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Magnesium in PDB 1xyl: 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: 1xyl 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 (°) 87.720, 99.490, 94.210, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 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 1xyl). 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: 1xyl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1xyl

Go back to Magnesium Binding Sites List in 1xyl
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:2.7
occ:1.00
 HE2 A:HIS219 1.8 0.0 1.0
O A:OH1700 1.9 21.5 1.0
OD2 A:ASP254 2.4 25.0 1.0
OD1 A:ASP254 2.5 22.7 1.0
OD1 A:ASP256 2.5 22.2 1.0
OE2 A:GLU216 2.5 18.2 1.0
HO A:OH1700 2.5 0.0 1.0
NE2 A:HIS219 2.6 14.0 1.0
CG A:ASP254 2.8 20.7 1.0
H2 A:HOH1275 3.1 0.0 1.0
CG A:ASP256 3.3 16.7 1.0
OD2 A:ASP256 3.3 22.7 1.0
CD A:GLU216 3.3 19.1 1.0
CD2 A:HIS219 3.4 11.3 1.0
H1 A:HOH1265 3.4 0.0 1.0
OE1 A:GLU216 3.4 15.3 1.0
HD21 A:ASN246 3.5 0.0 1.0
CE1 A:HIS219 3.6 13.4 1.0
O A:HOH1275 3.8 21.2 1.0
HZ3 A:LYS182 3.9 0.0 1.0
HD22 A:ASN246 4.1 0.0 1.0
ND2 A:ASN246 4.2 10.4 1.0
CB A:ASP254 4.3 17.5 1.0
O A:HOH1265 4.4 17.6 1.0
CG A:HIS219 4.5 11.8 1.0
H1 A:HOH1275 4.6 0.0 1.0
HZ2 A:LYS182 4.6 0.0 1.0
ND1 A:HIS219 4.6 13.1 1.0
NZ A:LYS182 4.7 10.0 1.0
CB A:ASP256 4.7 12.1 1.0
H A:ASP256 4.7 0.0 1.0
HZ3 A:LYS180 4.7 0.0 1.0
CG A:GLU216 4.7 13.8 1.0
HZ1 A:LYS180 4.8 0.0 1.0
H2 A:HOH1265 4.9 0.0 1.0
CE A:LYS182 4.9 11.0 1.0

Magnesium binding site 2 out of 2 in 1xyl

Go back to Magnesium Binding Sites List in 1xyl
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:2.9
occ:1.00
 O B:OH1800 1.9 23.1 1.0
HE2 B:HIS719 2.0 0.0 1.0
OD2 B:ASP754 2.4 25.7 1.0
H2 B:HOH1120 2.5 0.0 1.0
OD1 B:ASP756 2.5 21.9 1.0
HO B:OH1800 2.5 0.0 1.0
OE2 B:GLU716 2.5 21.0 1.0
OD1 B:ASP754 2.6 22.3 1.0
CG B:ASP754 2.9 20.2 1.0
NE2 B:HIS719 2.9 14.0 1.0
CG B:ASP756 3.2 19.4 1.0
OD2 B:ASP756 3.3 22.9 1.0
CD B:GLU716 3.3 14.2 1.0
O B:HOH1120 3.4 23.9 1.0
OE1 B:GLU716 3.4 14.9 1.0
CD2 B:HIS719 3.5 13.7 1.0
HD21 B:ASN746 3.6 0.0 1.0
H1 B:HOH1120 3.8 0.0 1.0
CE1 B:HIS719 3.9 15.6 1.0
HZ3 B:LYS682 4.0 0.0 1.0
H2 B:HOH1122 4.0 0.0 1.0
H2 B:HOH1111 4.0 0.0 1.0
HD22 B:ASN746 4.1 0.0 1.0
ND2 B:ASN746 4.2 7.2 1.0
CB B:ASP754 4.4 13.7 1.0
O B:HOH1111 4.4 19.7 1.0
CB B:ASP756 4.7 14.4 1.0
HZ1 B:LYS680 4.7 0.0 1.0
NZ B:LYS682 4.7 15.2 1.0
HZ2 B:LYS682 4.7 0.0 1.0
CG B:GLU716 4.7 12.1 1.0
OD2 B:ASP786 4.8 22.6 1.0
CG B:HIS719 4.8 11.3 1.0
H B:ASP756 4.8 0.0 1.0
HZ1 B:LYS788 4.9 0.0 1.0
ND1 B:HIS719 4.9 15.8 1.0
CE B:LYS682 4.9 11.4 1.0
O B:HOH1122 5.0 45.3 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: Tue Aug 13 18:27:58 2024

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