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Calcium in PDB 1nqd: Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 Angstrom Resolution in Presence of Calcium

Enzymatic activity of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 Angstrom Resolution in Presence of Calcium

All present enzymatic activity of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 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 1.65 Angstrom Resolution in Presence of Calcium, PDB code: 1nqd was solved by J.J.Wilson, O.Matsushita, A.Okabe, J.Sakon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.867, 59.401, 48.572, 90.00, 98.73, 90.00
R / Rfree (%) 18.5 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 Angstrom Resolution in Presence of Calcium (pdb code 1nqd). 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 1.65 Angstrom Resolution in Presence of Calcium, PDB code: 1nqd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1nqd

Go back to Calcium Binding Sites List in 1nqd
Calcium binding site 1 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 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 1.65 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:12.9
occ:1.00
 OE2 A:GLU901 2.2 13.9 1.0
OD2 A:ASP927 2.3 13.0 1.0
O A:SER922 2.4 13.6 1.0
OE1 A:GLU899 2.5 16.0 1.0
OD1 A:ASP930 2.5 10.9 1.0
O A:HOH2066 2.5 16.6 1.0
OE2 A:GLU899 2.5 13.8 1.0
OD2 A:ASP930 2.6 13.1 1.0
CD A:GLU899 2.8 11.7 1.0
CG A:ASP930 2.9 8.2 1.0
CG A:ASP927 3.4 13.6 1.0
CD A:GLU901 3.4 16.9 1.0
C A:SER922 3.6 13.8 1.0
CA A:CA1010 3.7 13.2 1.0
OD1 A:ASP927 3.8 13.1 1.0
O A:HOH2010 4.0 14.3 1.0
N A:SER922 4.0 15.6 1.0
CG A:GLU901 4.1 20.2 1.0
CG A:GLU899 4.3 18.1 1.0
CB A:ASP930 4.3 9.8 1.0
OE1 A:GLU901 4.4 13.0 1.0
CA A:SER922 4.4 19.9 1.0
CD2 A:LEU923 4.5 11.4 1.0
O A:HOH2169 4.5 28.2 1.0
O A:HOH2058 4.5 29.1 1.0
OG A:SER922 4.5 12.5 0.7
OD1 A:ASN903 4.6 18.1 1.0
N A:LEU923 4.6 13.6 1.0
CB A:ASP927 4.7 11.0 1.0
ND2 A:ASN903 4.8 13.9 1.0
CA A:LEU923 4.8 9.8 1.0
OH A:TYR1002 4.8 13.7 1.0
CG A:LEU923 4.9 10.0 1.0

Calcium binding site 2 out of 4 in 1nqd

Go back to Calcium Binding Sites List in 1nqd
Calcium binding site 2 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 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 1.65 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1010

b:13.2
occ:1.00
 OD2 A:ASP904 2.3 17.8 1.0
O A:ARG929 2.3 10.5 1.0
OD1 A:ASP930 2.3 10.9 1.0
OD1 A:ASN903 2.3 18.1 1.0
OD1 A:ASP927 2.4 13.1 1.0
OE2 A:GLU901 2.5 13.9 1.0
OE1 A:GLU901 2.6 13.0 1.0
CD A:GLU901 2.9 16.9 1.0
CG A:ASP927 3.4 13.6 1.0
C A:ARG929 3.4 12.1 1.0
CG A:ASP930 3.5 8.2 1.0
CG A:ASP904 3.5 28.7 1.0
CG A:ASN903 3.6 11.0 1.0
OD2 A:ASP927 3.6 13.0 1.0
CA A:CA1009 3.7 12.9 1.0
CA A:ASP930 3.8 8.1 1.0
O A:HOH2065 4.0 20.4 1.0
N A:ASP930 4.0 7.2 1.0
OD1 A:ASP904 4.2 24.6 1.0
CB A:ASP930 4.2 9.8 1.0
N A:ASN903 4.2 17.8 1.0
C A:ASN903 4.2 15.1 1.0
ND2 A:ASN903 4.3 13.9 1.0
N A:ASP904 4.4 12.7 1.0
CG A:GLU901 4.4 20.2 1.0
O A:ASN903 4.4 12.2 1.0
OE1 A:GLU899 4.4 16.0 1.0
O A:HOH2094 4.4 27.6 1.0
OD2 A:ASP930 4.5 13.1 1.0
CA A:ASP904 4.5 13.6 1.0
CB A:ASP904 4.6 27.3 1.0
CA A:ARG929 4.6 10.9 1.0
CA A:ASN903 4.6 18.9 1.0
N A:ARG929 4.6 10.4 1.0
CB A:ASN903 4.7 10.9 1.0
CB A:ASP927 4.8 11.0 1.0
CD2 A:LEU923 4.9 11.4 1.0
O A:HOH2039 5.0 23.0 1.0

