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Cobalt in PDB 4xim: 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: 4xim 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 / 2.30
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

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co395

b:24.9
occ:1.00
 OD2 A:ASP245 1.9 18.9 1.0
OE1 A:GLU217 2.0 17.8 1.0
OD2 A:ASP292 2.0 15.2 1.0
OE2 A:GLU181 2.2 23.5 1.0
CG A:ASP292 3.0 14.7 1.0
CG A:ASP245 3.0 16.7 1.0
CD A:GLU181 3.1 22.4 1.0
CD A:GLU217 3.2 16.7 1.0
OE1 A:GLU181 3.2 23.3 1.0
CB A:ASP245 3.5 14.9 1.0
CB A:ASP292 3.5 14.2 1.0
CG A:GLU217 3.8 15.6 1.0
CB A:GLU217 3.9 14.3 1.0
O A:HOH530 3.9 11.9 1.0
O A:HOH576 3.9 33.7 1.0
O A:HOH453 3.9 23.3 1.0
O A:HOH575 3.9 28.0 1.0
OD1 A:ASP292 4.1 14.7 1.0
OD1 A:ASP245 4.1 17.7 1.0
O A:HOH577 4.1 31.6 1.0
OE2 A:GLU217 4.2 16.2 1.0
CE1 A:HIS220 4.3 16.1 1.0
CG A:GLU181 4.4 20.2 1.0
ND2 A:ASN215 4.7 10.0 1.0
NE2 A:HIS220 4.8 15.7 1.0
CA A:ASP292 4.9 14.8 1.0
ND1 A:HIS220 4.9 16.5 1.0
CA A:ASP245 4.9 13.9 1.0
CA A:GLU217 5.0 12.6 1.0

Cobalt binding site 2 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co396

b:20.4
occ:1.00
 OE2 A:GLU217 1.9 16.2 1.0
OD1 A:ASP257 2.0 18.9 1.0
O A:HOH530 2.1 11.9 1.0
OD1 A:ASP255 2.2 19.2 1.0
OD2 A:ASP255 2.2 18.8 1.0
NE2 A:HIS220 2.4 15.7 1.0
CG A:ASP255 2.6 16.4 1.0
CD A:GLU217 3.0 16.7 1.0
CD2 A:HIS220 3.0 13.0 1.0
CG A:ASP257 3.1 19.0 1.0
OD2 A:ASP257 3.4 20.2 1.0
OE1 A:GLU217 3.4 17.8 1.0
CE1 A:HIS220 3.5 16.1 1.0
O A:HOH574 3.6 23.4 1.0
ND2 A:ASN247 3.9 11.8 1.0
CB A:ASP255 4.1 14.9 1.0
O A:HOH426 4.1 10.1 1.0
CG A:HIS220 4.2 14.9 1.0
CG A:GLU217 4.4 15.6 1.0
CB A:ASP257 4.4 16.7 1.0
ND1 A:HIS220 4.5 16.5 1.0
O A:HOH575 4.5 28.0 1.0
CE A:LYS183 4.8 8.1 1.0
NZ A:LYS183 4.8 11.5 1.0
CA A:ASP255 5.0 13.4 1.0
CA A:ASP257 5.0 14.6 1.0

Cobalt binding site 3 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co395

b:30.2
occ:1.00
 OE1 B:GLU217 1.8 21.2 1.0
OD2 B:ASP245 1.9 24.6 1.0
OD2 B:ASP292 2.2 19.2 1.0
OE2 B:GLU181 2.3 25.6 1.0
CG B:ASP245 3.0 21.1 1.0
CD B:GLU217 3.1 17.9 1.0
CD B:GLU181 3.1 24.3 1.0
OE1 B:GLU181 3.1 24.5 1.0
CG B:ASP292 3.1 19.3 1.0
CB B:ASP245 3.5 18.9 1.0
CB B:ASP292 3.5 17.8 1.0
CG B:GLU217 3.7 15.9 1.0
CB B:GLU217 3.8 15.5 1.0
O B:HOH458 3.8 22.9 1.0
O B:HOH587 3.9 31.3 1.0
O B:HOH538 3.9 16.1 1.0
OE2 B:GLU217 4.0 19.8 1.0
O B:HOH585 4.0 39.3 1.0
O B:HOH586 4.0 42.4 1.0
OD1 B:ASP245 4.1 22.3 1.0
CE1 B:HIS220 4.2 15.9 1.0
OD1 B:ASP292 4.3 19.4 1.0
CG B:GLU181 4.4 21.9 1.0
ND2 B:ASN215 4.7 14.6 1.0
NE2 B:HIS220 4.8 16.1 1.0
ND1 B:HIS220 4.9 16.2 1.0
CA B:ASP245 5.0 16.5 1.0
CA B:ASP292 5.0 16.3 1.0

