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Cadmium in PDB 3jqx: Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium

Enzymatic activity of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium

All present enzymatic activity of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium:
3.4.24.3;

Protein crystallography data

The structure of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium, PDB code: 3jqx was solved by J.Sakon, S.T.L.Philominathan, R.Bauer, O.Matsushita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.68 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.567, 64.589, 96.010, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 25

Other elements in 3jqx:

The structure of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium (pdb code 3jqx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium, PDB code: 3jqx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 1 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:22.0
occ:0.70
 OD2 A:ASP897 2.4 13.3 1.0
O A:THR891 2.5 10.7 1.0
OD1 A:ASP899 2.5 13.8 1.0
OE2 A:GLU870 2.5 19.6 1.0
OD2 A:ASP899 2.6 12.3 1.0
OE1 A:GLU868 2.6 17.8 1.0
OE2 A:GLU868 2.7 14.6 1.0
CG A:ASP899 2.9 12.8 1.0
CD A:GLU868 3.0 19.4 1.0
O A:HOH1123 3.1 26.5 1.0
CG A:ASP897 3.3 14.8 1.0
OD1 A:ASP897 3.6 13.8 1.0
C A:THR891 3.6 10.7 1.0
CA A:CA1001 3.7 15.1 1.0
CD A:GLU870 3.8 24.2 1.0
N A:THR891 4.3 11.2 1.0
CA A:ILE892 4.3 12.0 1.0
OH A:TYR971 4.3 9.2 1.0
N A:ILE892 4.3 11.4 1.0
CB A:ASP899 4.4 12.4 1.0
CG A:GLU868 4.5 20.0 1.0
CA A:THR891 4.5 11.4 1.0
OD1 A:ASN872 4.6 14.1 1.0
CG A:GLU870 4.6 26.4 1.0
N A:GLU893 4.6 12.9 1.0
OE1 A:GLU870 4.7 25.6 1.0
CG A:GLU893 4.7 26.8 1.0
CB A:ASP897 4.7 15.2 1.0
CB A:THR891 5.0 12.7 1.0
C A:ILE892 5.0 13.4 1.0

Cadmium binding site 2 out of 9 in 3jqx

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Cadmium binding site 2 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:68.0
occ:0.50
 OE2 A:GLU876 2.2 38.0 1.0
O A:HOH1136 2.7 30.4 1.0
OE1 A:GLU876 2.8 38.9 1.0
CD A:GLU876 2.9 36.4 1.0
CG A:GLU876 4.4 28.5 1.0
N A:LYS875 4.6 18.9 1.0
CB A:LYS875 4.6 20.4 1.0
CB A:SER874 4.7 19.1 1.0
O A:HOH1153 4.8 39.3 1.0

Cadmium binding site 3 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 3 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:61.5
occ:0.50
 OE2 A:GLU930 2.2 41.6 1.0
CD A:GLU930 3.2 38.5 1.0
OE1 A:GLU930 3.4 39.5 1.0
CA A:GLY955 4.2 23.7 1.0
CG A:GLU930 4.5 34.1 1.0
N A:ARG956 4.5 21.3 1.0
C A:GLY955 4.9 22.4 1.0

Cadmium binding site 4 out of 9 in 3jqx

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Cadmium binding site 4 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1002

b:23.6
occ:0.70
 O B:THR891 2.4 14.3 1.0
OE2 B:GLU870 2.4 21.2 1.0
OD1 B:ASP899 2.5 17.0 1.0
OD2 B:ASP897 2.5 11.2 1.0
OD2 B:ASP899 2.5 11.8 1.0
OE2 B:GLU868 2.5 17.1 1.0
OE1 B:GLU868 2.8 15.6 1.0
CG B:ASP899 2.8 12.2 1.0
O B:HOH1104 2.9 13.6 1.0
CD B:GLU868 3.0 19.8 1.0
CG B:ASP897 3.3 14.7 1.0
C B:THR891 3.5 14.4 1.0
OD1 B:ASP897 3.6 9.6 1.0
CD B:GLU870 3.6 21.4 1.0
CA B:CA1001 3.6 16.4 1.0
CA B:ILE892 4.3 13.8 1.0
N B:ILE892 4.3 13.9 1.0
OH B:TYR971 4.3 12.9 1.0
N B:THR891 4.3 14.7 1.0
CB B:ASP899 4.3 11.7 1.0
CG B:GLU870 4.4 21.4 1.0
CA B:THR891 4.4 16.1 1.0
OE1 B:GLU870 4.5 16.7 1.0
N B:GLU893 4.5 15.5 1.0
CG B:GLU868 4.5 19.3 1.0
OD1 B:ASN872 4.6 13.6 1.0
O B:HOH1122 4.6 21.4 1.0
CB B:ASP897 4.7 14.2 1.0
CG B:GLU893 4.8 30.4 1.0
C B:ILE892 4.9 14.6 1.0
ND2 B:ASN872 5.0 13.2 1.0
CE2 B:TYR971 5.0 14.4 1.0

