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Calcium in PDB 5nh8: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose:
5.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose, PDB code: 5nh8 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) 46.70 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.764, 79.337, 91.926, 115.41, 89.91, 117.16
R / Rfree (%) 17.6 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose (pdb code 5nh8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose, PDB code: 5nh8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5nh8

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Calcium binding site 1 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:23.6
occ:1.00
 OD2 A:ASP297 2.2 15.7 1.0
OE2 A:GLU233 2.2 16.6 1.0
OE1 A:GLU269 2.3 17.7 1.0
OD2 A:ASP340 2.3 17.2 1.0
O4 A:XLS503 2.3 30.1 1.0
O2 A:XLS503 2.3 31.2 1.0
CD A:GLU233 3.0 16.9 1.0
OE1 A:GLU233 3.2 18.2 1.0
C4 A:XLS503 3.3 31.6 1.0
CG A:ASP297 3.3 15.0 1.0
C2 A:XLS503 3.3 32.6 1.0
CG A:ASP340 3.4 16.2 1.0
CD A:GLU269 3.5 16.6 1.0
C3 A:XLS503 3.6 32.2 1.0
O3 A:XLS503 3.7 33.9 1.0
CB A:ASP340 4.0 15.4 1.0
CB A:ASP297 4.0 14.2 1.0
O A:HOH666 4.0 30.4 1.0
CE1 A:HIS272 4.1 19.2 1.0
CB A:GLU269 4.3 14.9 1.0
OD1 A:ASP297 4.3 16.2 1.0
CG A:GLU269 4.4 15.4 1.0
OE2 A:GLU269 4.4 16.7 1.0
CG A:GLU233 4.4 16.7 1.0
OD1 A:ASP340 4.4 16.6 1.0
NE2 A:HIS272 4.5 19.4 1.0
C5 A:XLS503 4.6 30.5 1.0
C1 A:XLS503 4.7 34.7 1.0
ND2 A:ASN267 4.7 15.3 1.0
O A:HOH606 4.8 29.3 1.0
ND1 A:HIS272 4.9 19.4 1.0

Calcium binding site 2 out of 10 in 5nh8

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Calcium binding site 2 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:42.5
occ:1.00
 OD2 A:ASP308 2.2 35.3 1.0
OE2 A:GLU269 2.3 16.7 1.0
OD1 A:ASP310 2.4 18.8 1.0
O A:HOH666 2.4 30.4 1.0
O A:HOH606 2.5 29.3 1.0
O A:HOH777 2.7 26.2 1.0
CG A:ASP308 2.9 29.1 1.0
CG A:ASP310 3.3 18.3 1.0
CD A:GLU269 3.4 16.6 1.0
CB A:ASP308 3.4 30.0 1.0
OD2 A:ASP310 3.5 21.1 1.0
NE2 A:HIS272 3.5 19.4 1.0
OE1 A:GLU269 3.7 17.7 1.0
OD1 A:ASP308 3.8 34.6 1.0
O1 A:XLS503 4.0 36.8 1.0
CD2 A:HIS272 4.0 18.9 1.0
O2 A:XLS503 4.1 31.2 1.0
ND2 A:ASN299 4.2 13.4 1.0
CB A:ASN271 4.5 20.7 1.0
NZ A:LYS235 4.6 16.9 1.0
CE1 A:HIS272 4.7 19.2 1.0
CB A:ASP310 4.7 16.9 1.0
CG A:GLU269 4.7 15.4 1.0
CA A:ASP308 4.7 27.3 1.0
OD1 A:ASN271 4.9 24.7 1.0
C1 A:XLS503 4.9 34.7 1.0
CG A:ASN271 5.0 22.9 1.0

