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Magnesium in PDB 6xim: Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites

Enzymatic activity of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites

All present enzymatic activity of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites:
5.3.1.5;

Protein crystallography data

The structure of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites, PDB code: 6xim was solved by J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.450, 143.450, 231.500, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites (pdb code 6xim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites, PDB code: 6xim:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6xim

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Magnesium binding site 1 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg395

b:18.2
occ:1.00
 OD2 A:ASP292 2.0 12.5 1.0
OE1 A:GLU217 2.1 16.9 1.0
OE2 A:GLU181 2.1 16.8 1.0
OD2 A:ASP245 2.1 17.8 1.0
O4 A:XLS397 2.3 26.7 1.0
O2 A:XLS397 2.3 24.7 1.0
CD A:GLU181 3.1 16.5 1.0
CG A:ASP292 3.1 12.0 1.0
OE1 A:GLU181 3.2 16.6 1.0
CG A:ASP245 3.3 16.0 1.0
CD A:GLU217 3.3 17.6 1.0
C2 A:XLS397 3.3 25.4 1.0
C4 A:XLS397 3.4 26.8 1.0
C3 A:XLS397 3.6 26.2 1.0
O3 A:XLS397 3.6 26.2 1.0
CB A:ASP292 3.8 11.5 1.0
CB A:ASP245 3.8 13.8 1.0
O A:HOH455 4.0 17.3 1.0
OE2 A:GLU217 4.0 19.6 1.0
O A:HOH540 4.1 30.2 1.0
OD1 A:ASP292 4.1 12.3 1.0
CG A:GLU217 4.1 15.9 1.0
CE1 A:HIS220 4.2 16.1 1.0
OD1 A:ASP245 4.2 16.9 1.0
CB A:GLU217 4.2 13.7 1.0
CG A:GLU181 4.4 15.2 1.0
NE2 A:HIS220 4.5 16.1 1.0
MG A:MG396 4.5 23.0 1.0
C1 A:XLS397 4.6 23.6 1.0
C5 A:XLS397 4.7 25.5 1.0
ND2 A:ASN215 4.7 7.7 1.0
O1 A:XLS397 4.8 24.6 1.0

Magnesium binding site 2 out of 8 in 6xim

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Magnesium binding site 2 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:23.0
occ:1.00
 OE2 A:GLU217 2.0 19.6 1.0
O A:HOH540 2.1 30.2 1.0
O1 A:XLS397 2.4 24.6 1.0
NE2 A:HIS220 2.5 16.1 1.0
OD1 A:ASP255 2.8 28.7 1.0
OD2 A:ASP255 2.9 28.7 1.0
O2 A:XLS397 3.0 24.7 1.0
CD A:GLU217 3.0 17.6 1.0
OD1 A:ASP257 3.0 21.3 1.0
CG A:ASP255 3.2 25.7 1.0
CD2 A:HIS220 3.3 15.8 1.0
OE1 A:GLU217 3.4 16.9 1.0
C1 A:XLS397 3.5 23.6 1.0
CE1 A:HIS220 3.6 16.1 1.0
C2 A:XLS397 3.9 25.4 1.0
CG A:ASP257 3.9 21.0 1.0
OD2 A:ASP257 4.0 23.1 1.0
NZ A:LYS183 4.3 8.0 1.0
CG A:GLU217 4.4 15.9 1.0
O A:HOH591 4.4 73.0 1.0
ND2 A:ASN247 4.4 9.5 1.0
CE A:LYS183 4.5 7.0 1.0
MG A:MG395 4.5 18.2 1.0
CG A:HIS220 4.5 14.7 1.0
ND1 A:HIS220 4.7 16.0 1.0
CB A:ASP255 4.7 19.0 1.0
OD2 A:ASP292 4.7 12.5 1.0

Magnesium binding site 3 out of 8 in 6xim

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Magnesium binding site 3 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg395

b:16.0
occ:1.00
 OE1 B:GLU217 2.0 21.5 1.0
OD2 B:ASP245 2.1 19.0 1.0
OD2 B:ASP292 2.2 17.7 1.0
O4 B:XLS397 2.3 27.6 1.0
OE2 B:GLU181 2.3 18.8 1.0
O2 B:XLS397 2.4 28.6 1.0
CD B:GLU181 3.0 19.0 1.0
OE1 B:GLU181 3.1 19.2 1.0
CD B:GLU217 3.2 21.4 1.0
CG B:ASP292 3.2 17.1 1.0
CG B:ASP245 3.3 16.3 1.0
C4 B:XLS397 3.4 28.0 1.0
C2 B:XLS397 3.4 27.4 1.0
C3 B:XLS397 3.6 27.6 1.0
O3 B:XLS397 3.6 27.6 1.0
O B:HOH458 3.8 22.7 1.0
CB B:ASP292 3.8 15.2 1.0
OE2 B:GLU217 3.9 25.0 1.0
CB B:ASP245 4.0 15.3 1.0
O B:HOH537 4.1 26.7 1.0
CG B:GLU217 4.2 18.3 1.0
OD1 B:ASP245 4.2 16.7 1.0
CE1 B:HIS220 4.2 14.8 1.0
CB B:GLU217 4.3 16.3 1.0
OD1 B:ASP292 4.3 18.1 1.0
CG B:GLU181 4.5 18.3 1.0
C5 B:XLS397 4.6 27.1 1.0
C1 B:XLS397 4.6 26.4 1.0
NE2 B:HIS220 4.7 15.2 1.0
O1 B:XLS397 4.7 24.1 1.0
MG B:MG396 4.8 19.2 1.0
ND2 B:ASN215 4.8 14.6 1.0

