystallography data

The structure of The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid, PDB code: 1xym was solved by K.N.Allen, A.Lavie, 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 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.120, 99.530, 94.790, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid (pdb code 1xym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid, PDB code: 1xym:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1xym

Go back to Magnesium Binding Sites List in 1xym
Magnesium binding site 1 out of 2 in the The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:2.6
occ:1.00
 O A:OH1700 1.9 25.9 1.0
HE2 A:HIS219 2.3 0.0 1.0
OD2 A:ASP254 2.4 27.1 1.0
OE2 A:GLU216 2.4 26.4 1.0
OD1 A:ASP256 2.4 26.1 1.0
HO A:OH1700 2.6 0.0 1.0
NE2 A:HIS219 2.7 12.3 1.0
OD1 A:ASP254 2.7 25.1 1.0
CG A:ASP254 2.9 24.3 1.0
CD A:GLU216 3.2 26.6 1.0
CG A:ASP256 3.2 25.5 1.0
OE1 A:GLU216 3.2 19.2 1.0
CD2 A:HIS219 3.3 12.7 1.0
HD21 A:ASN246 3.3 0.0 1.0
OD2 A:ASP256 3.4 26.7 1.0
HO2 A:GLO950 3.5 0.0 1.0
CE1 A:HIS219 3.7 9.9 1.0
H1 A:HOH1542 3.8 0.0 1.0
O2 A:GLO950 3.8 67.2 1.0
O1 A:GLO950 3.9 55.1 1.0
ND2 A:ASN246 4.1 13.1 1.0
O A:HOH1241 4.1 24.6 1.0
HZ1 A:LYS182 4.2 0.0 1.0
HD22 A:ASN246 4.2 0.0 1.0
C1 A:GLO950 4.3 61.5 1.0
CB A:ASP254 4.3 20.6 1.0
CG A:HIS219 4.4 10.6 1.0
H2 A:HOH1542 4.6 0.0 1.0
CG A:GLU216 4.6 19.6 1.0
H A:ASP256 4.6 0.0 1.0
ND1 A:HIS219 4.6 13.5 1.0
CB A:ASP256 4.6 16.6 1.0
O A:HOH1542 4.6 42.7 1.0
C2 A:GLO950 4.7 63.6 1.0
HZ1 A:LYS180 4.7 0.0 1.0
H2 A:HOH1241 4.7 0.0 1.0
HZ3 A:LYS180 4.7 0.0 1.0
H1 A:HOH1241 4.7 0.0 1.0
O A:HOH1247 4.8 43.2 1.0
NZ A:LYS182 4.9 22.0 1.0
HZ3 A:LYS182 4.9 0.0 1.0
N A:ASP256 5.0 14.4 1.0
H1 A:GLO950 5.0 0.0 1.0
CA A:ASP256 5.0 16.7 1.0

Magnesium binding site 2 out of 2 in 1xym

Go back to Magnesium Binding Sites List in 1xym
Magnesium binding site 2 out of 2 in the The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino-Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:2.0
occ:1.00
 O B:OH1800 1.9 28.9 1.0
OD2 B:ASP754 2.3 26.0 1.0
HE2 B:HIS719 2.4 0.0 1.0
OD1 B:ASP756 2.4 27.3 1.0
OE2 B:GLU716 2.4 20.9 1.0
HO B:OH1800 2.6 0.0 1.0
OD1 B:ASP754 2.7 25.0 1.0
NE2 B:HIS719 2.8 15.1 1.0
HO2 B:GLO960 2.8 0.0 1.0
CG B:ASP754 2.8 26.7 1.0
CD B:GLU716 3.2 17.4 1.0
O1 B:GLO960 3.2 63.1 1.0
OE1 B:GLU716 3.3 18.1 1.0
CG B:ASP756 3.3 25.4 1.0
HD21 B:ASN746 3.4 0.0 1.0
CD2 B:HIS719 3.4 16.9 1.0
OD2 B:ASP756 3.5 28.3 1.0
H1 B:HOH1541 3.6 0.0 1.0
O2 B:GLO960 3.7 73.7 1.0
H2 B:HOH1109 3.7 0.0 1.0
CE1 B:HIS719 3.8 13.5 1.0
C1 B:GLO960 3.8 68.6 1.0
HZ1 B:LYS682 4.0 0.0 1.0
ND2 B:ASN746 4.1 13.7 1.0
HD22 B:ASN746 4.1 0.0 1.0
CB B:ASP754 4.3 18.6 1.0
H1 B:HOH1109 4.3 0.0 1.0
H2 B:HOH1541 4.4 0.0 1.0
C2 B:GLO960 4.4 70.6 1.0
O B:HOH1541 4.4 48.5 1.0
O B:HOH1109 4.5 23.2 1.0
HZ3 B:LYS680 4.5 0.0 1.0
CG B:GLU716 4.6 15.3 1.0
H1 B:GLO960 4.6 0.0 1.0
CG B:HIS719 4.6 13.1 1.0
CB B:ASP756 4.6 17.9 1.0
H B:ASP756 4.7 0.0 1.0
ND1 B:HIS719 4.8 17.8 1.0
NZ B:LYS682 4.8 19.3 1.0
H2 B:HOH1332 4.8 0.0 1.0
HZ3 B:LYS682 4.9 0.0 1.0
HO3 B:GLO960 4.9 0.0 1.0

Reference:

K.N.Allen, A.Lavie, A.Glasfeld, T.N.Tanada, D.P.Gerrity, S.C.Carlson, G.K.Farber, G.A.Petsko, D.Ringe. Role of the Divalent Metal Ion in Sugar Binding, Ring Opening, and Isomerization By D-Xylose Isomerase: Replacement of A Catalytic Metal By An Amino Acid. Biochemistry V. 33 1488 1994.
ISSN: ISSN 0006-2960
PubMed: 7906142
DOI: 10.1021/BI00172A027
Page generated: Mon Dec 14 07:06:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy