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Calcium in PDB 6t8e: Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose

Enzymatic activity of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose

All present enzymatic activity of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose, PDB code: 6t8e was solved by H.J.Rozeboom, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.454, 79.267, 91.878, 115.46, 89.99, 117.07
R / Rfree (%) 13.9 / 17.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose (pdb code 6t8e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose, PDB code: 6t8e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6t8e

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Calcium binding site 1 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:13.8
occ:1.00
 OD2 A:ASP297 2.1 13.9 1.0
OD2 A:ASP340 2.2 18.6 1.0
OE2 A:GLU233 2.2 16.8 1.0
OE1 A:GLU269 2.2 13.3 1.0
O2 A:XLS503 2.3 25.9 1.0
O4 A:XLS503 2.3 24.8 1.0
CD A:GLU233 3.0 15.7 1.0
OE1 A:GLU233 3.1 16.9 1.0
CG A:ASP340 3.3 15.6 1.0
CG A:ASP297 3.3 13.7 1.0
C4 A:XLS503 3.3 27.3 1.0
C2 A:XLS503 3.3 28.4 1.0
CD A:GLU269 3.5 12.7 1.0
C3 A:XLS503 3.6 29.1 1.0
O3 A:XLS503 3.7 34.7 1.0
CB A:ASP340 3.8 14.4 1.0
CB A:ASP297 3.9 12.8 1.0
O A:HOH635 3.9 18.8 1.0
CE1 A:HIS272 4.0 13.2 1.0
CB A:GLU269 4.1 11.9 1.0
CG A:GLU269 4.2 12.4 1.0
OD1 A:ASP297 4.3 14.6 1.0
OD1 A:ASP340 4.4 16.5 1.0
CG A:GLU233 4.4 15.1 1.0
OE2 A:GLU269 4.4 13.3 1.0
NE2 A:HIS272 4.5 14.1 1.0
ND2 A:ASN267 4.6 13.0 1.0
C5 A:XLS503 4.7 27.2 1.0
C1 A:XLS503 4.7 29.5 1.0
ND1 A:HIS272 4.7 12.8 1.0
CA A:CA502 4.9 18.0 1.0

Calcium binding site 2 out of 8 in 6t8e

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Calcium binding site 2 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:18.0
occ:1.00
 OD1 A:ASP310 1.9 18.7 1.0
OD2 A:ASP308 2.0 23.8 1.0
OE2 A:GLU269 2.0 13.3 1.0
O A:HOH635 2.1 18.8 1.0
OD1 A:ASP308 2.6 25.2 1.0
CG A:ASP308 2.6 22.1 1.0
CD A:GLU269 2.9 12.7 1.0
CG A:ASP310 2.9 17.5 1.0
OE1 A:GLU269 3.1 13.3 1.0
NE2 A:HIS272 3.2 14.1 1.0
OD2 A:ASP310 3.2 20.5 1.0
O A:HOH610 3.5 26.1 1.0
CD2 A:HIS272 3.7 12.7 1.0
ND2 A:ASN299 3.8 11.8 1.0
O2 A:XLS503 3.9 25.9 1.0
O A:HOH837 3.9 32.2 1.0
CB A:ASP308 4.0 19.5 1.0
CE1 A:HIS272 4.2 13.2 1.0
CG A:GLU269 4.3 12.4 1.0
CB A:ASP310 4.3 16.4 1.0
CB A:ASN271 4.5 11.5 1.0
OD2 A:ASP340 4.6 18.6 1.0
O1 A:XLS503 4.7 31.0 1.0
CG A:ASP340 4.7 15.6 1.0
O A:ASP340 4.8 12.4 1.0
CA A:ASP310 4.8 15.0 1.0
OD1 A:ASP340 4.8 16.5 1.0
OD1 A:ASN271 4.8 11.9 1.0
O A:HOH608 4.8 37.0 1.0
C1 A:XLS503 4.9 29.5 1.0
CG A:HIS272 4.9 12.5 1.0
CA A:CA501 4.9 13.8 1.0
N A:ASP310 4.9 14.3 1.0
C2 A:XLS503 4.9 28.4 1.0
CA A:ASP308 5.0 17.4 1.0
CG A:ASN271 5.0 11.6 1.0

