Atomistry » Calcium » PDB 1nmb-1nxc » 1nqd
Atomistry »
  Calcium »
    PDB 1nmb-1nxc »
      1nqd »

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: Sat Dec 12 03:09:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy