Calcium in PDB 4hpk: Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium Nitrate

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 Nitrate, PDB code: 4hpk was solved by S.T.L.Philominathan, J.J.Wilson, R.Bauer, O.Matsushita, J.Sakon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.61 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.866, 59.170, 48.800, 90.00, 100.77, 90.00
R / Rfree (%) 17.9 / 21

Other elements in 4hpk:

The structure of Crystal Structure of Clostridium Histolyticum Colg Collagenase Collagen-Binding Domain 3B at 1.35 Angstrom Resolution in Presence of Calcium Nitrate 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 Nitrate (pdb code 4hpk). 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 Nitrate, PDB code: 4hpk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4hpk

Go back to Calcium Binding Sites List in 4hpk
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 Nitrate


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 Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:8.2
occ:1.00
 O A:ARG929 2.3 8.5 1.0
OD2 A:ASP904 2.4 12.5 1.0
OD1 A:ASP930 2.4 7.8 1.0
OD1 A:ASN903 2.4 9.6 1.0
OD1 A:ASP927 2.4 9.0 1.0
OE2 A:GLU901 2.4 8.7 1.0
OE1 A:GLU901 2.6 11.4 1.0
CD A:GLU901 2.9 9.0 1.0
CG A:ASP927 3.4 7.6 1.0
C A:ARG929 3.5 8.5 1.0
CG A:ASP930 3.6 8.5 1.0
CG A:ASN903 3.6 9.2 1.0
CG A:ASP904 3.6 14.2 1.0
OD2 A:ASP927 3.6 8.5 1.0
CA A:CA1102 3.8 8.4 1.0
CA A:ASP930 3.9 7.4 1.0
O A:HOH1231 4.0 18.3 1.0
N A:ASP930 4.1 7.9 1.0
C A:ASN903 4.2 11.5 1.0
ND2 A:ASN903 4.3 10.2 1.0
N A:ASN903 4.3 12.1 1.0
CB A:ASP930 4.3 7.7 1.0
OD1 A:ASP904 4.3 17.6 1.0
N A:ASP904 4.4 13.2 1.0
CG A:GLU901 4.4 12.0 1.0
OE1 A:GLU899 4.4 11.0 1.0
O A:ASN903 4.5 11.2 1.0
O A:HOH1286 4.5 29.9 1.0
CA A:ASP904 4.5 14.5 1.0
OD2 A:ASP930 4.5 8.6 1.0
CA A:ASN903 4.6 10.8 1.0
CA A:ARG929 4.7 8.9 1.0
CB A:ASP904 4.7 14.6 1.0
N A:ARG929 4.7 8.6 1.0
CB A:ASN903 4.7 9.8 1.0
O A:HOH1232 4.7 18.4 1.0
CB A:ASP927 4.8 8.2 1.0
CD2 A:LEU923 5.0 9.5 1.0

Calcium binding site 2 out of 4 in 4hpk

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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 Nitrate


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 Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:8.4
occ:1.00
 OE2 A:GLU901 2.4 8.7 1.0
O A:SER922 2.4 8.1 1.0
OD2 A:ASP927 2.4 8.5 1.0
O A:HOH1205 2.4 11.9 1.0
OE2 A:GLU899 2.4 10.7 1.0
OD1 A:ASP930 2.5 7.8 1.0
OE1 A:GLU899 2.5 11.0 1.0
OD2 A:ASP930 2.6 8.6 1.0
CD A:GLU899 2.8 11.1 1.0
CG A:ASP930 2.8 8.5 1.0
CG A:ASP927 3.5 7.6 1.0
CD A:GLU901 3.5 9.0 1.0
C A:SER922 3.6 7.5 1.0
CA A:CA1101 3.8 8.2 1.0
OD1 A:ASP927 3.8 9.0 1.0
N A:SER922 4.0 8.5 1.0
O A:HOH1203 4.0 8.9 1.0
CG A:GLU901 4.2 12.0 1.0
OG A:SER922 4.2 11.0 1.0
CG A:GLU899 4.3 11.6 1.0
CB A:ASP930 4.3 7.7 1.0
CD2 A:LEU923 4.3 9.5 1.0
CA A:SER922 4.4 8.8 1.0
OE1 A:GLU901 4.5 11.4 1.0
O A:HOH1246 4.6 22.4 1.0
N A:LEU923 4.6 8.5 1.0
OD1 A:ASN903 4.6 9.6 1.0
CB A:ASP927 4.8 8.2 1.0
ND2 A:ASN903 4.8 10.2 1.0
CA A:LEU923 4.8 8.8 1.0
OH A:TYR1002 4.9 8.9 1.0
CB A:SER922 4.9 10.1 1.0
CG A:LEU923 5.0 9.7 1.0