Calcium binding site 3 out of 10 in 5nh8

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Calcium binding site 3 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:30.0
occ:1.00
 O A:HOH954 2.2 15.7 1.0
O A:HOH882 2.5 25.7 1.0
O B:HOH903 2.5 26.9 1.0
O A:HOH928 2.6 15.3 1.0
O B:HOH949 2.6 18.6 1.0
O B:ALA276 2.7 20.0 1.0
O A:ALA276 2.8 16.8 1.0
C B:ALA276 3.2 18.9 1.0
C A:ALA276 3.4 16.4 1.0
CA B:ALA276 3.9 18.8 1.0
N B:GLY277 3.9 17.4 1.0
N A:GLY277 4.0 15.2 1.0
O B:HOH926 4.0 27.4 1.0
CA A:ALA276 4.1 16.8 1.0
O A:HOH897 4.2 21.7 1.0
CA B:GLY277 4.3 16.9 1.0
CA A:GLY277 4.3 15.2 1.0
O B:HOH877 4.3 24.4 1.0
CB B:ALA276 4.6 18.6 1.0
O A:HOH805 4.7 15.1 1.0
O B:LEU275 4.8 21.4 1.0
CB A:ALA276 4.8 16.6 1.0
O A:LEU275 4.9 21.0 1.0

Calcium binding site 4 out of 10 in 5nh8

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Calcium binding site 4 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:21.1
occ:1.00
 OD2 B:ASP297 2.2 17.1 1.0
OE2 B:GLU233 2.2 18.3 1.0
OE1 B:GLU269 2.2 14.5 1.0
O4 B:XLS504 2.3 21.8 1.0
OD2 B:ASP340 2.3 19.4 1.0
O2 B:XLS504 2.3 24.8 1.0
CD B:GLU233 3.0 17.5 1.0
OE1 B:GLU233 3.2 18.2 1.0
C4 B:XLS504 3.3 24.1 1.0
CG B:ASP297 3.4 15.5 1.0
CG B:ASP340 3.4 17.0 1.0
C2 B:XLS504 3.5 27.2 1.0
CD B:GLU269 3.5 15.1 1.0
C3 B:XLS504 3.7 25.6 1.0
O3 B:XLS504 3.8 28.8 1.0
CB B:ASP340 3.9 15.6 1.0
O B:HOH687 4.0 24.9 1.0
CB B:ASP297 4.0 14.4 1.0
CE1 B:HIS272 4.1 16.8 1.0
CB B:GLU269 4.3 13.8 1.0
CG B:GLU269 4.4 14.0 1.0
OD1 B:ASP297 4.4 15.9 1.0
CG B:GLU233 4.4 16.8 1.0
OE2 B:GLU269 4.4 14.4 1.0
OD1 B:ASP340 4.4 17.5 1.0
NE2 B:HIS272 4.5 17.1 1.0
C5 B:XLS504 4.6 22.7 1.0
C1 B:XLS504 4.7 29.1 1.0
ND2 B:ASN267 4.7 17.2 1.0
ND1 B:HIS272 4.9 17.6 1.0

Calcium binding site 5 out of 10 in 5nh8

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Calcium binding site 5 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:29.4
occ:1.00
 O B:HOH687 2.1 24.9 1.0
OD2 B:ASP308 2.2 32.6 1.0
OE2 B:GLU269 2.3 14.4 1.0
OD1 B:ASP310 2.4 15.9 1.0
O B:HOH672 2.7 26.7 1.0
CG B:ASP308 2.9 30.6 1.0
CG B:ASP310 3.3 16.8 1.0
CD B:GLU269 3.4 15.1 1.0
CB B:ASP308 3.4 29.9 1.0
NE2 B:HIS272 3.5 17.1 1.0
OD2 B:ASP310 3.5 18.9 1.0
O1 B:XLS504 3.7 35.9 1.0
OE1 B:GLU269 3.7 14.5 1.0
OD1 B:ASP308 3.8 36.8 1.0
CD2 B:HIS272 4.0 16.9 1.0
O2 B:XLS504 4.1 24.8 1.0
ND2 B:ASN299 4.2 13.7 1.0
CB B:ASN271 4.5 18.0 1.0
NZ B:LYS235 4.6 16.0 1.0
C1 B:XLS504 4.6 29.1 1.0
CE1 B:HIS272 4.6 16.8 1.0
CG B:GLU269 4.7 14.0 1.0
CB B:ASP310 4.7 15.7 1.0
CA B:ASP308 4.7 26.4 1.0
OD1 B:ASN271 4.9 22.0 1.0
CG B:ASN271 4.9 20.5 1.0
CE B:LYS235 5.0 16.0 1.0
C2 B:XLS504 5.0 27.2 1.0