Cobalt binding site 4 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co396

b:19.9
occ:1.00
 O B:HOH538 2.0 16.1 1.0
OE2 B:GLU217 2.1 19.8 1.0
OD1 B:ASP257 2.1 20.9 1.0
OD2 B:ASP255 2.3 17.3 1.0
OD1 B:ASP255 2.3 14.7 1.0
NE2 B:HIS220 2.4 16.1 1.0
CG B:ASP255 2.6 15.4 1.0
CD2 B:HIS220 3.0 13.2 1.0
CD B:GLU217 3.2 17.9 1.0
CG B:ASP257 3.2 20.2 1.0
OD2 B:ASP257 3.5 23.3 1.0
CE1 B:HIS220 3.5 15.9 1.0
O B:HOH584 3.8 21.7 1.0
OE1 B:GLU217 3.8 21.2 1.0
ND2 B:ASN247 3.9 14.5 1.0
O B:HOH431 4.0 11.0 1.0
CB B:ASP255 4.1 13.7 1.0
CG B:HIS220 4.2 13.1 1.0
O B:HOH561 4.3 32.7 1.0
ND1 B:HIS220 4.4 16.2 1.0
CG B:GLU217 4.5 15.9 1.0
NZ B:LYS183 4.6 9.1 1.0
CB B:ASP257 4.6 17.1 1.0
CE B:LYS183 4.6 10.5 1.0
O B:HOH585 4.9 39.3 1.0
CA B:ASP255 5.0 11.5 1.0

Cobalt binding site 5 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co395

b:25.7
occ:1.00
 OD2 C:ASP245 1.9 21.6 1.0
OD2 C:ASP292 2.0 16.6 1.0
OE1 C:GLU217 2.0 16.5 1.0
OE2 C:GLU181 2.2 22.3 1.0
CG C:ASP292 3.1 16.2 1.0
CG C:ASP245 3.1 18.7 1.0
CD C:GLU181 3.1 22.6 1.0
CD C:GLU217 3.2 14.8 1.0
OE1 C:GLU181 3.4 24.0 1.0
CB C:ASP292 3.5 13.9 1.0
CB C:ASP245 3.6 16.1 1.0
O C:HOH598 3.8 35.2 1.0
CG C:GLU217 3.8 12.2 1.0
CB C:GLU217 3.9 9.8 1.0
O C:HOH549 4.0 14.6 1.0
O C:HOH600 4.0 27.8 1.0
O C:HOH467 4.1 23.6 1.0
OD1 C:ASP245 4.1 18.4 1.0
OD1 C:ASP292 4.1 14.0 1.0
CE1 C:HIS220 4.1 11.5 1.0
OE2 C:GLU217 4.2 14.5 1.0
O C:HOH599 4.3 35.5 1.0
CG C:GLU181 4.4 20.1 1.0
NE2 C:HIS220 4.6 11.6 1.0
ND2 C:ASN215 4.7 11.2 1.0
ND1 C:HIS220 4.9 12.0 1.0
CO C:CO396 5.0 18.2 1.0