Calcium binding site 3 out of 4 in 1nqd

Go back to Calcium Binding Sites List in 1nqd
Calcium binding site 3 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 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 1.65 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1009

b:14.5
occ:1.00
 OD2 B:ASP927 2.4 14.9 1.0
OE2 B:GLU901 2.4 17.3 1.0
O B:SER922 2.4 14.7 1.0
O B:HOH2126 2.5 15.2 1.0
OD1 B:ASP930 2.5 13.9 1.0
OE1 B:GLU899 2.5 15.7 1.0
OE2 B:GLU899 2.5 14.8 1.0
OD2 B:ASP930 2.7 13.7 1.0
CG B:ASP930 2.9 12.6 1.0
CD B:GLU899 2.9 15.3 1.0
CG B:ASP927 3.5 16.6 1.0
CD B:GLU901 3.6 15.1 1.0
C B:SER922 3.6 16.3 1.0
CA B:CA1010 3.7 14.7 1.0
O B:HOH2013 3.9 17.4 1.0
OD1 B:ASP927 3.9 16.7 1.0
N B:SER922 4.0 12.7 1.0
CG B:GLU901 4.2 20.8 1.0
CB B:ASP930 4.4 12.5 1.0
CG B:GLU899 4.4 14.5 1.0
CA B:SER922 4.4 17.6 1.0
OG B:SER922 4.5 22.9 1.0
CD2 B:LEU923 4.5 15.1 1.0
OE1 B:GLU901 4.5 18.4 1.0
N B:LEU923 4.6 15.1 1.0
OD1 B:ASN903 4.7 14.9 1.0
O B:HOH2102 4.7 22.6 1.0
O B:HOH2076 4.7 27.4 1.0
CB B:ASP927 4.7 12.1 1.0
O B:HOH2158 4.8 33.0 1.0
ND2 B:ASN903 4.8 13.3 1.0
CA B:LEU923 4.8 10.5 1.0
OH B:TYR1002 4.8 15.3 1.0
CG B:LEU923 4.9 8.5 1.0

Calcium binding site 4 out of 4 in 1nqd

Go back to Calcium Binding Sites List in 1nqd
Calcium binding site 4 out of 4 in the Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.65 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 1.65 Angstrom Resolution in Presence of Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1010

b:14.7
occ:1.00
 OD1 B:ASN903 2.3 14.9 1.0
OE2 B:GLU901 2.4 17.3 1.0
OD1 B:ASP930 2.4 13.9 1.0
OD2 B:ASP904 2.4 17.8 1.0
O B:ARG929 2.5 16.7 1.0
OD1 B:ASP927 2.6 16.7 1.0
OE1 B:GLU901 2.7 18.4 1.0
CD B:GLU901 2.9 15.1 1.0
CG B:ASP927 3.4 16.6 1.0
CG B:ASN903 3.5 11.3 1.0
C B:ARG929 3.5 13.2 1.0
CG B:ASP930 3.6 12.6 1.0
OD2 B:ASP927 3.6 14.9 1.0
CG B:ASP904 3.6 25.5 1.0
CA B:CA1009 3.7 14.5 1.0
CA B:ASP930 3.9 14.6 1.0
O B:HOH2048 4.0 26.8 1.0
N B:ASP930 4.1 12.5 1.0
O B:HOH2188 4.2 36.0 1.0
ND2 B:ASN903 4.2 13.3 1.0
C B:ASN903 4.3 17.7 1.0
CB B:ASP930 4.3 12.5 1.0
OD1 B:ASP904 4.3 31.7 1.0
N B:ASN903 4.3 21.6 1.0
N B:ASP904 4.4 17.1 1.0
CG B:GLU901 4.4 20.8 1.0
OE1 B:GLU899 4.4 15.7 1.0
O B:ASN903 4.4 18.1 1.0
OD2 B:ASP930 4.6 13.7 1.0
CA B:ASP904 4.6 19.2 1.0
O B:HOH2052 4.6 25.0 1.0
CA B:ASN903 4.7 16.9 1.0
CB B:ASN903 4.7 15.6 1.0
N B:ARG929 4.7 10.4 1.0
CA B:ARG929 4.7 11.5 1.0
CB B:ASP904 4.7 17.6 1.0
CB B:ASP927 4.8 12.1 1.0

Reference:

J.J.Wilson, O.Matsushita, A.Okabe, J.Sakon. A Bacterial Collagen-Binding Domain with Novel Calcium-Binding Motif Controls Domain Orientation Embo J. V. 22 1743 2003.
ISSN: ISSN 0261-4189
PubMed: 12682007
DOI: 10.1093/EMBOJ/CDG172
Page generated: Mon Jul 7 17:38:25 2025

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