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Calcium in PDB 6t8f: Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose

Enzymatic activity of Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose

All present enzymatic activity of Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose, PDB code: 6t8f 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 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.598, 79.372, 91.982, 115.46, 89.98, 117.13
R / Rfree (%) 14.9 / 18.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose (pdb code 6t8f). 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose, PDB code: 6t8f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6t8f

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Calcium binding site 1 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:16.5
occ:1.00
 OD2 A:ASP297 2.1 19.7 1.0
OE2 A:GLU233 2.1 19.9 1.0
OE1 A:GLU269 2.1 21.7 1.0
O2 A:XLS503 2.2 29.7 1.0
OD2 A:ASP340 2.2 20.9 1.0
O4 A:XLS503 2.3 29.4 1.0
CD A:GLU233 2.9 18.5 1.0
OE1 A:GLU233 3.1 21.1 1.0
C2 A:XLS503 3.2 33.8 1.0
CG A:ASP297 3.2 19.9 1.0
C4 A:XLS503 3.3 32.5 1.0
CG A:ASP340 3.3 19.1 1.0
CD A:GLU269 3.3 19.3 1.0
C3 A:XLS503 3.5 34.6 1.0
O3 A:XLS503 3.6 36.9 1.0
CB A:ASP297 3.8 17.9 1.0
CB A:ASP340 3.8 17.4 1.0
O A:HOH614 3.9 20.3 1.0
CE1 A:HIS272 3.9 17.5 1.0
CG A:GLU269 4.1 18.6 1.0
CB A:GLU269 4.1 17.8 1.0
OE2 A:GLU269 4.3 20.2 1.0
CG A:GLU233 4.3 18.4 1.0
OD1 A:ASP297 4.3 20.1 1.0
OD1 A:ASP340 4.4 19.7 1.0
NE2 A:HIS272 4.5 17.9 1.0
ND1 A:HIS272 4.6 16.1 1.0
C1 A:XLS503 4.6 32.9 1.0
ND2 A:ASN267 4.6 16.4 1.0
C5 A:XLS503 4.7 32.2 1.0
CA A:CA502 4.8 21.0 1.0

Calcium binding site 2 out of 8 in 6t8f

Go back to Calcium Binding Sites List in 6t8f
Calcium binding site 2 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:21.0
occ:1.00
 OD1 A:ASP310 1.9 22.0 1.0
OD2 A:ASP308 1.9 33.0 1.0
O A:HOH614 2.0 20.3 1.0
OE2 A:GLU269 2.0 20.2 1.0
CG A:ASP308 2.6 29.8 1.0
OD1 A:ASP308 2.7 35.7 1.0
CG A:ASP310 2.9 21.0 1.0
CD A:GLU269 2.9 19.3 1.0
NE2 A:HIS272 3.1 17.9 1.0
OD2 A:ASP310 3.1 21.4 1.0
OE1 A:GLU269 3.2 21.7 1.0
O A:HOH675 3.5 25.4 1.0
CD2 A:HIS272 3.6 16.5 1.0
O2 A:XLS503 3.7 29.7 1.0
ND2 A:ASN299 3.8 13.6 1.0
O A:HOH898 4.0 37.7 1.0
CB A:ASP308 4.1 25.6 1.0
CE1 A:HIS272 4.1 17.5 1.0
CG A:GLU269 4.3 18.6 1.0
OD2 A:ASP340 4.3 20.9 1.0
CB A:ASP310 4.3 20.0 1.0
CG A:ASP340 4.5 19.1 1.0
OD1 A:ASP340 4.6 19.7 1.0
CB A:ASN271 4.6 17.2 1.0
O1 A:XLS503 4.7 33.8 1.0
O A:ASP340 4.7 15.6 1.0
C2 A:XLS503 4.8 33.8 1.0
CA A:ASP310 4.8 18.6 1.0
CA A:CA501 4.8 16.5 1.0
CG A:HIS272 4.8 16.7 1.0
C1 A:XLS503 4.9 32.9 1.0
N A:ASP310 5.0 17.3 1.0