Calcium binding site 6 out of 10 in 5nh8

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Calcium binding site 6 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:21.9
occ:1.00
 OE1 C:GLU269 2.2 15.4 1.0
OD2 C:ASP340 2.2 17.6 1.0
OD2 C:ASP297 2.2 16.0 1.0
O2 C:XLS503 2.3 26.8 1.0
OE2 C:GLU233 2.3 17.7 1.0
O4 C:XLS503 2.4 24.2 1.0
CD C:GLU233 3.1 17.0 1.0
CG C:ASP340 3.3 16.6 1.0
OE1 C:GLU233 3.3 17.8 1.0
C4 C:XLS503 3.4 26.0 1.0
CG C:ASP297 3.4 15.4 1.0
C2 C:XLS503 3.4 28.7 1.0
CD C:GLU269 3.4 15.2 1.0
C3 C:XLS503 3.7 27.6 1.0
O3 C:XLS503 3.8 29.6 1.0
CB C:ASP340 3.9 15.2 1.0
CB C:ASP297 4.0 14.8 1.0
CE1 C:HIS272 4.1 16.8 1.0
CB C:GLU269 4.3 13.8 1.0
OD1 C:ASP340 4.3 17.9 1.0
OE2 C:GLU269 4.3 14.3 1.0
CG C:GLU269 4.3 14.1 1.0
OD1 C:ASP297 4.4 15.5 1.0
CG C:GLU233 4.5 16.8 1.0
NE2 C:HIS272 4.5 17.2 1.0
C1 C:XLS503 4.6 28.8 1.0
C5 C:XLS503 4.8 25.0 1.0
ND2 C:ASN267 4.8 15.6 1.0
O1 C:XLS503 4.9 31.2 1.0
ND1 C:HIS272 4.9 17.6 1.0

Calcium binding site 7 out of 10 in 5nh8

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Calcium binding site 7 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:37.2
occ:1.00
 OE2 C:GLU269 2.2 14.3 1.0
OD2 C:ASP308 2.3 41.2 1.0
OD1 C:ASP310 2.4 18.3 1.0
O C:HOH657 2.7 24.5 1.0
CG C:ASP308 3.0 34.5 1.0
CD C:GLU269 3.3 15.2 1.0
CG C:ASP310 3.4 18.3 1.0
NE2 C:HIS272 3.4 17.2 1.0
CB C:ASP308 3.6 33.8 1.0
O1 C:XLS503 3.6 31.2 1.0
OE1 C:GLU269 3.6 15.4 1.0
OD2 C:ASP310 3.6 19.9 1.0
OD1 C:ASP308 3.9 40.1 1.0
CD2 C:HIS272 3.9 16.5 1.0
O2 C:XLS503 4.0 26.8 1.0
ND2 C:ASN299 4.2 12.8 1.0
CE1 C:HIS272 4.5 16.8 1.0
CB C:ASN271 4.6 19.0 1.0
CG C:GLU269 4.6 14.1 1.0
NZ C:LYS235 4.6 17.8 1.0
C1 C:XLS503 4.6 28.8 1.0
CB C:ASP310 4.8 17.8 1.0
CA C:ASP308 4.9 29.6 1.0
C2 C:XLS503 4.9 28.7 1.0
OD1 C:ASP340 5.0 17.9 1.0
OD1 C:ASN271 5.0 21.8 1.0

Calcium binding site 8 out of 10 in 5nh8

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Calcium binding site 8 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and 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 Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca507

b:38.0
occ:1.00
 O C:HOH958 2.3 24.0 1.0
O C:HOH931 2.5 20.9 1.0
O C:HOH904 2.6 27.8 1.0
O D:HOH930 2.6 15.3 1.0
O C:ALA276 2.7 19.8 1.0
O D:ALA276 2.7 19.8 1.0
O D:HOH914 2.8 32.2 1.0
C C:ALA276 3.3 19.3 1.0
C D:ALA276 3.3 18.5 1.0
CA C:ALA276 3.9 19.4 1.0
N C:GLY277 4.0 17.8 1.0
N D:GLY277 4.0 16.9 1.0
CA D:ALA276 4.0 18.3 1.0
O D:HOH789 4.2 17.7 1.0
CA C:GLY277 4.3 16.8 1.0
CA D:GLY277 4.3 16.2 1.0
O C:HOH806 4.3 24.1 1.0
CB C:ALA276 4.7 19.5 1.0
CB D:ALA276 4.7 18.1 1.0
O C:HOH782 4.7 15.3 1.0
O C:LEU275 4.8 21.8 1.0
O D:LEU275 4.9 20.9 1.0

