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Calcium in PDB 2o8o: Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium

Enzymatic activity of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium

All present enzymatic activity of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium:
3.4.24.3;

Protein crystallography data

The structure of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium, PDB code: 2o8o was solved by S.T.L.Philominathan, J.J.Wilson, O.Matsushita, J.Sakon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.866, 59.170, 48.801, 90.00, 100.77, 90.00
R / Rfree (%) 14.7 / 21

Other elements in 2o8o:

The structure of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium (pdb code 2o8o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium, PDB code: 2o8o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2o8o

Go back to Calcium Binding Sites List in 2o8o
Calcium binding site 1 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 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 Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:10.9
occ:1.00
 OD2 A:ASP904 2.3 13.2 1.0
O A:ARG929 2.3 10.8 1.0
OD1 A:ASN903 2.4 11.2 1.0
OD1 A:ASP930 2.4 10.8 1.0
OE2 A:GLU901 2.4 11.0 1.0
OD1 A:ASP927 2.4 11.8 1.0
OE1 A:GLU901 2.5 14.3 1.0
CD A:GLU901 2.8 12.0 1.0
CG A:ASP927 3.4 10.3 1.0
C A:ARG929 3.4 9.8 1.0
CG A:ASN903 3.5 10.5 1.0
CG A:ASP930 3.6 10.2 1.0
CG A:ASP904 3.6 17.3 1.0
OD2 A:ASP927 3.6 10.8 1.0
CA A:CA1010 3.8 11.2 1.0
CA A:ASP930 3.9 9.5 1.0
O A:HOH3061 4.0 25.6 1.0
N A:ASP930 4.0 9.2 1.0
CB A:ASP930 4.2 10.0 1.0
ND2 A:ASN903 4.2 13.4 1.0
C A:ASN903 4.2 12.0 1.0
N A:ASN903 4.2 13.8 1.0
OD1 A:ASP904 4.3 26.9 1.0
CG A:GLU901 4.3 16.3 1.0
N A:ASP904 4.4 16.2 1.0
O A:HOH3151 4.4 39.0 1.0
OE1 A:GLU899 4.4 13.9 1.0
O A:ASN903 4.4 13.0 1.0
OD2 A:ASP930 4.5 11.2 1.0
CA A:ASP904 4.6 16.3 1.0
CA A:ASN903 4.6 12.0 1.0
CA A:ARG929 4.6 11.1 1.0
CB A:ASP904 4.7 19.8 1.0
CB A:ASN903 4.7 11.6 1.0
N A:ARG929 4.7 9.5 1.0
CB A:ASP927 4.7 11.2 1.0
O A:HOH3031 4.8 21.6 1.0
CD2 A:LEU923 5.0 11.7 1.0

Calcium binding site 2 out of 4 in 2o8o

Go back to Calcium Binding Sites List in 2o8o
Calcium binding site 2 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 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 Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1010

b:11.2
occ:1.00
 OE2 A:GLU901 2.3 11.0 1.0
O A:SER922 2.3 10.9 1.0
OD2 A:ASP927 2.4 10.8 1.0
O A:HOH3018 2.4 15.0 1.0
OE2 A:GLU899 2.4 13.0 1.0
OD1 A:ASP930 2.5 10.8 1.0
OE1 A:GLU899 2.5 13.9 1.0
OD2 A:ASP930 2.6 11.2 1.0
CD A:GLU899 2.8 13.6 1.0
CG A:ASP930 2.8 10.2 1.0
CG A:ASP927 3.5 10.3 1.0
CD A:GLU901 3.5 12.0 1.0
C A:SER922 3.6 9.3 1.0
CA A:CA1009 3.8 10.9 1.0
OD1 A:ASP927 3.9 11.8 1.0
N A:SER922 4.0 11.2 1.0
O A:HOH3002 4.1 11.3 1.0
CG A:GLU901 4.2 16.3 1.0
CG A:GLU899 4.2 14.2 1.0
CB A:ASP930 4.3 10.0 1.0
OG A:SER922 4.3 14.8 1.0
CD2 A:LEU923 4.3 11.7 1.0
CA A:SER922 4.3 11.7 1.0
OE1 A:GLU901 4.5 14.3 1.0
N A:LEU923 4.6 10.4 1.0
O A:HOH3108 4.6 27.0 1.0
OD1 A:ASN903 4.6 11.2 1.0
ND2 A:ASN903 4.8 13.4 1.0
CB A:ASP927 4.8 11.2 1.0
CA A:LEU923 4.8 11.0 1.0
OH A:TYR1002 4.9 11.7 1.0
CG A:LEU923 5.0 11.1 1.0
CB A:SER922 5.0 13.7 1.0

