Atomistry » Calcium » PDB 2o8o-2ovu » 2o8o
Atomistry »
  Calcium »
    PDB 2o8o-2ovu »
      2o8o »

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

Last articles

Cl in 5J59
Cl in 5J5J
Cl in 5J57
Cl in 5J58
Cl in 5IZ0
Cl in 5J56
Cl in 5J4L
Cl in 5J48
Cl in 5J2Z
Cl in 5J3B
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy