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Cadmium in PDB 5nhe: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose

Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose

All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ 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 CD2+ Ions and Xylose, PDB code: 5nhe 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) 45.10 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.640, 79.370, 92.010, 115.37, 89.97, 117.16
R / Rfree (%) 14 / 16.5

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose (pdb code 5nhe). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose, PDB code: 5nhe:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 5nhe

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Cadmium binding site 1 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:16.4
occ:0.50
OE1 A:GLU269 2.0 17.5 1.0
OD2 A:ASP340 2.2 16.9 1.0
OD2 A:ASP297 2.2 17.9 1.0
OE2 A:GLU233 2.2 18.1 1.0
O2 A:XLS503 2.3 29.5 1.0
O4 A:XLS503 2.4 29.4 1.0
CD A:GLU233 3.1 16.8 1.0
CG A:ASP297 3.2 16.2 1.0
CG A:ASP340 3.2 15.1 1.0
CD A:GLU269 3.3 15.4 1.0
OE1 A:GLU233 3.4 17.7 1.0
C4 A:XLS503 3.4 32.8 1.0
C2 A:XLS503 3.4 37.6 1.0
CB A:ASP340 3.7 13.9 1.0
CB A:ASP297 3.7 14.8 1.0
C3 A:XLS503 3.7 35.3 1.0
O3 A:XLS503 3.8 41.4 1.0
CD A:CD502 4.0 30.4 0.3
CG A:GLU269 4.0 13.5 1.0
CE1 A:HIS272 4.1 13.4 1.0
CB A:GLU269 4.1 12.3 1.0
O A:HOH795 4.1 28.1 1.0
OE2 A:GLU269 4.2 16.2 1.0
OD1 A:ASP297 4.3 16.5 1.0
OD1 A:ASP340 4.3 16.8 1.0
CG A:GLU233 4.4 15.2 1.0
NE2 A:HIS272 4.5 13.9 1.0
C1 A:XLS503 4.6 39.2 1.0
CD A:CD502 4.7 15.2 0.4
C5 A:XLS503 4.8 33.0 1.0
ND1 A:HIS272 4.8 13.1 1.0
ND2 A:ASN267 4.9 14.7 1.0

Cadmium binding site 2 out of 12 in 5nhe

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Cadmium binding site 2 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:15.2
occ:0.40
CD A:CD502 0.0 15.2 0.4
CD A:CD502 1.4 30.4 0.3
OE2 A:GLU269 1.9 16.2 1.0
OD2 A:ASP308 2.3 25.4 1.0
OD1 A:ASP310 2.4 22.2 1.0
O A:HOH795 2.4 28.1 1.0
OD1 A:ASP308 2.6 20.5 1.0
CG A:ASP308 2.7 21.4 1.0
CD A:GLU269 2.9 15.4 1.0
NE2 A:HIS272 2.9 13.9 1.0
OE1 A:GLU269 3.2 17.5 1.0
CD2 A:HIS272 3.4 13.2 1.0
CG A:ASP310 3.4 19.5 1.0
O A:HOH785 3.6 29.9 1.0
OD2 A:ASP310 3.7 22.8 1.0
O2 A:XLS503 3.7 29.5 1.0
ND2 A:ASN299 3.9 11.2 1.0
CE1 A:HIS272 4.0 13.4 1.0
CB A:ASP308 4.1 18.5 1.0
O A:HOH744 4.2 28.8 1.0
CG A:GLU269 4.2 13.5 1.0
CB A:ASN271 4.4 11.4 1.0
OD2 A:ASP340 4.4 16.9 1.0
C1 A:XLS503 4.5 39.2 1.0
CG A:HIS272 4.6 12.5 1.0
C2 A:XLS503 4.7 37.6 1.0
CD A:CD501 4.7 16.4 0.5
CB A:ASP310 4.8 17.1 1.0
OD1 A:ASN271 4.8 12.3 1.0
ND1 A:HIS272 4.8 13.1 1.0
CG A:ASP340 4.9 15.1 1.0
CG A:ASN271 4.9 11.7 1.0