Calcium binding site 3 out of 8 in 6t8f

Go back to Calcium Binding Sites List in 6t8f
Calcium binding site 3 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:16.5
occ:1.00
 OE2 B:GLU233 2.1 19.4 1.0
OD2 B:ASP297 2.1 22.1 1.0
O2 B:XLS503 2.1 34.5 1.0
OE1 B:GLU269 2.1 23.9 1.0
OD2 B:ASP340 2.2 19.9 1.0
O4 B:XLS503 2.4 32.3 1.0
CD B:GLU233 2.9 18.4 1.0
OE1 B:GLU233 3.1 18.3 1.0
CG B:ASP297 3.2 19.1 1.0
C2 B:XLS503 3.3 38.2 1.0
CG B:ASP340 3.3 19.6 1.0
CD B:GLU269 3.3 22.4 1.0
C4 B:XLS503 3.4 35.3 1.0
CB B:ASP297 3.7 17.6 1.0
O B:HOH637 3.7 26.3 1.0
CB B:ASP340 3.8 18.0 1.0
C3 B:XLS503 3.8 38.0 1.0
CE1 B:HIS272 4.0 22.3 1.0
CG B:GLU269 4.1 20.6 1.0
CB B:GLU269 4.1 18.7 1.0
OD1 B:ASP297 4.3 19.0 1.0
OE2 B:GLU269 4.3 23.6 1.0
CG B:GLU233 4.3 18.7 1.0
OD1 B:ASP340 4.4 21.8 1.0
NE2 B:HIS272 4.5 23.0 1.0
C1 B:XLS503 4.6 38.7 1.0
ND1 B:HIS272 4.6 20.9 1.0
ND2 B:ASN267 4.6 17.8 1.0
C5 B:XLS503 4.8 33.8 1.0
CA B:CA502 4.8 21.1 1.0
O3 B:XLS503 4.9 40.9 1.0

Calcium binding site 4 out of 8 in 6t8f

Go back to Calcium Binding Sites List in 6t8f
Calcium binding site 4 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:21.1
occ:1.00
 O B:HOH637 1.9 26.3 1.0
OE2 B:GLU269 1.9 23.6 1.0
OD2 B:ASP308 1.9 30.1 1.0
OD1 B:ASP310 1.9 22.5 1.0
CG B:ASP308 2.6 30.4 1.0
OD1 B:ASP308 2.6 33.5 1.0
CD B:GLU269 2.9 22.4 1.0
CG B:ASP310 2.9 22.0 1.0
NE2 B:HIS272 3.0 23.0 1.0
OE1 B:GLU269 3.2 23.9 1.0
OD2 B:ASP310 3.2 24.7 1.0
O B:HOH610 3.5 27.9 1.0
CD2 B:HIS272 3.6 20.2 1.0
ND2 B:ASN299 3.8 13.9 1.0
O2 B:XLS503 3.9 34.5 1.0
CB B:ASP308 4.0 25.8 1.0
CE1 B:HIS272 4.1 22.3 1.0
CG B:GLU269 4.2 20.6 1.0
OD2 B:ASP340 4.3 19.9 1.0
CB B:ASP310 4.3 20.8 1.0
CG B:ASP340 4.5 19.6 1.0
C1 B:XLS503 4.6 38.7 1.0
CB B:ASN271 4.6 17.3 1.0
OD1 B:ASP340 4.6 21.8 1.0
O B:ASP340 4.7 15.9 1.0
CG B:HIS272 4.8 20.0 1.0
C2 B:XLS503 4.8 38.2 1.0
CA B:ASP310 4.8 19.9 1.0
CA B:CA501 4.8 16.5 1.0
ND2 B:ASN271 4.9 15.5 1.0
O B:HOH603 4.9 32.3 1.0
O1 B:XLS503 4.9 43.1 1.0
N B:ASP310 5.0 18.3 1.0
ND1 B:HIS272 5.0 20.9 1.0

