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Calcium in PDB 1cqr: Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution

Enzymatic activity of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution

All present enzymatic activity of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution, PDB code: 1cqr was solved by L.Chen, T.J.Rydel, F.Gu, C.M.Dunaway, S.Pikul, K.M.Dunham, B.L.Barnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.200, 79.100, 107.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26.6

Other elements in 1cqr:

The structure of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution (pdb code 1cqr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution, PDB code: 1cqr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1cqr

Go back to Calcium Binding Sites List in 1cqr
Calcium binding site 1 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


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 the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:21.4
occ:1.00
 OD2 A:ASP181 2.3 9.2 1.0
OE2 A:GLU184 2.3 11.7 1.0
O A:GLY159 2.3 15.6 1.0
O A:VAL163 2.3 14.6 1.0
OD1 A:ASP158 2.3 14.2 1.0
O A:GLY161 2.4 15.9 1.0
CG A:ASP181 3.3 8.9 1.0
CD A:GLU184 3.5 10.2 1.0
C A:VAL163 3.5 11.1 1.0
C A:GLY161 3.5 11.0 1.0
C A:GLY159 3.5 14.4 1.0
CG A:ASP158 3.5 10.4 1.0
N A:GLY161 3.9 10.0 1.0
CB A:ASP181 4.0 4.9 1.0
C A:PRO160 4.1 10.4 1.0
OE1 A:GLU184 4.1 8.2 1.0
N A:VAL163 4.1 11.3 1.0
N A:GLY159 4.2 14.0 1.0
OD1 A:ASP181 4.2 9.7 1.0
OD2 A:ASP158 4.2 14.6 1.0
CA A:GLY161 4.2 11.0 1.0
CA A:VAL163 4.3 10.4 1.0
N A:PRO160 4.4 14.1 1.0
C A:ASP158 4.4 14.1 1.0
CA A:PRO160 4.4 12.1 1.0
N A:LEU164 4.4 10.9 1.0
N A:ASP158 4.5 12.9 1.0
CG A:GLU184 4.5 9.5 1.0
CA A:GLY159 4.5 12.6 1.0
C A:ASN162 4.5 8.3 1.0
O A:PRO160 4.5 11.3 1.0
CA A:LEU164 4.6 10.2 1.0
N A:ASN162 4.6 10.1 1.0
CB A:ASP158 4.6 14.8 1.0
CA A:ASP158 4.7 12.9 1.0
CB A:VAL163 4.7 8.8 1.0
O A:ASP158 4.8 16.2 1.0

Calcium binding site 2 out of 6 in 1cqr

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Calcium binding site 2 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


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 the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1304

b:21.6
occ:1.00
 OD2 A:ASP107 2.4 10.8 1.0
O A:ASP182 2.4 11.9 1.0
OD1 A:ASP182 2.4 10.3 1.0
OD1 A:ASP107 2.4 16.2 1.0
O A:GLU184 2.4 14.4 1.0
O A:HOH43 2.4 21.2 1.0
O A:HOH6 2.4 10.8 1.0
CG A:ASP107 2.7 6.1 1.0
C A:ASP182 3.3 8.9 1.0
CG A:ASP182 3.4 8.0 1.0
C A:GLU184 3.5 10.8 1.0
CA A:ASP182 3.8 7.4 1.0
CB A:ASP182 4.0 8.4 1.0
OG1 A:THR105 4.2 8.8 1.0
CB A:ASP107 4.2 10.1 1.0
CA A:GLN185 4.3 12.6 1.0
N A:GLN185 4.3 12.3 1.0
CD1 A:TRP186 4.3 8.9 1.0
OD2 A:ASP182 4.3 11.2 1.0
N A:GLU184 4.4 13.1 1.0
N A:ASP183 4.4 9.2 1.0
C A:ASP183 4.6 11.6 1.0
CA A:GLU184 4.6 12.1 1.0
CA A:ASP183 4.7 10.5 1.0
OE1 A:GLN185 4.7 22.6 1.0
N A:TRP186 4.8 9.9 1.0
NE1 A:TRP186 4.9 5.7 1.0