Cadmium binding site 5 out of 9 in 3jqx

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Cadmium binding site 5 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1003

b:58.5
occ:0.50
 OE1 B:GLU876 2.3 44.5 1.0
OE2 B:GLU876 2.4 44.9 1.0
CD B:GLU876 2.6 40.1 1.0
CG B:GLU876 4.0 31.4 1.0
CB B:SER874 4.4 19.8 1.0
N B:LYS875 4.5 19.6 1.0
N B:GLU876 4.5 22.8 1.0
CB B:LYS875 4.6 21.8 1.0
OG B:SER874 4.8 18.7 1.0
CA B:LYS875 5.0 22.2 1.0

Cadmium binding site 6 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 6 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1004

b:71.6
occ:1.00
 OE2 B:GLU930 2.5 31.3 1.0
OE1 B:GLU930 2.8 39.5 1.0
CD B:GLU930 3.0 35.2 1.0
O B:HOH1151 3.2 29.9 1.0
O B:HOH1166 3.7 38.4 1.0
CG B:GLU930 4.5 33.0 1.0
N B:ARG956 4.6 15.0 1.0
O B:HOH1157 4.7 31.8 1.0
CA B:GLY955 4.9 18.4 1.0
CB B:ARG956 4.9 14.1 1.0

Cadmium binding site 7 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 7 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1002

b:25.6
occ:0.70
 O C:THR891 2.3 12.9 1.0
OD2 C:ASP897 2.4 10.4 1.0
OD1 C:ASP899 2.5 10.3 1.0
OE2 C:GLU868 2.5 10.7 1.0
OD2 C:ASP899 2.6 12.6 1.0
OE2 C:GLU870 2.6 20.0 1.0
OE1 C:GLU868 2.6 14.9 1.0
CG C:ASP899 2.9 11.3 1.0
CD C:GLU868 2.9 14.4 1.0
O C:HOH1119 3.0 22.0 1.0
CG C:ASP897 3.3 14.2 1.0
OD1 C:ASP897 3.5 12.1 1.0
C C:THR891 3.5 13.3 1.0
CA C:CA1001 3.6 12.7 1.0
CD C:GLU870 3.7 21.0 1.0
N C:THR891 4.3 13.2 1.0
N C:ILE892 4.3 13.9 1.0
CA C:ILE892 4.3 14.0 1.0
OH C:TYR971 4.3 7.6 1.0
CG C:GLU870 4.3 23.4 1.0
OE2 C:GLU893 4.4 39.2 1.0
CB C:ASP899 4.4 10.8 1.0
CG C:GLU893 4.4 27.4 1.0
CG C:GLU868 4.5 14.3 1.0
CA C:THR891 4.5 14.3 1.0
OD1 C:ASN872 4.6 15.3 1.0
N C:GLU893 4.7 15.9 1.0
CB C:ASP897 4.7 13.3 1.0
OE1 C:GLU870 4.7 25.6 1.0
CD C:GLU893 4.8 36.6 1.0
ND2 C:ASN872 5.0 13.9 1.0
CE2 C:TYR971 5.0 9.4 1.0

Cadmium binding site 8 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 8 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1003

b:48.6
occ:0.50
 OE1 C:GLU876 2.2 24.9 1.0
OE2 C:GLU876 2.6 23.6 1.0
CD C:GLU876 2.8 25.1 1.0
O C:HOH1114 2.9 19.6 1.0
O C:HOH1144 3.1 29.5 1.0
O C:HOH1158 4.1 32.9 1.0
CG C:GLU876 4.3 19.9 1.0
N C:LYS875 4.4 16.5 1.0
CB C:LYS875 4.5 20.0 1.0
NZ C:LYS875 4.5 46.6 1.0
CB C:SER874 4.6 13.6 1.0
N C:GLU876 4.8 18.1 1.0
CA C:LYS875 5.0 18.7 1.0
CG C:LYS875 5.0 24.4 1.0

Cadmium binding site 9 out of 9 in 3jqx

Go back to Cadmium Binding Sites List in 3jqx
Cadmium binding site 9 out of 9 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium


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 Clostridium Histolyticum Colh Collagenase Collagen Binding Domain 3 at 2.2 Angstrom Resolution in the Presence of Calcium and Cadmium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1004

b:40.6
occ:0.50
 OE2 C:GLU930 2.4 34.4 1.0
OE1 C:GLU930 2.7 38.9 1.0
O C:HOH1151 2.7 31.4 1.0
CD C:GLU930 2.8 36.1 1.0
CA C:GLY955 4.2 23.0 1.0
CG C:GLU930 4.4 31.2 1.0
N C:ARG956 4.6 20.2 1.0
O C:PRO954 4.6 26.0 1.0
C C:GLY955 5.0 22.2 1.0

Reference:

R.Bauer, J.J.Wilson, S.T.Philominathan, D.Davis, O.Matsushita, J.Sakon. Structural Comparison of Colh and Colg Collagen-Binding Domains From Clostridium Histolyticum. J.Bacteriol. V. 195 318 2013.
ISSN: ISSN 0021-9193
PubMed: 23144249
DOI: 10.1128/JB.00010-12
Page generated: Thu Jul 10 12:43:02 2025

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