Calcium binding site 3 out of 8 in 6t8e

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Calcium binding site 3 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:14.1
occ:1.00
 OD2 B:ASP297 2.1 14.9 1.0
OD2 B:ASP340 2.2 15.2 1.0
OE2 B:GLU233 2.2 16.2 1.0
OE1 B:GLU269 2.3 14.8 1.0
O2 B:XLS503 2.3 29.6 1.0
O4 B:XLS503 2.3 25.7 1.0
CD B:GLU233 3.0 14.9 1.0
OE1 B:GLU233 3.1 15.8 1.0
CG B:ASP340 3.3 14.0 1.0
CG B:ASP297 3.3 13.7 1.0
C4 B:XLS503 3.3 29.3 1.0
C2 B:XLS503 3.4 31.8 1.0
CD B:GLU269 3.5 13.3 1.0
C3 B:XLS503 3.7 32.2 1.0
CB B:ASP340 3.8 13.3 1.0
CB B:ASP297 3.8 12.8 1.0
O3 B:XLS503 3.8 37.6 1.0
O B:HOH635 3.8 22.4 1.0
CE1 B:HIS272 4.0 14.7 1.0
CB B:GLU269 4.2 11.9 1.0
CG B:GLU269 4.2 12.6 1.0
OD1 B:ASP340 4.3 15.1 1.0
OD1 B:ASP297 4.3 13.8 1.0
CG B:GLU233 4.4 13.8 1.0
OE2 B:GLU269 4.4 14.2 1.0
NE2 B:HIS272 4.6 15.1 1.0
ND2 B:ASN267 4.6 11.3 1.0
C5 B:XLS503 4.7 28.5 1.0
C1 B:XLS503 4.7 32.7 1.0
ND1 B:HIS272 4.7 14.0 1.0
CA B:CA502 4.9 16.6 1.0

Calcium binding site 4 out of 8 in 6t8e

Go back to Calcium Binding Sites List in 6t8e
Calcium binding site 4 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:16.6
occ:1.00
 OD2 B:ASP308 1.9 25.5 1.0
O B:HOH635 1.9 22.4 1.0
OE2 B:GLU269 1.9 14.2 1.0
OD1 B:ASP310 2.0 18.0 1.0
OD1 B:ASP308 2.4 27.7 1.0
CG B:ASP308 2.5 23.1 1.0
CD B:GLU269 2.8 13.3 1.0
CG B:ASP310 2.9 17.0 1.0
NE2 B:HIS272 3.1 15.1 1.0
OE1 B:GLU269 3.1 14.8 1.0
OD2 B:ASP310 3.2 18.2 1.0
O B:HOH648 3.6 22.6 1.0
CD2 B:HIS272 3.7 13.8 1.0
ND2 B:ASN299 3.7 10.4 1.0
CB B:ASP308 4.0 20.2 1.0
O2 B:XLS503 4.0 29.6 1.0
CE1 B:HIS272 4.1 14.7 1.0
CG B:GLU269 4.2 12.6 1.0
CB B:ASP310 4.3 15.7 1.0
OD2 B:ASP340 4.5 15.2 1.0
CB B:ASN271 4.5 11.6 1.0
CG B:ASP340 4.6 14.0 1.0
OD1 B:ASP340 4.7 15.1 1.0
O B:HOH646 4.7 31.9 1.0
CA B:ASP310 4.8 14.5 1.0
O B:ASP340 4.8 12.3 1.0
CG B:HIS272 4.8 13.2 1.0
CA B:CA501 4.9 14.1 1.0
O1 B:XLS503 4.9 32.5 1.0
ND2 B:ASN271 4.9 11.0 1.0
C1 B:XLS503 5.0 32.7 1.0
CA B:ASP308 5.0 17.4 1.0
N B:ASP310 5.0 13.5 1.0

