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Calcium in PDB 3jqw: Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium

Enzymatic activity of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium

All present enzymatic activity of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium:
3.4.24.3;

Protein crystallography data

The structure of Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium, PDB code: 3jqw was solved by J.Sakon, S.T.L.Philominathan, O.Matsushita, R.Bauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.50 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.001, 64.180, 95.375, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 1 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:16.1
occ:1.00
 OD1 A:ASP897 2.3 15.8 1.0
OD1 A:ASP899 2.3 15.2 1.0
O A:GLN898 2.4 14.0 1.0
OD1 A:ASN872 2.4 14.9 1.0
OD1 A:ASN873 2.4 22.9 1.0
OE2 A:GLU870 2.5 14.3 1.0
OE1 A:GLU870 2.6 17.0 1.0
CD A:GLU870 2.9 16.1 1.0
CG A:ASP897 3.3 18.0 1.0
C A:GLN898 3.4 15.7 1.0
CG A:ASP899 3.5 15.2 1.0
CG A:ASN873 3.6 24.1 1.0
CG A:ASN872 3.6 17.4 1.0
CA A:CA1002 3.7 14.8 1.0
OD2 A:ASP897 3.8 16.1 1.0
CA A:ASP899 3.9 16.1 1.0
N A:ASP899 4.0 16.2 1.0
O A:HOH1132 4.0 33.5 1.0
N A:GLN898 4.1 17.5 1.0
N A:ASN872 4.2 19.2 1.0
C A:ASN872 4.2 18.5 1.0
O A:ASN872 4.2 17.0 1.0
ND2 A:ASN872 4.3 16.3 1.0
CB A:ASP899 4.3 16.1 1.0
N A:ASN873 4.3 18.8 1.0
OE1 A:GLU868 4.4 16.5 1.0
CA A:ASN873 4.4 20.8 1.0
CG A:GLU870 4.4 19.2 1.0
CA A:GLN898 4.4 16.0 1.0
OD2 A:ASP899 4.4 19.0 1.0
O A:HOH1129 4.4 32.5 1.0
C A:ASP897 4.4 17.6 1.0
CB A:ASN873 4.5 21.9 1.0
ND2 A:ASN873 4.5 31.2 1.0
O A:HOH1121 4.5 28.5 1.0
CA A:ASN872 4.6 18.4 1.0
CB A:ASP897 4.6 17.3 1.0
CB A:ASN872 4.7 17.2 1.0
CA A:ASP897 4.7 17.7 1.0

Calcium binding site 2 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 2 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:14.8
occ:1.00
 OE2 A:GLU870 2.2 14.3 1.0
O A:THR891 2.4 15.4 1.0
O A:HOH1103 2.4 16.9 1.0
OD2 A:ASP899 2.5 19.0 1.0
OD2 A:ASP897 2.5 16.1 1.0
OE2 A:GLU868 2.5 16.8 1.0
OD1 A:ASP899 2.6 15.2 1.0
OE1 A:GLU868 2.6 16.5 1.0
CG A:ASP899 2.9 15.2 1.0
CD A:GLU868 2.9 18.5 1.0
CG A:ASP897 3.4 18.0 1.0
CD A:GLU870 3.5 16.1 1.0
C A:THR891 3.6 16.1 1.0
OD1 A:ASP897 3.7 15.8 1.0
CA A:CA1001 3.7 16.1 1.0
CG A:GLU870 4.1 19.2 1.0
N A:THR891 4.3 14.9 1.0
OH A:TYR971 4.3 17.1 1.0
CB A:ASP899 4.4 16.1 1.0
CA A:ILE892 4.4 16.8 1.0
N A:ILE892 4.4 16.0 1.0
CG A:GLU868 4.4 17.5 1.0
OE1 A:GLU870 4.4 17.0 1.0
CA A:THR891 4.5 16.6 1.0
OD1 A:ASN872 4.7 14.9 1.0
N A:GLU893 4.7 18.7 1.0
O A:HOH1177 4.7 42.7 1.0
O A:HOH1165 4.7 41.3 1.0
CG A:GLU893 4.8 27.8 1.0
CB A:ASP897 4.8 17.3 1.0
ND2 A:ASN872 5.0 16.3 1.0