Cadmium binding site 3 out of 12 in 5nhe

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Cadmium binding site 3 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:30.4
occ:0.35
CD A:CD502 0.0 30.4 0.3
CD A:CD502 1.4 15.2 0.4
O A:HOH795 2.2 28.1 1.0
NE2 A:HIS272 2.3 13.9 1.0
O A:HOH785 2.5 29.9 1.0
OD2 A:ASP308 2.5 25.4 1.0
O2 A:XLS503 2.6 29.5 1.0
OE2 A:GLU269 2.7 16.2 1.0
OE1 A:GLU269 2.9 17.5 1.0
CE1 A:HIS272 3.1 13.4 1.0
CD A:GLU269 3.1 15.4 1.0
CD2 A:HIS272 3.3 13.2 1.0
C1 A:XLS503 3.3 39.2 1.0
C2 A:XLS503 3.4 37.6 1.0
CG A:ASP308 3.4 21.4 1.0
OD1 A:ASP310 3.5 22.2 1.0
OD1 A:ASP308 3.6 20.5 1.0
OD2 A:ASP340 3.9 16.9 1.0
CD A:CD501 4.0 16.4 0.5
O A:HOH744 4.2 28.8 1.0
ND1 A:HIS272 4.2 13.1 1.0
OD2 A:ASP310 4.3 22.8 1.0
CG A:HIS272 4.3 12.5 1.0
CG A:ASP310 4.3 19.5 1.0
O1 A:XLS503 4.4 51.4 1.0
NZ A:LYS235 4.5 14.9 1.0
CG A:GLU269 4.6 13.5 1.0
CE A:LYS235 4.6 14.6 1.0
CG A:ASP340 4.7 15.1 1.0
C3 A:XLS503 4.7 35.3 1.0
OE2 A:GLU233 4.7 18.1 1.0
CB A:ASP308 4.8 18.5 1.0
CD A:LYS235 4.8 13.9 1.0
O3 A:XLS503 4.9 41.4 1.0
ND2 A:ASN299 5.0 11.2 1.0

Cadmium binding site 4 out of 12 in 5nhe

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Cadmium binding site 4 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:15.0
occ:0.50
OE1 B:GLU269 2.0 17.8 1.0
OD2 B:ASP340 2.1 17.5 1.0
OD2 B:ASP297 2.2 15.5 1.0
OE2 B:GLU233 2.2 18.7 1.0
O2 B:XLS503 2.4 29.1 1.0
O4 B:XLS503 2.5 28.1 1.0
CD B:GLU233 3.1 15.8 1.0
CG B:ASP340 3.2 14.5 1.0
CG B:ASP297 3.3 13.9 1.0
CD B:GLU269 3.3 17.9 1.0
C4 B:XLS503 3.3 33.8 1.0
OE1 B:GLU233 3.4 15.8 1.0
C2 B:XLS503 3.6 37.0 1.0
CB B:ASP340 3.7 13.5 1.0
O3 B:XLS503 3.7 46.1 1.0
C3 B:XLS503 3.7 36.4 1.0
CB B:ASP297 3.7 12.8 1.0
CD B:CD502 3.9 23.7 0.2
O B:HOH830 3.9 21.9 1.0
CE1 B:HIS272 4.1 12.0 1.0
CG B:GLU269 4.1 14.9 1.0
CB B:GLU269 4.1 13.4 1.0
OE2 B:GLU269 4.2 19.0 1.0
OD1 B:ASP340 4.3 15.8 1.0
OD1 B:ASP297 4.3 14.1 1.0
CG B:GLU233 4.5 14.6 1.0
NE2 B:HIS272 4.5 12.6 1.0
CD B:CD502 4.7 12.4 0.4
C5 B:XLS503 4.8 34.4 1.0
C1 B:XLS503 4.8 35.1 1.0
ND1 B:HIS272 4.9 12.2 1.0
ND2 B:ASN267 5.0 16.3 1.0