Calcium binding site 5 out of 8 in 6t8e

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Calcium binding site 5 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:11.2
occ:1.00
 OD2 C:ASP297 2.1 13.7 1.0
O2 C:XLS503 2.1 26.0 1.0
OE1 C:GLU269 2.1 13.2 1.0
OE2 C:GLU233 2.2 16.8 1.0
OD2 C:ASP340 2.3 14.0 1.0
O4 C:XLS503 2.3 20.4 1.0
CD C:GLU233 2.9 15.3 1.0
OE1 C:GLU233 3.1 17.1 1.0
C2 C:XLS503 3.2 26.7 1.0
CG C:ASP297 3.3 13.6 1.0
C4 C:XLS503 3.3 23.7 1.0
CG C:ASP340 3.3 13.3 1.0
CD C:GLU269 3.4 12.8 1.0
C3 C:XLS503 3.6 26.6 1.0
O3 C:XLS503 3.7 30.6 1.0
O C:HOH610 3.8 19.6 1.0
CB C:ASP340 3.8 12.8 1.0
CB C:ASP297 3.8 12.9 1.0
CE1 C:HIS272 4.1 11.3 1.0
CB C:GLU269 4.1 11.7 1.0
CG C:GLU269 4.1 12.1 1.0
OD1 C:ASP297 4.3 14.2 1.0
OE2 C:GLU269 4.3 13.5 1.0
CG C:GLU233 4.3 14.1 1.0
OD1 C:ASP340 4.5 14.1 1.0
C1 C:XLS503 4.5 26.8 1.0
NE2 C:HIS272 4.6 11.8 1.0
C5 C:XLS503 4.7 23.6 1.0
ND2 C:ASN267 4.7 11.8 1.0
ND1 C:HIS272 4.7 11.1 1.0
CA C:CA502 4.9 15.8 1.0

Calcium binding site 6 out of 8 in 6t8e

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Calcium binding site 6 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:15.8
occ:1.00
 OD1 C:ASP310 2.0 16.6 1.0
OE2 C:GLU269 2.0 13.5 1.0
O C:HOH610 2.0 19.6 1.0
OD2 C:ASP308 2.1 22.1 1.0
OD1 C:ASP308 2.4 20.7 1.0
CG C:ASP308 2.5 18.9 1.0
CG C:ASP310 2.9 15.5 1.0
CD C:GLU269 3.0 12.8 1.0
NE2 C:HIS272 3.1 11.8 1.0
OD2 C:ASP310 3.2 17.5 1.0
OE1 C:GLU269 3.3 13.2 1.0
O C:HOH628 3.6 22.2 1.0
CD2 C:HIS272 3.6 11.2 1.0
ND2 C:ASN299 3.8 11.7 1.0
O2 C:XLS503 3.9 26.0 1.0
CB C:ASP308 4.0 17.4 1.0
CE1 C:HIS272 4.2 11.3 1.0
CG C:GLU269 4.3 12.1 1.0
CB C:ASP310 4.3 14.5 1.0
CB C:ASN271 4.5 10.4 1.0
C1 C:XLS503 4.5 26.8 1.0
OD2 C:ASP340 4.6 14.0 1.0
CA C:ASP310 4.7 13.3 1.0
CG C:ASP340 4.7 13.3 1.0
O C:HOH620 4.8 31.8 1.0
O C:ASP340 4.8 12.6 1.0
CG C:HIS272 4.8 11.2 1.0
C2 C:XLS503 4.8 26.7 1.0
OD1 C:ASN271 4.9 10.2 1.0
OD1 C:ASP340 4.9 14.1 1.0
N C:ASP310 4.9 12.6 1.0
CA C:CA501 4.9 11.2 1.0
CA C:ASP308 5.0 15.4 1.0
CG C:ASN271 5.0 10.4 1.0
O1 C:XLS503 5.0 28.6 1.0

