Manganese in PDB 9xim: 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: 9xim 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 / 2.40
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

Manganese Binding Sites:

The binding sites of Manganese atom in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites (pdb code 9xim). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese 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: 9xim:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn395

b:16.7
occ:1.00
 OE1 A:GLU217 2.0 13.6 1.0
OD2 A:ASP292 2.0 11.5 1.0
OD2 A:ASP245 2.1 14.2 1.0
O2 A:XLS397 2.2 19.2 1.0
OE2 A:GLU181 2.2 13.2 1.0
O4 A:XLS397 2.4 19.1 1.0
CD A:GLU181 3.0 13.7 1.0
OE1 A:GLU181 3.1 12.9 1.0
CG A:ASP292 3.2 10.8 1.0
CD A:GLU217 3.2 13.8 1.0
CG A:ASP245 3.3 15.0 1.0
C2 A:XLS397 3.3 19.2 1.0
C4 A:XLS397 3.4 20.7 1.0
C3 A:XLS397 3.7 20.6 1.0
O3 A:XLS397 3.8 22.1 1.0
CB A:ASP245 3.8 13.0 1.0
CB A:ASP292 3.8 10.4 1.0
O A:HOH454 4.0 15.0 1.0
OE2 A:GLU217 4.1 15.3 1.0
CG A:GLU217 4.1 12.6 1.0
CE1 A:HIS220 4.2 14.7 1.0
OD1 A:ASP292 4.2 10.4 1.0
OD1 A:ASP245 4.2 17.2 1.0
CB A:GLU217 4.3 11.2 1.0
O A:HOH530 4.3 12.6 1.0
CG A:GLU181 4.4 12.4 1.0
C1 A:XLS397 4.6 18.9 1.0
ND2 A:ASN215 4.6 7.3 1.0
NE2 A:HIS220 4.6 12.9 1.0
C5 A:XLS397 4.7 19.2 1.0
ND1 A:HIS220 5.0 14.8 1.0

Manganese binding site 2 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn396

b:24.9
occ:1.00
 OE2 A:GLU217 2.1 15.3 1.0
O A:HOH530 2.3 12.6 1.0
OD2 A:ASP255 2.3 17.2 1.0
OD1 A:ASP257 2.5 14.8 1.0
OD1 A:ASP255 2.5 21.5 1.0
NE2 A:HIS220 2.7 12.9 1.0
CG A:ASP255 2.7 17.2 1.0
CD A:GLU217 3.1 13.8 1.0
CD2 A:HIS220 3.2 11.7 1.0
CG A:ASP257 3.5 14.1 1.0
OD2 A:ASP257 3.6 18.4 1.0
OE1 A:GLU217 3.6 13.6 1.0
O1 A:XLS397 3.7 23.7 1.0
ND2 A:ASN247 3.7 7.0 1.0
CE1 A:HIS220 3.9 14.7 1.0
O2 A:XLS397 4.0 19.2 1.0
O A:HOH426 4.2 2.3 1.0
CB A:ASP255 4.2 12.7 1.0
CG A:GLU217 4.3 12.6 1.0
C1 A:XLS397 4.4 18.9 1.0
CG A:HIS220 4.4 13.0 1.0
CE A:LYS183 4.6 4.8 1.0
NZ A:LYS183 4.7 7.9 1.0
CB A:ASP257 4.8 13.1 1.0
ND1 A:HIS220 4.8 14.8 1.0
C2 A:XLS397 4.8 19.2 1.0

Manganese binding site 3 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn395

b:17.1
occ:1.00
 OE1 B:GLU217 1.9 15.7 1.0
OD2 B:ASP245 2.0 17.1 1.0
OE2 B:GLU181 2.1 11.5 1.0
OD2 B:ASP292 2.2 16.6 1.0
O2 B:XLS397 2.2 23.8 1.0
O4 B:XLS397 2.4 15.6 1.0
CD B:GLU181 3.0 12.9 1.0
CG B:ASP245 3.2 14.9 1.0
CD B:GLU217 3.2 13.8 1.0
CG B:ASP292 3.3 14.8 1.0
OE1 B:GLU181 3.3 13.7 1.0
C2 B:XLS397 3.4 20.5 1.0
C4 B:XLS397 3.4 18.9 1.0
O3 B:XLS397 3.5 20.3 1.0
C3 B:XLS397 3.6 19.6 1.0
CB B:ASP292 3.7 13.1 1.0
O B:HOH457 3.8 11.6 1.0
CB B:ASP245 3.8 13.2 1.0
OE2 B:GLU217 4.0 16.8 1.0
OD1 B:ASP245 4.1 15.1 1.0
CG B:GLU217 4.2 11.2 1.0
O B:HOH534 4.2 21.6 1.0
CB B:GLU217 4.2 12.2 1.0
CE1 B:HIS220 4.2 12.3 1.0
OD1 B:ASP292 4.3 15.3 1.0
CG B:GLU181 4.4 12.5 1.0
C1 B:XLS397 4.6 20.2 1.0
C5 B:XLS397 4.7 18.7 1.0
NE2 B:HIS220 4.7 12.1 1.0
ND2 B:ASN215 4.8 13.2 1.0
O1 B:XLS397 4.9 20.3 1.0