Cobalt binding site 6 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co396

b:18.2
occ:1.00
 OE2 C:GLU217 2.1 14.5 1.0
O C:HOH549 2.1 14.6 1.0
OD1 C:ASP255 2.1 10.8 1.0
OD1 C:ASP257 2.2 15.9 1.0
OD2 C:ASP255 2.2 13.3 1.0
NE2 C:HIS220 2.5 11.6 1.0
CG C:ASP255 2.6 11.6 1.0
CD2 C:HIS220 3.1 11.5 1.0
CD C:GLU217 3.1 14.8 1.0
CG C:ASP257 3.2 15.5 1.0
OD2 C:ASP257 3.4 18.3 1.0
OE1 C:GLU217 3.5 16.5 1.0
O C:HOH597 3.6 28.4 1.0
CE1 C:HIS220 3.6 11.5 1.0
ND2 C:ASN247 4.0 11.0 1.0
CB C:ASP255 4.1 10.8 1.0
O C:HOH438 4.1 10.6 1.0
CG C:HIS220 4.3 11.3 1.0
CG C:GLU217 4.4 12.2 1.0
ND1 C:HIS220 4.5 12.0 1.0
CB C:ASP257 4.6 14.1 1.0
O C:HOH592 4.6 34.6 1.0
NZ C:LYS183 4.7 10.6 1.0
O C:HOH598 4.8 35.2 1.0
CE C:LYS183 4.8 10.6 1.0
CO C:CO395 5.0 25.7 1.0

Cobalt binding site 7 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co395

b:23.9
occ:1.00
 OE1 D:GLU217 2.0 15.9 1.0
OD2 D:ASP245 2.0 21.7 1.0
OD2 D:ASP292 2.0 13.3 1.0
OE2 D:GLU181 2.1 22.8 1.0
CG D:ASP292 2.9 12.8 1.0
CG D:ASP245 3.0 19.2 1.0
CD D:GLU217 3.2 13.8 1.0
CD D:GLU181 3.2 22.0 1.0
CB D:ASP292 3.3 12.2 1.0
CB D:ASP245 3.4 16.7 1.0
OE1 D:GLU181 3.6 24.7 1.0
O D:HOH591 3.8 44.6 1.0
CG D:GLU217 3.8 11.2 1.0
O D:HOH469 3.9 21.9 1.0
CB D:GLU217 3.9 10.8 1.0
OD1 D:ASP292 4.0 12.6 1.0
O D:HOH590 4.0 25.5 1.0
OD1 D:ASP245 4.1 19.1 1.0
O D:HOH548 4.1 13.1 1.0
OE2 D:GLU217 4.1 10.3 1.0
O D:HOH592 4.2 36.2 1.0
CE1 D:HIS220 4.4 8.2 1.0
CG D:GLU181 4.4 18.2 1.0
ND2 D:ASN215 4.6 13.0 1.0
CA D:ASP292 4.8 12.9 1.0
NE2 D:HIS220 4.9 6.1 1.0
CA D:ASP245 4.9 14.8 1.0

Cobalt binding site 8 out of 8 in 4xim

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Cobalt 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 Cobalt with other atoms in the Co 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:Co396

b:9.5
occ:1.00
 OE2 D:GLU217 2.0 10.3 1.0
OD2 D:ASP255 2.1 17.6 1.0
O D:HOH548 2.1 13.1 1.0
OD1 D:ASP257 2.1 12.1 1.0
OD1 D:ASP255 2.2 15.2 1.0
NE2 D:HIS220 2.3 6.1 1.0
CG D:ASP255 2.5 15.1 1.0
CD2 D:HIS220 3.0 7.7 1.0
CD D:GLU217 3.0 13.8 1.0
CG D:ASP257 3.2 16.0 1.0
CE1 D:HIS220 3.4 8.2 1.0
OD2 D:ASP257 3.4 18.2 1.0
OE1 D:GLU217 3.5 15.9 1.0
O D:HOH589 3.7 22.3 1.0
ND2 D:ASN247 3.9 8.4 1.0
CB D:ASP255 4.0 12.7 1.0
O D:HOH441 4.1 10.1 1.0
CG D:HIS220 4.2 6.5 1.0
ND1 D:HIS220 4.3 7.7 1.0
CG D:GLU217 4.3 11.2 1.0
CB D:ASP257 4.5 13.8 1.0
CE D:LYS183 4.6 9.9 1.0
O D:HOH590 4.8 25.5 1.0
NZ D:LYS183 4.8 9.8 1.0
CA D:ASP257 5.0 12.8 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 Jul 30 17:40:33 2024

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