Calcium binding site 7 out of 8 in 6t8e

Go back to Calcium Binding Sites List in 6t8e
Calcium binding site 7 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:11.9
occ:1.00
 OE1 D:GLU269 2.1 12.5 1.0
OD2 D:ASP297 2.1 12.5 1.0
OE2 D:GLU233 2.2 14.7 1.0
OD2 D:ASP340 2.2 14.9 1.0
O4 D:XLS503 2.3 19.2 1.0
O2 D:XLS503 2.3 21.1 1.0
CD D:GLU233 3.0 13.8 1.0
OE1 D:GLU233 3.2 14.8 1.0
C4 D:XLS503 3.3 22.4 1.0
CG D:ASP340 3.3 13.1 1.0
CG D:ASP297 3.3 12.2 1.0
CD D:GLU269 3.4 12.1 1.0
C2 D:XLS503 3.5 24.9 1.0
C3 D:XLS503 3.6 24.4 1.0
O3 D:XLS503 3.6 29.1 1.0
CB D:ASP340 3.8 12.5 1.0
CB D:ASP297 3.9 11.6 1.0
O D:HOH775 4.0 19.8 1.0
CE1 D:HIS272 4.0 11.8 1.0
CB D:GLU269 4.2 10.7 1.0
CG D:GLU269 4.2 11.3 1.0
OE2 D:GLU269 4.3 12.6 1.0
OD1 D:ASP297 4.4 12.3 1.0
CG D:GLU233 4.4 13.1 1.0
OD1 D:ASP340 4.4 14.0 1.0
NE2 D:HIS272 4.5 13.2 1.0
ND2 D:ASN267 4.6 13.9 1.0
C5 D:XLS503 4.6 22.1 1.0
ND1 D:HIS272 4.7 12.3 1.0
C1 D:XLS503 4.8 24.3 1.0
CA D:CA502 4.9 16.1 1.0

Calcium binding site 8 out of 8 in 6t8e

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Calcium binding site 8 out of 8 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Native Xylose Isomerase From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:16.1
occ:1.00
 O D:HOH775 1.9 19.8 1.0
OD2 D:ASP308 2.0 22.1 1.0
OD1 D:ASP310 2.0 15.9 1.0
OE2 D:GLU269 2.0 12.6 1.0
OD1 D:ASP308 2.5 22.9 1.0
CG D:ASP308 2.5 19.1 1.0
CG D:ASP310 2.9 14.8 1.0
CD D:GLU269 3.0 12.1 1.0
NE2 D:HIS272 3.1 13.2 1.0
OD2 D:ASP310 3.1 17.2 1.0
OE1 D:GLU269 3.3 12.5 1.0
CD2 D:HIS272 3.6 11.9 1.0
O D:HOH607 3.6 23.8 1.0
ND2 D:ASN299 3.8 10.4 1.0
O2 D:XLS503 4.0 21.1 1.0
CB D:ASP308 4.0 16.7 1.0
CE1 D:HIS272 4.1 11.8 1.0
O1 D:XLS503 4.3 27.4 1.0
CG D:GLU269 4.3 11.3 1.0
CB D:ASP310 4.3 14.1 1.0
CB D:ASN271 4.5 10.4 1.0
OD2 D:ASP340 4.5 14.9 1.0
CG D:ASP340 4.7 13.1 1.0
CA D:ASP310 4.8 12.8 1.0
CG D:HIS272 4.8 11.7 1.0
OD1 D:ASP340 4.8 14.0 1.0
O D:ASP340 4.8 11.8 1.0
CA D:CA501 4.9 11.9 1.0
OD1 D:ASN271 4.9 10.7 1.0
N D:ASP310 4.9 12.1 1.0
CA D:ASP308 5.0 14.8 1.0
CG D:ASN271 5.0 10.7 1.0

Reference:

M.Lee, H.J.Rozeboom, E.Keuning, P.De Waal, D.B.Janssen. Disconnection Between in Vitro Catalytic Properties of Engineered Xylose Isomerases and Rates of Xylose Metabolism in Yeast Biotechnol Biofuels 2020.
ISSN: ESSN 1754-6834
DOI: 10.1186/S13068-019-1643-0
Page generated: Tue Jul 16 15:12:20 2024

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