Calcium binding site 3 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 3 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:17.5
occ:1.00
 OD1 B:ASP897 2.2 17.4 1.0
OD1 B:ASN873 2.3 21.7 1.0
O B:GLN898 2.4 15.7 1.0
OD1 B:ASN872 2.4 14.2 1.0
OD1 B:ASP899 2.4 10.7 1.0
OE2 B:GLU870 2.5 19.5 1.0
OE1 B:GLU870 2.5 20.4 1.0
CD B:GLU870 2.9 22.3 1.0
CG B:ASP897 3.3 19.6 1.0
C B:GLN898 3.4 16.6 1.0
CG B:ASN873 3.5 25.0 1.0
CG B:ASN872 3.6 19.3 1.0
CG B:ASP899 3.6 16.4 1.0
CA B:CA1002 3.8 16.0 1.0
OD2 B:ASP897 3.8 19.5 1.0
CA B:ASP899 3.9 15.7 1.0
N B:ASP899 4.0 16.1 1.0
N B:GLN898 4.1 17.4 1.0
N B:ASN872 4.2 20.4 1.0
C B:ASN872 4.2 20.2 1.0
ND2 B:ASN872 4.3 19.0 1.0
N B:ASN873 4.3 20.7 1.0
O B:HOH1124 4.3 25.7 1.0
O B:ASN872 4.3 19.6 1.0
OE1 B:GLU868 4.3 20.0 1.0
CA B:ASN873 4.4 21.2 1.0
O B:HOH1147 4.4 31.2 1.0
CB B:ASP899 4.4 16.0 1.0
CA B:GLN898 4.4 17.9 1.0
CG B:GLU870 4.4 23.1 1.0
CB B:ASN873 4.4 21.1 1.0
ND2 B:ASN873 4.4 28.5 1.0
C B:ASP897 4.5 19.0 1.0
O B:HOH1171 4.5 37.5 1.0
OD2 B:ASP899 4.6 13.5 1.0
CB B:ASP897 4.6 18.9 1.0
O B:HOH1184 4.6 41.9 1.0
CA B:ASN872 4.6 20.5 1.0
CA B:ASP897 4.7 18.5 1.0
CB B:ASN872 4.7 19.6 1.0

Calcium binding site 4 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 4 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:16.0
occ:1.00
 O B:THR891 2.3 15.2 1.0
OE2 B:GLU870 2.3 19.5 1.0
OE2 B:GLU868 2.4 17.1 1.0
OD2 B:ASP897 2.4 19.5 1.0
O B:HOH1107 2.5 19.4 1.0
OD2 B:ASP899 2.5 13.5 1.0
OD1 B:ASP899 2.5 10.7 1.0
OE1 B:GLU868 2.6 20.0 1.0
CD B:GLU868 2.8 19.1 1.0
CG B:ASP899 2.9 16.4 1.0
CG B:ASP897 3.4 19.6 1.0
C B:THR891 3.5 15.8 1.0
CD B:GLU870 3.5 22.3 1.0
OD1 B:ASP897 3.6 17.4 1.0
CA B:CA1001 3.8 17.5 1.0
CG B:GLU870 4.1 23.1 1.0
N B:THR891 4.2 16.3 1.0
OH B:TYR971 4.3 13.6 1.0
N B:ILE892 4.3 15.9 1.0
CG B:GLU868 4.3 20.1 1.0
CB B:ASP899 4.4 16.0 1.0
CA B:ILE892 4.4 16.2 1.0
O B:HOH1171 4.4 37.5 1.0
O B:HOH1149 4.4 31.9 1.0
CA B:THR891 4.4 16.4 1.0
OE1 B:GLU870 4.4 20.4 1.0
N B:GLU893 4.6 18.3 1.0
OD1 B:ASN872 4.7 14.2 1.0
CB B:ASP897 4.8 18.9 1.0
OE2 B:GLU893 4.8 32.9 1.0
CG B:GLU893 4.8 24.4 1.0
ND2 B:ASN872 4.9 19.0 1.0