Calcium binding site 5 out of 8 in 6t8f

Go back to Calcium Binding Sites List in 6t8f
Calcium binding site 5 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:13.5
occ:1.00
 O2 C:XLS503 2.0 30.9 1.0
OD2 C:ASP297 2.1 20.6 1.0
OE2 C:GLU233 2.1 19.1 1.0
OE1 C:GLU269 2.2 22.2 1.0
OD2 C:ASP340 2.2 18.2 1.0
O4 C:XLS503 2.2 27.6 1.0
CD C:GLU233 2.9 17.7 1.0
OE1 C:GLU233 3.1 20.1 1.0
C4 C:XLS503 3.2 30.9 1.0
CG C:ASP297 3.2 18.9 1.0
C2 C:XLS503 3.2 32.1 1.0
CG C:ASP340 3.3 17.1 1.0
CD C:GLU269 3.4 18.9 1.0
C3 C:XLS503 3.7 33.1 1.0
CB C:ASP297 3.8 18.0 1.0
CB C:ASP340 3.8 16.5 1.0
O C:HOH732 3.8 20.8 1.0
CE1 C:HIS272 4.0 16.4 1.0
CG C:GLU269 4.1 17.9 1.0
CB C:GLU269 4.2 16.2 1.0
OD1 C:ASP297 4.3 19.9 1.0
CG C:GLU233 4.3 17.2 1.0
OE2 C:GLU269 4.3 21.1 1.0
C1 C:XLS503 4.4 33.7 1.0
OD1 C:ASP340 4.4 17.0 1.0
NE2 C:HIS272 4.5 17.5 1.0
C5 C:XLS503 4.6 31.2 1.0
ND2 C:ASN267 4.6 14.2 1.0
ND1 C:HIS272 4.7 16.3 1.0
O3 C:XLS503 4.7 37.9 1.0
CA C:CA502 4.8 18.6 1.0

Calcium binding site 6 out of 8 in 6t8f

Go back to Calcium Binding Sites List in 6t8f
Calcium binding site 6 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:18.6
occ:1.00
 OE2 C:GLU269 1.9 21.1 1.0
O C:HOH732 1.9 20.8 1.0
OD1 C:ASP310 1.9 22.1 1.0
OD2 C:ASP308 2.0 26.5 1.0
CG C:ASP308 2.6 25.6 1.0
OD1 C:ASP308 2.7 31.3 1.0
CD C:GLU269 2.8 18.9 1.0
CG C:ASP310 2.9 20.6 1.0
NE2 C:HIS272 3.0 17.5 1.0
OE1 C:GLU269 3.1 22.2 1.0
OD2 C:ASP310 3.2 21.9 1.0
CD2 C:HIS272 3.6 16.7 1.0
ND2 C:ASN299 3.7 13.8 1.0
O C:HOH714 3.8 24.3 1.0
O2 C:XLS503 3.9 30.9 1.0
CB C:ASP308 4.1 22.9 1.0
CE1 C:HIS272 4.1 16.4 1.0
CG C:GLU269 4.2 17.9 1.0
OD2 C:ASP340 4.3 18.2 1.0
CB C:ASP310 4.3 18.8 1.0
C1 C:XLS503 4.3 33.7 1.0
CG C:ASP340 4.5 17.1 1.0
CB C:ASN271 4.6 16.0 1.0
OD1 C:ASP340 4.6 17.0 1.0
C2 C:XLS503 4.7 32.1 1.0
O C:ASP340 4.7 16.0 1.0
CG C:HIS272 4.7 16.3 1.0
CA C:ASP310 4.8 17.3 1.0
CA C:CA501 4.8 13.5 1.0
ND1 C:HIS272 5.0 16.3 1.0
OD1 C:ASN271 5.0 16.9 1.0
N C:ASP310 5.0 17.1 1.0