Manganese binding site 4 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn396

b:25.5
occ:1.00
 OD2 B:ASP255 1.9 28.3 1.0
OE2 B:GLU217 2.2 16.8 1.0
O B:HOH534 2.3 21.6 1.0
OD1 B:ASP257 2.5 14.8 1.0
NE2 B:HIS220 2.7 12.1 1.0
CG B:ASP255 2.8 26.4 1.0
OD1 B:ASP255 3.1 31.7 1.0
CD B:GLU217 3.3 13.8 1.0
CD2 B:HIS220 3.3 9.7 1.0
CG B:ASP257 3.4 16.4 1.0
O1 B:XLS397 3.4 20.3 1.0
OD2 B:ASP257 3.4 20.2 1.0
CE1 B:HIS220 3.8 12.3 1.0
OE1 B:GLU217 3.8 15.7 1.0
O2 B:XLS397 3.9 23.8 1.0
ND2 B:ASN247 3.9 7.5 1.0
CB B:ASP255 4.2 20.1 1.0
C1 B:XLS397 4.4 20.2 1.0
O B:HOH430 4.4 7.3 1.0
CG B:GLU217 4.4 11.2 1.0
NZ B:LYS183 4.5 7.4 1.0
CE B:LYS183 4.5 8.9 1.0
CG B:HIS220 4.6 11.5 1.0
ND1 B:HIS220 4.8 13.3 1.0
C2 B:XLS397 4.8 20.5 1.0
CB B:ASP257 4.8 15.1 1.0
O B:HOH547 4.9 38.8 1.0

Manganese binding site 5 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn395

b:14.9
occ:1.00
 OD2 C:ASP292 2.0 17.1 1.0
OE1 C:GLU217 2.0 15.2 1.0
OD2 C:ASP245 2.1 15.8 1.0
O2 C:XLS397 2.2 20.5 1.0
OE2 C:GLU181 2.2 13.1 1.0
O4 C:XLS397 2.3 15.6 1.0
CD C:GLU181 3.1 13.5 1.0
CG C:ASP292 3.1 16.3 1.0
OE1 C:GLU181 3.2 14.1 1.0
CD C:GLU217 3.3 13.1 1.0
CG C:ASP245 3.3 14.8 1.0
C2 C:XLS397 3.4 17.1 1.0
C4 C:XLS397 3.5 15.8 1.0
C3 C:XLS397 3.7 16.4 1.0
CB C:ASP292 3.7 13.3 1.0
CB C:ASP245 3.8 12.4 1.0
O3 C:XLS397 3.9 16.8 1.0
OE2 C:GLU217 4.1 15.0 1.0
O C:HOH471 4.1 16.3 1.0
CG C:GLU217 4.1 10.6 1.0
O C:HOH538 4.1 11.5 1.0
OD1 C:ASP292 4.2 12.6 1.0
CE1 C:HIS220 4.2 12.4 1.0
CB C:GLU217 4.2 9.1 1.0
OD1 C:ASP245 4.2 16.0 1.0
CG C:GLU181 4.4 12.5 1.0
C1 C:XLS397 4.6 17.7 1.0
NE2 C:HIS220 4.6 10.5 1.0
ND2 C:ASN215 4.6 8.6 1.0
C5 C:XLS397 4.7 14.2 1.0
ND1 C:HIS220 5.0 12.2 1.0

