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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: Sun Aug 10 07:39:19 2025

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