Calcium binding site 7 out of 8 in 6t8f

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Calcium binding site 7 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:15.3
occ:1.00
 OD2 D:ASP297 2.1 19.8 1.0
OE2 D:GLU233 2.1 19.4 1.0
OE1 D:GLU269 2.1 21.4 1.0
OD2 D:ASP340 2.1 19.9 1.0
O2 D:XLS503 2.2 32.8 1.0
O4 D:XLS503 2.3 26.0 1.0
CD D:GLU233 2.9 18.3 1.0
OE1 D:GLU233 3.1 19.4 1.0
C2 D:XLS503 3.2 34.1 1.0
CG D:ASP297 3.2 18.7 1.0
CG D:ASP340 3.2 19.0 1.0
C4 D:XLS503 3.3 31.4 1.0
CD D:GLU269 3.3 20.4 1.0
C3 D:XLS503 3.6 33.8 1.0
O D:HOH604 3.7 20.2 1.0
CB D:ASP340 3.7 17.5 1.0
CB D:ASP297 3.8 17.0 1.0
O3 D:XLS503 3.8 40.0 1.0
CE1 D:HIS272 4.0 18.8 1.0
CG D:GLU269 4.1 18.6 1.0
CB D:GLU269 4.2 17.2 1.0
OE2 D:GLU269 4.3 21.1 1.0
OD1 D:ASP297 4.3 17.4 1.0
OD1 D:ASP340 4.3 20.3 1.0
CG D:GLU233 4.3 17.7 1.0
NE2 D:HIS272 4.5 20.0 1.0
C1 D:XLS503 4.6 34.8 1.0
ND1 D:HIS272 4.6 18.5 1.0
ND2 D:ASN267 4.7 18.3 1.0
C5 D:XLS503 4.7 31.4 1.0
CA D:CA502 4.8 20.0 1.0

Calcium binding site 8 out of 8 in 6t8f

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Calcium binding site 8 out of 8 in the Crystal Structure of Mutant Xylose Isomerase (V270A/A273G) 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 Mutant Xylose Isomerase (V270A/A273G) From Piromyces E2 Grown in Yeast, in Complex with Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:20.0
occ:1.00
 O D:HOH604 1.8 20.2 1.0
OD2 D:ASP308 1.9 32.3 1.0
OD1 D:ASP310 2.0 21.5 1.0
OE2 D:GLU269 2.0 21.1 1.0
CG D:ASP308 2.6 27.5 1.0
OD1 D:ASP308 2.6 34.2 1.0
CD D:GLU269 2.9 20.4 1.0
CG D:ASP310 2.9 20.4 1.0
NE2 D:HIS272 3.0 20.0 1.0
OE1 D:GLU269 3.2 21.4 1.0
OD2 D:ASP310 3.2 23.4 1.0
CD2 D:HIS272 3.6 18.5 1.0
O D:HOH806 3.7 27.6 1.0
O2 D:XLS503 3.7 32.8 1.0
ND2 D:ASN299 3.8 14.5 1.0
CB D:ASP308 4.0 24.5 1.0
CE1 D:HIS272 4.1 18.8 1.0
CG D:GLU269 4.3 18.6 1.0
CB D:ASP310 4.3 18.8 1.0
OD2 D:ASP340 4.3 19.9 1.0
CG D:ASP340 4.6 19.0 1.0
CB D:ASN271 4.6 17.2 1.0
OD1 D:ASP340 4.7 20.3 1.0
O1 D:XLS503 4.7 36.0 1.0
C2 D:XLS503 4.7 34.1 1.0
O D:ASP340 4.7 15.3 1.0
CG D:HIS272 4.8 18.2 1.0
C1 D:XLS503 4.8 34.8 1.0
CA D:ASP310 4.8 17.2 1.0
CA D:CA501 4.8 15.3 1.0
OD1 D:ASN271 5.0 17.1 1.0
ND1 D:HIS272 5.0 18.5 1.0
N D:ASP310 5.0 15.9 1.0
CA D:ASP308 5.0 21.2 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: Wed Jul 9 18:05:50 2025

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