Magnesium binding site 4 out of 8 in 6xim

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Magnesium binding site 4 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg396

b:19.2
occ:1.00
 O B:HOH537 2.1 26.7 1.0
OE2 B:GLU217 2.2 25.0 1.0
O1 B:XLS397 2.5 24.1 1.0
NE2 B:HIS220 2.6 15.2 1.0
OD1 B:ASP255 2.7 29.1 1.0
OD2 B:ASP255 2.8 29.4 1.0
CG B:ASP255 3.1 28.0 1.0
OD1 B:ASP257 3.1 21.4 1.0
O2 B:XLS397 3.2 28.6 1.0
CD B:GLU217 3.3 21.4 1.0
CD2 B:HIS220 3.4 13.2 1.0
CE1 B:HIS220 3.6 14.8 1.0
C1 B:XLS397 3.7 26.4 1.0
OD2 B:ASP257 3.8 25.2 1.0
OE1 B:GLU217 3.8 21.5 1.0
CG B:ASP257 3.9 20.6 1.0
NZ B:LYS183 4.1 6.7 1.0
C2 B:XLS397 4.2 27.4 1.0
CE B:LYS183 4.2 8.1 1.0
ND2 B:ASN247 4.4 11.1 1.0
CG B:HIS220 4.6 13.8 1.0
CB B:ASP255 4.6 20.9 1.0
CG B:GLU217 4.6 18.3 1.0
ND1 B:HIS220 4.7 14.5 1.0
O B:HOH589 4.7 43.3 1.0
O B:HOH431 4.7 19.4 1.0
MG B:MG395 4.8 16.0 1.0
CD B:LYS183 4.9 8.6 1.0
OD2 B:ASP292 5.0 17.7 1.0

Magnesium binding site 5 out of 8 in 6xim

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Magnesium binding site 5 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg395

b:14.0
occ:1.00
 OD2 C:ASP245 2.1 19.4 1.0
OD2 C:ASP292 2.1 14.5 1.0
OE1 C:GLU217 2.2 20.0 1.0
OE2 C:GLU181 2.2 18.5 1.0
O2 C:XLS397 2.2 24.5 1.0
O4 C:XLS397 2.4 23.0 1.0
CD C:GLU181 3.1 17.2 1.0
CG C:ASP292 3.2 14.1 1.0
CG C:ASP245 3.2 17.0 1.0
OE1 C:GLU181 3.3 17.3 1.0
CD C:GLU217 3.4 19.6 1.0
C2 C:XLS397 3.5 23.6 1.0
C4 C:XLS397 3.5 22.4 1.0
C3 C:XLS397 3.8 23.0 1.0
CB C:ASP292 3.8 11.8 1.0
O3 C:XLS397 3.8 23.5 1.0
CB C:ASP245 3.8 15.1 1.0
O C:HOH468 3.9 18.9 1.0
O C:HOH551 4.1 28.9 1.0
OD1 C:ASP245 4.1 18.2 1.0
OE2 C:GLU217 4.2 23.5 1.0
CG C:GLU217 4.2 15.2 1.0
CE1 C:HIS220 4.2 12.1 1.0
OD1 C:ASP292 4.3 14.1 1.0
CB C:GLU217 4.3 11.3 1.0
CG C:GLU181 4.4 15.7 1.0
NE2 C:HIS220 4.6 12.7 1.0
ND2 C:ASN215 4.6 6.8 1.0
C1 C:XLS397 4.6 23.6 1.0
MG C:MG396 4.7 24.9 1.0
C5 C:XLS397 4.8 21.0 1.0
O1 C:XLS397 4.8 21.9 1.0