Cadmium binding site 5 out of 12 in 5nhe

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Cadmium binding site 5 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:12.4
occ:0.40
CD B:CD502 0.0 12.4 0.4
CD B:CD502 1.4 23.7 0.2
OE2 B:GLU269 2.0 19.0 1.0
OD2 B:ASP308 2.2 23.3 1.0
O B:HOH830 2.3 21.9 1.0
OD1 B:ASP310 2.5 18.6 1.0
OD1 B:ASP308 2.6 23.4 1.0
CG B:ASP308 2.7 20.2 1.0
NE2 B:HIS272 2.8 12.6 1.0
CD B:GLU269 2.9 17.9 1.0
OE1 B:GLU269 3.2 17.8 1.0
CD2 B:HIS272 3.3 11.5 1.0
CG B:ASP310 3.5 18.2 1.0
OD2 B:ASP310 3.7 25.3 1.0
O2 B:XLS503 3.8 29.1 1.0
CE1 B:HIS272 3.9 12.0 1.0
ND2 B:ASN299 4.0 11.1 1.0
O B:HOH655 4.1 26.4 1.0
CB B:ASP308 4.1 18.1 1.0
O1 B:XLS503 4.2 47.5 1.0
CG B:GLU269 4.2 14.9 1.0
CB B:ASN271 4.4 10.7 1.0
OD2 B:ASP340 4.4 17.5 1.0
CG B:HIS272 4.6 11.6 1.0
CD B:CD501 4.7 15.0 0.5
ND1 B:HIS272 4.8 12.2 1.0
CB B:ASP310 4.9 15.5 1.0
OD1 B:ASN271 4.9 10.6 1.0
CG B:ASN271 4.9 10.6 1.0
C2 B:XLS503 4.9 37.0 1.0
CG B:ASP340 4.9 14.5 1.0
NZ B:LYS235 4.9 13.6 1.0
CE B:LYS235 4.9 13.1 1.0
C1 B:XLS503 5.0 35.1 1.0

Cadmium binding site 6 out of 12 in 5nhe

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Cadmium binding site 6 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:23.7
occ:0.25
CD B:CD502 0.0 23.7 0.2
CD B:CD502 1.4 12.4 0.4
O B:HOH830 2.0 21.9 1.0
NE2 B:HIS272 2.2 12.6 1.0
OD2 B:ASP308 2.5 23.3 1.0
O2 B:XLS503 2.6 29.1 1.0
OE2 B:GLU269 2.8 19.0 1.0
OE1 B:GLU269 3.0 17.8 1.0
CE1 B:HIS272 3.0 12.0 1.0
O1 B:XLS503 3.1 47.5 1.0
CD B:GLU269 3.2 17.9 1.0
CD2 B:HIS272 3.3 11.5 1.0
CG B:ASP308 3.4 20.2 1.0
C2 B:XLS503 3.6 37.0 1.0
OD1 B:ASP308 3.6 23.4 1.0
OD1 B:ASP310 3.6 18.6 1.0
C1 B:XLS503 3.8 35.1 1.0
CD B:CD501 3.9 15.0 0.5
OD2 B:ASP340 3.9 17.5 1.0
O B:HOH655 4.1 26.4 1.0
ND1 B:HIS272 4.2 12.2 1.0
CG B:HIS272 4.3 11.6 1.0
OD2 B:ASP310 4.3 25.3 1.0
CG B:ASP310 4.4 18.2 1.0
NZ B:LYS235 4.5 13.6 1.0
CE B:LYS235 4.6 13.1 1.0
CG B:GLU269 4.6 14.9 1.0
OE2 B:GLU233 4.7 18.7 1.0
CG B:ASP340 4.7 14.5 1.0
CD B:LYS235 4.8 12.2 1.0
CB B:ASP308 4.8 18.1 1.0
C3 B:XLS503 4.8 36.4 1.0
O3 B:XLS503 4.8 46.1 1.0