Calcium binding site 3 out of 4 in 4hpk

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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 Nitrate


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 Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1101

b:10.5
occ:1.00
 O B:ARG929 2.3 9.6 1.0
OD1 B:ASN903 2.3 10.9 1.0
OD2 B:ASP904 2.3 12.0 1.0
OD1 B:ASP930 2.4 9.6 1.0
OE2 B:GLU901 2.4 11.1 1.0
OD1 B:ASP927 2.4 11.0 1.0
OE1 B:GLU901 2.6 13.0 1.0
CD B:GLU901 2.8 11.9 1.0
CG B:ASP927 3.4 11.0 1.0
C B:ARG929 3.4 9.6 1.0
CG B:ASN903 3.5 11.2 1.0
CG B:ASP930 3.6 9.6 1.0
CG B:ASP904 3.6 15.2 1.0
OD2 B:ASP927 3.6 11.7 1.0
CA B:CA1102 3.7 10.8 1.0
CA B:ASP930 3.8 9.1 1.0
O B:HOH1226 4.0 20.1 1.0
N B:ASP930 4.0 9.6 1.0
ND2 B:ASN903 4.2 12.2 1.0
C B:ASN903 4.3 14.8 1.0
N B:ASN903 4.3 15.0 1.0
CB B:ASP930 4.3 9.3 1.0
OD1 B:ASP904 4.3 18.2 1.0
N B:ASP904 4.3 15.7 1.0
CG B:GLU901 4.3 13.8 1.0
OE2 B:GLU899 4.4 12.2 1.0
O B:HOH1285 4.4 30.4 1.0
O B:ASN903 4.5 13.2 1.0
CA B:ASP904 4.5 16.0 1.0
OD2 B:ASP930 4.5 10.4 1.0
CA B:ASN903 4.6 14.4 1.0
CB B:ASP904 4.6 15.8 1.0
CA B:ARG929 4.7 10.3 1.0
CB B:ASN903 4.7 13.2 1.0
N B:ARG929 4.7 10.0 1.0
CB B:ASP927 4.8 10.8 1.0
O B:HOH1229 4.8 21.5 1.0

Calcium binding site 4 out of 4 in 4hpk

Go back to Calcium Binding Sites List in 4hpk
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 Nitrate


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 Nitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1102

b:10.8
occ:1.00
 OD2 B:ASP927 2.3 11.7 1.0
O B:SER922 2.3 9.9 1.0
OE2 B:GLU901 2.3 11.1 1.0
O B:HOH1204 2.4 13.2 1.0
OE1 B:GLU899 2.4 11.3 1.0
OD1 B:ASP930 2.5 9.6 1.0
OE2 B:GLU899 2.5 12.2 1.0
OD2 B:ASP930 2.6 10.4 1.0
CD B:GLU899 2.8 12.8 1.0
CG B:ASP930 2.8 9.6 1.0
CG B:ASP927 3.4 11.0 1.0
CD B:GLU901 3.5 11.9 1.0
C B:SER922 3.6 11.1 1.0
CA B:CA1101 3.7 10.5 1.0
OD1 B:ASP927 3.8 11.0 1.0
O B:HOH1210 4.0 14.5 1.0
N B:SER922 4.0 11.7 1.0
CG B:GLU901 4.1 13.8 1.0
OG B:SER922 4.3 18.2 1.0
CG B:GLU899 4.3 13.1 1.0
CB B:ASP930 4.3 9.3 1.0
CA B:SER922 4.3 12.7 1.0
CD2 B:LEU923 4.3 12.1 1.0
OE1 B:GLU901 4.5 13.0 1.0
N B:LEU923 4.6 10.9 1.0
O B:HOH1227 4.6 20.1 1.0
O B:HOH1278 4.6 29.9 1.0
OD1 B:ASN903 4.6 10.9 1.0
CB B:ASP927 4.7 10.8 1.0
CA B:LEU923 4.8 10.5 1.0
ND2 B:ASN903 4.8 12.2 1.0
O B:HOH1242 4.8 24.6 1.0
CG B:LEU923 4.9 10.2 1.0
OH B:TYR1002 4.9 11.6 1.0
CB B:SER922 5.0 14.7 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: Sat Dec 12 04:50:33 2020

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