Manganese binding site 6 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn396

b:23.2
occ:1.00
 OD2 C:ASP255 1.8 18.7 1.0
OE2 C:GLU217 2.1 15.0 1.0
O C:HOH538 2.1 11.5 1.0
OD1 C:ASP257 2.4 11.8 1.0
CG C:ASP255 2.7 19.5 1.0
NE2 C:HIS220 2.8 10.5 1.0
OD1 C:ASP255 2.8 23.5 1.0
CD C:GLU217 3.2 13.1 1.0
CD2 C:HIS220 3.3 9.5 1.0
OD2 C:ASP257 3.3 14.1 1.0
CG C:ASP257 3.3 13.0 1.0
O1 C:XLS397 3.6 17.3 1.0
OE1 C:GLU217 3.7 15.2 1.0
CE1 C:HIS220 3.9 12.4 1.0
ND2 C:ASN247 4.0 6.3 1.0
O2 C:XLS397 4.1 20.5 1.0
CB C:ASP255 4.1 13.6 1.0
O C:HOH444 4.2 9.5 1.0
C1 C:XLS397 4.4 17.7 1.0
CG C:GLU217 4.4 10.6 1.0
NZ C:LYS183 4.5 7.8 1.0
CG C:HIS220 4.5 10.7 1.0
CE C:LYS183 4.7 7.6 1.0
CB C:ASP257 4.8 11.4 1.0
ND1 C:HIS220 4.8 12.2 1.0
C2 C:XLS397 4.8 17.1 1.0

Manganese binding site 7 out of 8 in 9xim

Go back to Manganese Binding Sites List in 9xim
Manganese 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 Manganese with other atoms in the Mn 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:Mn395

b:16.0
occ:1.00
 OE1 D:GLU217 2.0 13.5 1.0
OD2 D:ASP292 2.0 11.2 1.0
OD2 D:ASP245 2.1 15.1 1.0
OE2 D:GLU181 2.1 12.1 1.0
O4 D:XLS397 2.3 20.8 1.0
O2 D:XLS397 2.4 19.6 1.0
CG D:ASP292 3.1 11.4 1.0
CD D:GLU181 3.1 12.3 1.0
CG D:ASP245 3.2 13.5 1.0
CD D:GLU217 3.3 11.7 1.0
C4 D:XLS397 3.4 21.1 1.0
OE1 D:GLU181 3.4 14.1 1.0
C2 D:XLS397 3.5 20.0 1.0
O3 D:XLS397 3.6 22.8 1.0
CB D:ASP292 3.6 10.2 1.0
C3 D:XLS397 3.7 21.0 1.0
CB D:ASP245 3.8 11.7 1.0
O D:HOH482 4.0 12.3 1.0
O D:HOH549 4.1 15.6 1.0
OE2 D:GLU217 4.1 14.3 1.0
OD1 D:ASP292 4.1 10.0 1.0
CG D:GLU217 4.2 9.3 1.0
OD1 D:ASP245 4.2 13.4 1.0
CE1 D:HIS220 4.2 7.3 1.0
CB D:GLU217 4.3 9.4 1.0
CG D:GLU181 4.4 10.8 1.0
NE2 D:HIS220 4.6 5.3 1.0
C5 D:XLS397 4.7 20.6 1.0
C1 D:XLS397 4.7 18.6 1.0
ND2 D:ASN215 4.7 8.3 1.0
MN D:MN396 5.0 21.7 1.0

Manganese binding site 8 out of 8 in 9xim

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Manganese 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 Manganese with other atoms in the Mn 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:Mn396

b:21.7
occ:1.00
 OE2 D:GLU217 2.0 14.3 1.0
OD2 D:ASP255 2.1 21.2 1.0
O D:HOH549 2.3 15.6 1.0
OD1 D:ASP257 2.3 11.8 1.0
OD1 D:ASP255 2.6 19.1 1.0
NE2 D:HIS220 2.6 5.3 1.0
CG D:ASP255 2.7 18.3 1.0
CD D:GLU217 3.1 11.7 1.0
CD2 D:HIS220 3.1 5.0 1.0
CG D:ASP257 3.3 14.3 1.0
OD2 D:ASP257 3.5 15.9 1.0
O1 D:XLS397 3.6 19.8 1.0
OE1 D:GLU217 3.6 13.5 1.0
CE1 D:HIS220 3.8 7.3 1.0
ND2 D:ASN247 3.8 4.6 1.0
O2 D:XLS397 3.9 19.6 1.0
O D:HOH455 4.2 9.1 1.0
CB D:ASP255 4.2 14.5 1.0
CG D:GLU217 4.3 9.3 1.0
CG D:HIS220 4.4 6.7 1.0
C1 D:XLS397 4.6 18.6 1.0
NZ D:LYS183 4.6 8.8 1.0
CE D:LYS183 4.7 6.5 1.0
ND1 D:HIS220 4.7 8.6 1.0
O D:HOH587 4.7 35.7 1.0
CB D:ASP257 4.7 12.1 1.0
C2 D:XLS397 4.9 20.0 1.0
OD2 D:ASP292 5.0 11.2 1.0
CG D:ASN247 5.0 2.0 1.0
MN D:MN395 5.0 16.0 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 Dec 15 05:15:06 2020

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