Cadmium binding site 7 out of 12 in 5nhe

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Cadmium binding site 7 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:14.8
occ:0.50
OE1 C:GLU269 2.1 18.0 1.0
OD2 C:ASP297 2.2 18.1 1.0
OD2 C:ASP340 2.2 15.9 1.0
OE2 C:GLU233 2.2 19.8 1.0
O4 C:XYS503 2.3 31.9 1.0
O3 C:XYS503 2.4 32.2 1.0
C3 C:XYS503 2.9 37.0 1.0
C4 C:XYS503 3.0 34.8 1.0
CD C:GLU233 3.1 17.4 1.0
CG C:ASP297 3.2 15.4 1.0
CG C:ASP340 3.2 14.5 1.0
CD C:GLU269 3.3 16.1 1.0
OE1 C:GLU233 3.4 17.5 1.0
CB C:ASP297 3.7 13.9 1.0
CB C:ASP340 3.7 13.5 1.0
O C:HOH765 3.9 28.7 1.0
CD C:CD502 3.9 24.8 0.2
CG C:GLU269 4.1 14.9 1.0
CE1 C:HIS272 4.1 13.2 1.0
CB C:GLU269 4.1 13.4 1.0
OE2 C:GLU269 4.2 18.7 1.0
OD1 C:ASP297 4.3 14.5 1.0
OD1 C:ASP340 4.3 15.2 1.0
C2 C:XYS503 4.3 38.7 1.0
CG C:GLU233 4.4 15.8 1.0
C5 C:XYS503 4.4 36.1 1.0
NE2 C:HIS272 4.5 13.4 1.0
CD C:CD502 4.7 14.3 0.4
ND1 C:HIS272 4.9 13.2 1.0
ND2 C:ASN267 4.9 14.5 1.0
O2 C:XYS503 5.0 37.8 1.0

Cadmium binding site 8 out of 12 in 5nhe

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Cadmium binding site 8 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd502

b:14.3
occ:0.40
CD C:CD502 0.0 14.3 0.4
CD C:CD502 1.4 24.8 0.2
OE2 C:GLU269 1.9 18.7 1.0
OD2 C:ASP308 2.2 25.6 1.0
O C:HOH765 2.3 28.7 1.0
OD1 C:ASP310 2.5 17.2 1.0
OD1 C:ASP308 2.6 24.3 1.0
CG C:ASP308 2.7 22.3 1.0
NE2 C:HIS272 2.8 13.4 1.0
CD C:GLU269 2.9 16.1 1.0
OE1 C:GLU269 3.2 18.0 1.0
CD2 C:HIS272 3.3 12.8 1.0
CG C:ASP310 3.5 17.3 1.0
O C:HOH605 3.5 26.7 1.0
OD2 C:ASP310 3.7 21.5 1.0
O3 C:XYS503 3.8 32.2 1.0
CE1 C:HIS272 3.9 13.2 1.0
ND2 C:ASN299 4.0 10.4 1.0
CB C:ASP308 4.1 18.9 1.0
CG C:GLU269 4.2 14.9 1.0
OD2 C:ASP340 4.4 15.9 1.0
CB C:ASN271 4.4 10.8 1.0
CG C:HIS272 4.5 12.4 1.0
O C:HOH929 4.5 41.2 1.0
CD C:CD501 4.7 14.8 0.5
O2 C:XYS503 4.7 37.8 1.0
ND1 C:HIS272 4.8 13.2 1.0
CB C:ASP310 4.9 15.4 1.0
OD1 C:ASN271 4.9 11.0 1.0
CG C:ASP340 4.9 14.5 1.0
CG C:ASN271 4.9 10.9 1.0
NZ C:LYS235 5.0 16.6 1.0
CE C:LYS235 5.0 15.2 1.0

