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Calcium 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:

Cadmium (Cd) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3jqx

Go back to Calcium Binding Sites List in 3jqx
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca1001

b:15.1
occ:1.00
 OD1 A:ASP897 2.3 13.8 1.0
OD1 A:ASP899 2.4 13.8 1.0
OD1 A:ASN872 2.4 14.1 1.0
O A:GLN898 2.4 11.7 1.0
OE2 A:GLU870 2.5 19.6 1.0
OD1 A:ASN873 2.5 18.9 1.0
OE1 A:GLU870 2.7 25.6 1.0
CD A:GLU870 3.0 24.2 1.0
CG A:ASP897 3.3 14.8 1.0
C A:GLN898 3.4 12.5 1.0
CG A:ASN873 3.4 20.8 1.0
CG A:ASP899 3.6 12.8 1.0
CG A:ASN872 3.6 16.9 1.0
CD A:CD1002 3.7 22.0 0.7
OD2 A:ASP897 3.7 13.3 1.0
O A:HOH1138 3.9 29.9 1.0
ND2 A:ASN873 3.9 17.4 1.0
CA A:ASP899 4.0 12.3 1.0
N A:GLN898 4.0 13.2 1.0
N A:ASP899 4.0 11.2 1.0
C A:ASN872 4.3 16.2 1.0
N A:ASN873 4.3 15.6 1.0
N A:ASN872 4.3 18.1 1.0
OE1 A:GLU868 4.3 17.8 1.0
CA A:GLN898 4.4 13.2 1.0
ND2 A:ASN872 4.4 14.5 1.0
CB A:ASP899 4.4 12.4 1.0
O A:ASN872 4.4 15.3 1.0
C A:ASP897 4.5 13.9 1.0
CA A:ASN873 4.5 17.7 1.0
OD2 A:ASP899 4.5 12.3 1.0
CB A:ASN873 4.6 16.8 1.0
CB A:ASP897 4.6 15.2 1.0
CG A:GLU870 4.6 26.4 1.0
CA A:ASP897 4.7 14.8 1.0
CA A:ASN872 4.7 15.8 1.0
CB A:ASN872 4.8 14.2 1.0

Calcium binding site 2 out of 3 in 3jqx

Go back to Calcium Binding Sites List in 3jqx
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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
B:Ca1001

b:16.4
occ:1.00
 OD1 B:ASN873 2.3 20.6 1.0
OD1 B:ASP897 2.3 9.6 1.0
OD1 B:ASN872 2.4 13.6 1.0
O B:GLN898 2.4 11.7 1.0
OD1 B:ASP899 2.4 17.0 1.0
OE2 B:GLU870 2.6 21.2 1.0
OE1 B:GLU870 2.6 16.7 1.0
CD B:GLU870 3.0 21.4 1.0
CG B:ASP897 3.3 14.7 1.0
C B:GLN898 3.4 12.4 1.0
CG B:ASN873 3.5 23.4 1.0
CG B:ASN872 3.6 14.4 1.0
CD B:CD1002 3.6 23.6 0.7
CG B:ASP899 3.6 12.2 1.0
OD2 B:ASP897 3.8 11.2 1.0
CA B:ASP899 4.0 12.6 1.0
N B:GLN898 4.0 13.8 1.0
N B:ASP899 4.0 12.0 1.0
O B:HOH1127 4.2 22.6 1.0
OE1 B:GLU868 4.2 15.6 1.0
C B:ASN872 4.2 16.6 1.0
N B:ASN872 4.3 15.1 1.0
ND2 B:ASN872 4.3 13.2 1.0
O B:ASN872 4.3 16.1 1.0
CA B:GLN898 4.4 12.3 1.0
CB B:ASP899 4.4 11.7 1.0
CB B:ASN873 4.4 19.3 1.0
C B:ASP897 4.5 14.0 1.0
ND2 B:ASN873 4.5 26.1 1.0
CG B:GLU870 4.5 21.4 1.0
N B:ASN873 4.5 17.9 1.0
OD2 B:ASP899 4.5 11.8 1.0
CA B:ASN873 4.5 19.3 1.0
CB B:ASP897 4.6 14.2 1.0
CA B:ASN872 4.6 14.7 1.0
CA B:ASP897 4.7 13.6 1.0
CB B:ASN872 4.7 14.0 1.0

Calcium binding site 3 out of 3 in 3jqx

Go back to Calcium Binding Sites List in 3jqx
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca 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
C:Ca1001

b:12.7
occ:1.00
 OD1 C:ASN873 2.2 20.8 1.0
OD1 C:ASN872 2.3 15.3 1.0
OE2 C:GLU870 2.3 20.0 1.0
O C:GLN898 2.3 13.4 1.0
OD1 C:ASP897 2.3 12.1 1.0
OD1 C:ASP899 2.4 10.3 1.0
OE1 C:GLU870 2.6 25.6 1.0
CD C:GLU870 2.8 21.0 1.0
C C:GLN898 3.3 11.8 1.0
CG C:ASN873 3.4 24.8 1.0
CG C:ASP897 3.4 14.2 1.0
CG C:ASN872 3.5 16.6 1.0
CG C:ASP899 3.6 11.3 1.0
CD C:CD1002 3.6 25.6 0.7
OD2 C:ASP897 3.9 10.4 1.0
CA C:ASP899 3.9 11.0 1.0
N C:ASP899 4.0 12.5 1.0
C C:ASN872 4.1 15.4 1.0
N C:ASN872 4.1 17.2 1.0
N C:GLN898 4.2 11.7 1.0
ND2 C:ASN872 4.2 13.9 1.0
OE1 C:GLU868 4.2 14.9 1.0
N C:ASN873 4.2 16.1 1.0
CG C:GLU870 4.3 23.4 1.0
O C:ASN872 4.3 14.9 1.0
ND2 C:ASN873 4.3 30.7 1.0
CA C:ASN873 4.3 17.2 1.0
CB C:ASP899 4.3 10.8 1.0
CB C:ASN873 4.4 17.6 1.0
CA C:GLN898 4.4 11.9 1.0
OD2 C:ASP899 4.5 12.6 1.0
CA C:ASN872 4.5 16.2 1.0
C C:ASP897 4.5 12.7 1.0
CB C:ASN872 4.6 14.3 1.0
CB C:ASP897 4.7 13.3 1.0
CA C:ASP897 4.7 13.3 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: Sat Jul 13 11:51:24 2024

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