Calcium binding site 3 out of 4 in 2o8o

Go back to Calcium Binding Sites List in 2o8o
Calcium binding site 3 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 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 Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2009

b:13.7
occ:1.00
 O B:SER1922 2.3 12.2 1.0
OD2 B:ASP1927 2.3 14.3 1.0
OE2 B:GLU1901 2.3 13.6 1.0
O B:HOH3025 2.4 16.2 1.0
OD1 B:ASP1930 2.4 12.4 1.0
OE1 B:GLU1899 2.5 14.3 1.0
OE2 B:GLU1899 2.5 14.6 1.0
OD2 B:ASP1930 2.6 13.8 1.0
CD B:GLU1899 2.8 15.2 1.0
CG B:ASP1930 2.9 12.7 1.0
CG B:ASP1927 3.4 13.7 1.0
C B:SER1922 3.5 11.6 1.0
CD B:GLU1901 3.6 14.4 1.0
CA B:CA2010 3.7 13.3 1.0
OD1 B:ASP1927 3.9 13.9 1.0
N B:SER1922 4.0 15.0 1.0
O B:HOH3013 4.0 17.4 1.0
CG B:GLU1901 4.2 17.4 1.0
CB B:ASP1930 4.3 12.0 1.0
CG B:GLU1899 4.3 15.3 1.0
CD2 B:LEU1923 4.3 15.6 1.0
CA B:SER1922 4.4 15.7 1.0
OG B:SER1922 4.4 24.5 1.0
N B:LEU1923 4.5 13.1 1.0
OE1 B:GLU1901 4.6 16.7 1.0
O B:HOH3103 4.6 23.0 1.0
OD1 B:ASN1903 4.6 14.0 1.0
O B:HOH3176 4.6 49.0 1.0
CB B:ASP1927 4.7 12.8 1.0
CA B:LEU1923 4.8 11.3 1.0
O B:HOH3080 4.8 27.4 1.0
ND2 B:ASN1903 4.8 16.0 1.0
CG B:LEU1923 4.9 12.0 1.0
OH B:TYR2002 5.0 15.6 1.0

Calcium binding site 4 out of 4 in 2o8o

Go back to Calcium Binding Sites List in 2o8o
Calcium binding site 4 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 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 Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2010

b:13.3
occ:1.00
 OD1 B:ASN1903 2.3 14.0 1.0
OD2 B:ASP1904 2.3 15.3 1.0
OD1 B:ASP1930 2.3 12.4 1.0
O B:ARG1929 2.4 11.7 1.0
OE2 B:GLU1901 2.4 13.6 1.0
OD1 B:ASP1927 2.4 13.9 1.0
OE1 B:GLU1901 2.6 16.7 1.0
CD B:GLU1901 2.8 14.4 1.0
CG B:ASP1927 3.4 13.7 1.0
C B:ARG1929 3.5 11.2 1.0
CG B:ASN1903 3.5 12.9 1.0
CG B:ASP1930 3.5 12.7 1.0
CG B:ASP1904 3.6 17.8 1.0
OD2 B:ASP1927 3.6 14.3 1.0
CA B:CA2009 3.7 13.7 1.0
CA B:ASP1930 3.9 11.9 1.0
N B:ASP1930 4.0 12.3 1.0
O B:HOH3109 4.1 28.5 1.0
CB B:ASP1930 4.2 12.0 1.0
ND2 B:ASN1903 4.2 16.0 1.0
N B:ASN1903 4.3 16.9 1.0
OD1 B:ASP1904 4.3 26.1 1.0
C B:ASN1903 4.3 16.6 1.0
CG B:GLU1901 4.3 17.4 1.0
N B:ASP1904 4.4 18.3 1.0
OE2 B:GLU1899 4.4 14.6 1.0
O B:ASN1903 4.5 15.8 1.0
OD2 B:ASP1930 4.5 13.8 1.0
CA B:ASP1904 4.5 17.9 1.0
O B:HOH3088 4.5 44.2 1.0
CA B:ASN1903 4.6 15.5 1.0
CA B:ARG1929 4.6 11.4 1.0
CB B:ASN1903 4.7 15.0 1.0
CB B:ASP1904 4.7 19.9 1.0
N B:ARG1929 4.7 11.4 1.0
CB B:ASP1927 4.8 12.8 1.0
O B:HOH3067 4.8 28.1 1.0
CD2 B:LEU1923 5.0 15.6 1.0

Reference:

S.T.L.Philominathan, J.J.Wilson, O.Matsushita, J.Sakon. Induction of Stable Beta-Sheet By CA2+ in Clostridial Collagen Binding Domain To Be Published.
Page generated: Tue Jul 8 07:18:18 2025

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