Cadmium binding site 9 out of 12 in 5nhe

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Cadmium binding site 9 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd502

b:24.8
occ:0.25
CD C:CD502 0.0 24.8 0.2
CD C:CD502 1.4 14.3 0.4
O C:HOH765 2.1 28.7 1.0
NE2 C:HIS272 2.2 13.4 1.0
O C:HOH605 2.4 26.7 1.0
OD2 C:ASP308 2.5 25.6 1.0
O3 C:XYS503 2.5 32.2 1.0
OE2 C:GLU269 2.7 18.7 1.0
OE1 C:GLU269 3.0 18.0 1.0
CE1 C:HIS272 3.0 13.2 1.0
CD C:GLU269 3.2 16.1 1.0
CD2 C:HIS272 3.3 12.8 1.0
CG C:ASP308 3.4 22.3 1.0
O2 C:XYS503 3.6 37.8 1.0
OD1 C:ASP308 3.6 24.3 1.0
OD1 C:ASP310 3.7 17.2 1.0
C3 C:XYS503 3.8 37.0 1.0
CD C:CD501 3.9 14.8 0.5
OD2 C:ASP340 4.0 15.9 1.0
ND1 C:HIS272 4.1 13.2 1.0
C2 C:XYS503 4.2 38.7 1.0
CG C:HIS272 4.3 12.4 1.0
OD2 C:ASP310 4.4 21.5 1.0
CG C:ASP310 4.5 17.3 1.0
NZ C:LYS235 4.5 16.6 1.0
CE C:LYS235 4.6 15.2 1.0
CG C:GLU269 4.6 14.9 1.0
O C:HOH929 4.6 41.2 1.0
OE2 C:GLU233 4.7 19.8 1.0
CD C:LYS235 4.7 14.4 1.0
CG C:ASP340 4.8 14.5 1.0
CB C:ASP308 4.8 18.9 1.0

Cadmium binding site 10 out of 12 in 5nhe

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Cadmium binding site 10 out of 12 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two CD2+ Ions and Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd501

b:14.0
occ:0.50
OE1 D:GLU269 2.1 18.4 1.0
OD2 D:ASP297 2.1 17.1 1.0
OE2 D:GLU233 2.2 17.4 1.0
OD2 D:ASP340 2.2 14.7 1.0
O3 D:XYS503 2.2 31.1 1.0
O4 D:XYS503 2.4 33.5 1.0
C3 D:XYS503 2.9 40.3 1.0
C4 D:XYS503 3.0 39.4 1.0
CD D:GLU233 3.1 16.1 1.0
CG D:ASP297 3.2 15.4 1.0
CG D:ASP340 3.3 13.7 1.0
CD D:GLU269 3.3 15.8 1.0
OE1 D:GLU233 3.3 17.1 1.0
CB D:ASP297 3.7 14.1 1.0
CB D:ASP340 3.7 12.2 1.0
CD D:CD502 3.9 21.3 0.2
O D:HOH848 4.0 22.1 1.0
CE1 D:HIS272 4.1 11.3 1.0
CG D:GLU269 4.1 14.1 1.0
CB D:GLU269 4.1 12.4 1.0
OE2 D:GLU269 4.2 16.4 1.0
OD1 D:ASP297 4.3 16.5 1.0
C2 D:XYS503 4.3 42.9 1.0
OD1 D:ASP340 4.3 15.2 1.0
CG D:GLU233 4.4 14.6 1.0
C5 D:XYS503 4.5 41.7 1.0
NE2 D:HIS272 4.5 11.6 1.0
CD D:CD502 4.7 18.1 0.5
ND1 D:HIS272 4.9 11.2 1.0
ND2 D:ASN267 4.9 12.8 1.0
O2 D:XYS503 4.9 42.9 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: Sat Dec 12 08:27:12 2020

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