Magnesium binding site 6 out of 8 in 6xim

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Magnesium binding site 6 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg396

b:24.9
occ:1.00
 O C:HOH551 1.9 28.9 1.0
OE2 C:GLU217 2.2 23.5 1.0
NE2 C:HIS220 2.5 12.7 1.0
OD1 C:ASP255 2.6 27.9 1.0
OD2 C:ASP255 2.7 28.9 1.0
O1 C:XLS397 2.7 21.9 1.0
OD1 C:ASP257 3.0 21.3 1.0
CG C:ASP255 3.0 26.3 1.0
CD2 C:HIS220 3.1 11.1 1.0
CD C:GLU217 3.1 19.6 1.0
OE1 C:GLU217 3.5 20.0 1.0
CE1 C:HIS220 3.6 12.1 1.0
O2 C:XLS397 3.6 24.5 1.0
C1 C:XLS397 3.7 23.6 1.0
CG C:ASP257 3.9 20.5 1.0
OD2 C:ASP257 3.9 24.3 1.0
ND2 C:ASN247 4.3 10.8 1.0
NZ C:LYS183 4.3 7.3 1.0
C2 C:XLS397 4.3 23.6 1.0
CG C:HIS220 4.4 10.6 1.0
CE C:LYS183 4.4 9.1 1.0
CG C:GLU217 4.5 15.2 1.0
CB C:ASP255 4.5 19.2 1.0
ND1 C:HIS220 4.6 10.9 1.0
O C:HOH439 4.7 22.0 1.0
MG C:MG395 4.7 14.0 1.0
O C:HOH608 4.8 57.0 1.0
OD2 C:ASP292 5.0 14.5 1.0

Magnesium binding site 7 out of 8 in 6xim

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Magnesium binding site 7 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg395

b:14.8
occ:1.00
 OD2 D:ASP292 2.1 12.5 1.0
OE1 D:GLU217 2.1 17.5 1.0
OE2 D:GLU181 2.1 22.4 1.0
OD2 D:ASP245 2.1 20.7 1.0
O4 D:XLS397 2.2 25.7 1.0
O2 D:XLS397 2.5 24.1 1.0
CD D:GLU181 3.1 20.1 1.0
CG D:ASP292 3.2 12.4 1.0
CG D:ASP245 3.2 19.2 1.0
CD D:GLU217 3.3 18.9 1.0
C2 D:XLS397 3.4 24.6 1.0
C4 D:XLS397 3.4 25.4 1.0
OE1 D:GLU181 3.5 20.5 1.0
O3 D:XLS397 3.5 26.6 1.0
C3 D:XLS397 3.6 25.5 1.0
CB D:ASP292 3.7 12.4 1.0
CB D:ASP245 3.8 17.8 1.0
O D:HOH470 4.0 23.7 1.0
CG D:GLU217 4.1 15.9 1.0
OE2 D:GLU217 4.1 22.9 1.0
OD1 D:ASP292 4.2 11.3 1.0
CB D:GLU217 4.2 14.3 1.0
O D:HOH550 4.2 36.2 1.0
CE1 D:HIS220 4.2 8.9 1.0
OD1 D:ASP245 4.3 16.6 1.0
CG D:GLU181 4.4 18.2 1.0
MG D:MG396 4.5 24.1 1.0
NE2 D:HIS220 4.5 11.3 1.0
C5 D:XLS397 4.7 24.6 1.0
ND2 D:ASN215 4.7 12.6 1.0
C1 D:XLS397 4.7 23.4 1.0
O1 D:XLS397 4.8 22.7 1.0

Magnesium binding site 8 out of 8 in 6xim

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Magnesium binding site 8 out of 8 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg396

b:24.1
occ:1.00
 OE2 D:GLU217 2.1 22.9 1.0
O D:HOH550 2.2 36.2 1.0
NE2 D:HIS220 2.5 11.3 1.0
O1 D:XLS397 2.6 22.7 1.0
OD2 D:ASP255 2.6 25.0 1.0
OD1 D:ASP255 2.7 22.4 1.0
OD1 D:ASP257 2.9 18.7 1.0
O2 D:XLS397 2.9 24.1 1.0
CD D:GLU217 3.0 18.9 1.0
CG D:ASP255 3.1 22.2 1.0
CD2 D:HIS220 3.4 10.3 1.0
OE1 D:GLU217 3.4 17.5 1.0
CE1 D:HIS220 3.5 8.9 1.0
C1 D:XLS397 3.6 23.4 1.0
CG D:ASP257 3.8 20.2 1.0
OD2 D:ASP257 3.8 25.0 1.0
C2 D:XLS397 4.0 24.6 1.0
ND2 D:ASN247 4.3 5.3 1.0
NZ D:LYS183 4.4 10.3 1.0
CG D:GLU217 4.4 15.9 1.0
CE D:LYS183 4.5 7.3 1.0
MG D:MG395 4.5 14.8 1.0
CG D:HIS220 4.6 9.4 1.0
CB D:ASP255 4.6 18.2 1.0
ND1 D:HIS220 4.6 8.5 1.0
OD2 D:ASP292 4.7 12.5 1.0
O D:HOH443 4.9 18.9 1.0

Reference:

J.Jenkins, J.Janin, F.Rey, M.Chiadmi, H.Van Tilbeurgh, I.Lasters, M.De Maeyer, D.Van Belle, S.J.Wodak, M.Lauwereys, P.Stanssens, G.Matthyssens, A.M.Lambeir. Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site-Directed Mutagenesis of Metal Binding Sites. Biochemistry V. 31 5449 1992.
ISSN: ISSN 0006-2960
PubMed: 1610791
DOI: 10.1021/BI00139A005
Page generated: Tue Oct 1 23:32:06 2024

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