Calcium binding site 5 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 5 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:15.8
occ:1.00
 OD1 C:ASN873 2.2 19.8 1.0
OD1 C:ASN872 2.3 19.3 1.0
OD1 C:ASP897 2.3 17.8 1.0
OD1 C:ASP899 2.4 9.8 1.0
O C:GLN898 2.4 16.5 1.0
OE2 C:GLU870 2.5 16.7 1.0
OE1 C:GLU870 2.5 21.1 1.0
CD C:GLU870 2.8 21.3 1.0
C C:GLN898 3.3 15.7 1.0
CG C:ASP897 3.4 17.9 1.0
CG C:ASN873 3.4 20.8 1.0
CG C:ASN872 3.5 17.2 1.0
CG C:ASP899 3.6 14.1 1.0
CA C:CA1002 3.8 15.4 1.0
CA C:ASP899 3.9 13.4 1.0
OD2 C:ASP897 3.9 15.7 1.0
N C:ASP899 4.0 14.6 1.0
N C:ASN872 4.1 19.6 1.0
N C:GLN898 4.1 16.4 1.0
C C:ASN872 4.2 17.7 1.0
ND2 C:ASN872 4.2 16.5 1.0
N C:ASN873 4.3 17.2 1.0
CB C:ASP899 4.3 12.5 1.0
CA C:ASN873 4.3 17.9 1.0
O C:ASN872 4.3 16.5 1.0
O C:HOH1111 4.4 23.2 1.0
ND2 C:ASN873 4.4 24.1 1.0
CG C:GLU870 4.4 22.6 1.0
OE1 C:GLU868 4.4 20.2 1.0
CB C:ASN873 4.4 17.8 1.0
CA C:GLN898 4.4 16.2 1.0
C C:ASP897 4.4 17.6 1.0
CA C:ASN872 4.5 18.2 1.0
O C:HOH1139 4.5 31.2 1.0
OD2 C:ASP899 4.5 15.2 1.0
CB C:ASN872 4.6 17.1 1.0
CB C:ASP897 4.6 18.6 1.0
CA C:ASP897 4.7 18.2 1.0
O C:HOH1170 4.8 38.1 1.0
O C:HOH1164 4.8 36.6 1.0

Calcium binding site 6 out of 6 in 3jqw

Go back to Calcium Binding Sites List in 3jqw
Calcium binding site 6 out of 6 in the Crystal Structure of Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium


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 Clostridium Histolyticum Colh Collagenase Collagen-Binding Domain 3 at 2 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1002

b:15.4
occ:1.00
 O C:THR891 2.3 15.6 1.0
OE2 C:GLU870 2.3 16.7 1.0
OE2 C:GLU868 2.5 13.6 1.0
OD2 C:ASP899 2.5 15.2 1.0
OD2 C:ASP897 2.5 15.7 1.0
O C:HOH1107 2.5 21.8 1.0
OD1 C:ASP899 2.5 9.8 1.0
OE1 C:GLU868 2.7 20.2 1.0
CG C:ASP899 2.8 14.1 1.0
CD C:GLU868 2.9 16.9 1.0
CG C:ASP897 3.4 17.9 1.0
CD C:GLU870 3.5 21.3 1.0
C C:THR891 3.5 16.6 1.0
OD1 C:ASP897 3.6 17.8 1.0
CA C:CA1001 3.8 15.8 1.0
CG C:GLU870 4.2 22.6 1.0
OH C:TYR971 4.3 14.8 1.0
N C:THR891 4.3 17.2 1.0
CB C:ASP899 4.3 12.5 1.0
CA C:ILE892 4.3 17.4 1.0
N C:ILE892 4.3 17.1 1.0
O C:HOH1164 4.4 36.6 1.0
CG C:GLU868 4.4 18.4 1.0
OE1 C:GLU870 4.5 21.1 1.0
CA C:THR891 4.5 16.3 1.0
N C:GLU893 4.6 18.4 1.0
O C:HOH1119 4.7 27.0 1.0
OD1 C:ASN872 4.7 19.3 1.0
CG C:GLU893 4.7 26.9 1.0
CB C:ASP897 4.8 18.6 1.0
OE2 C:GLU893 4.9 33.6 1.0
ND2 C:ASN872 5.0 16.5 1.0
CE2 C:TYR971 5.0 15.8 1.0
C C:ILE892 5.0 17.4 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: Tue Jul 8 13:32:16 2025

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