Calcium binding site 9 out of 10 in 5nh8

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Calcium binding site 9 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:22.4
occ:1.00
 OD2 D:ASP297 2.2 17.1 1.0
OE2 D:GLU233 2.2 19.9 1.0
OE1 D:GLU269 2.3 20.4 1.0
OD2 D:ASP340 2.3 18.9 1.0
O2 D:XLS503 2.4 26.8 1.0
O4 D:XLS503 2.4 25.8 1.0
CD D:GLU233 3.0 18.7 1.0
OE1 D:GLU233 3.2 20.0 1.0
CG D:ASP297 3.3 16.1 1.0
C4 D:XLS503 3.4 27.3 1.0
CG D:ASP340 3.4 15.9 1.0
C2 D:XLS503 3.4 28.7 1.0
CD D:GLU269 3.5 17.6 1.0
C3 D:XLS503 3.6 28.2 1.0
O3 D:XLS503 3.7 31.0 1.0
O D:HOH630 3.9 29.4 1.0
CB D:ASP340 3.9 15.2 1.0
CB D:ASP297 4.0 14.9 1.0
CE1 D:HIS272 4.1 16.0 1.0
CB D:GLU269 4.3 14.6 1.0
OD1 D:ASP297 4.3 18.2 1.0
CG D:GLU269 4.4 15.7 1.0
OE2 D:GLU269 4.4 18.9 1.0
OD1 D:ASP340 4.4 16.5 1.0
CG D:GLU233 4.4 17.2 1.0
NE2 D:HIS272 4.5 15.9 1.0
C5 D:XLS503 4.7 26.1 1.0
ND2 D:ASN267 4.7 15.0 1.0
C1 D:XLS503 4.7 30.3 1.0
ND1 D:HIS272 4.9 16.2 1.0

Calcium binding site 10 out of 10 in 5nh8

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Calcium binding site 10 out of 10 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CA2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:35.0
occ:1.00
 OD2 D:ASP308 2.2 37.4 1.0
OE2 D:GLU269 2.3 18.9 1.0
OD1 D:ASP310 2.3 17.4 1.0
O D:HOH630 2.4 29.4 1.0
O D:HOH687 2.7 30.5 1.0
CG D:ASP308 2.9 31.0 1.0
CG D:ASP310 3.3 18.1 1.0
CD D:GLU269 3.4 17.6 1.0
CB D:ASP308 3.4 31.6 1.0
NE2 D:HIS272 3.5 15.9 1.0
OD2 D:ASP310 3.5 20.6 1.0
OE1 D:GLU269 3.7 20.4 1.0
OD1 D:ASP308 3.8 34.4 1.0
O1 D:XLS503 3.9 32.4 1.0
CD2 D:HIS272 4.0 16.1 1.0
O2 D:XLS503 4.1 26.8 1.0
ND2 D:ASN299 4.2 12.9 1.0
CB D:ASN271 4.5 19.2 1.0
NZ D:LYS235 4.6 16.8 1.0
CE1 D:HIS272 4.6 16.0 1.0
CB D:ASP310 4.7 16.5 1.0
CG D:GLU269 4.7 15.7 1.0
CA D:ASP308 4.7 28.0 1.0
OD1 D:ASN271 4.9 24.9 1.0
C1 D:XLS503 4.9 30.3 1.0
CG D:ASN271 4.9 21.8 1.0

Reference:

M.Lee, H.J.Rozeboom, P.P.De Waal, R.M.De Jong, H.M.Dudek, D.B.Janssen. Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Mon Jul 15 09:04:28 2024

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