Calcium binding site 3 out of 6 in 1cqr

Go back to Calcium Binding Sites List in 1cqr
Calcium binding site 3 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


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 the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1305

b:25.0
occ:1.00
 OD1 A:ASP177 2.3 8.1 1.0
O A:GLY173 2.3 15.6 1.0
O A:ASP141 2.3 13.2 1.0
O A:HOH59 2.3 5.4 1.0
O A:ASN175 2.4 15.3 1.0
O A:HOH33 2.4 12.1 1.0
CG A:ASP177 3.3 5.5 1.0
C A:ASP141 3.4 10.5 1.0
C A:GLY173 3.5 13.3 1.0
C A:ASN175 3.5 9.2 1.0
OD2 A:ASP177 3.7 5.7 1.0
C A:ILE174 4.0 12.4 1.0
N A:ASN175 4.0 10.9 1.0
O A:ALA140 4.0 12.8 1.0
CA A:ASP141 4.2 12.1 1.0
N A:GLY173 4.2 16.9 1.0
N A:ASP177 4.2 10.2 1.0
O A:ILE174 4.3 11.4 1.0
CA A:GLY173 4.3 14.6 1.0
CA A:ILE174 4.4 11.9 1.0
N A:ILE174 4.4 14.6 1.0
CA A:ASN175 4.4 13.1 1.0
N A:ILE142 4.4 14.3 1.0
N A:GLY176 4.4 10.2 1.0
O A:GLY171 4.5 18.0 1.0
CB A:ASP177 4.5 7.4 1.0
C A:GLY176 4.5 8.8 1.0
CA A:GLY176 4.5 8.6 1.0
O A:HOH58 4.5 23.5 1.0
C A:PRO172 4.6 18.1 1.0
N A:MET143 4.7 10.7 1.0
CA A:ILE142 4.7 12.9 1.0
CA A:ASP177 4.8 9.4 1.0
O A:HOH36 4.8 22.0 1.0
CG A:MET143 4.8 7.3 1.0
OE2 A:GLU139 4.9 42.7 1.0
O A:PRO172 4.9 16.8 1.0
C A:ALA140 5.0 10.4 1.0
CH2 A:TRP92 5.0 9.6 1.0

Calcium binding site 4 out of 6 in 1cqr

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Calcium binding site 4 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


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 the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2303

b:25.9
occ:1.00
 O B:GLY159 2.3 17.9 1.0
O B:VAL163 2.3 17.1 1.0
OD2 B:ASP181 2.3 17.0 1.0
OD1 B:ASP158 2.3 18.8 1.0
OE2 B:GLU184 2.3 23.9 1.0
O B:GLY161 2.3 23.7 1.0
CG B:ASP181 3.3 12.1 1.0
C B:VAL163 3.4 15.6 1.0
CD B:GLU184 3.5 21.4 1.0
C B:GLY159 3.5 16.2 1.0
C B:GLY161 3.5 21.9 1.0
CG B:ASP158 3.5 15.9 1.0
N B:VAL163 3.9 20.4 1.0
N B:GLY161 4.0 18.3 1.0
N B:GLY159 4.0 18.1 1.0
OE1 B:GLU184 4.1 22.1 1.0
CB B:ASP181 4.1 10.0 1.0
CA B:VAL163 4.1 17.6 1.0
OD2 B:ASP158 4.1 19.7 1.0
OD1 B:ASP181 4.2 13.0 1.0
C B:PRO160 4.2 19.0 1.0
C B:ASP158 4.2 19.7 1.0
N B:ASP158 4.3 19.1 1.0
C B:ASN162 4.3 21.6 1.0
CA B:GLY161 4.3 20.4 1.0
N B:PRO160 4.4 18.6 1.0
CA B:GLY159 4.4 16.9 1.0
CA B:PRO160 4.4 17.4 1.0
N B:LEU164 4.5 15.3 1.0
CB B:VAL163 4.5 16.7 1.0
N B:ASN162 4.5 22.8 1.0
CG B:GLU184 4.5 16.7 1.0
O B:PRO160 4.5 20.9 1.0
CA B:ASP158 4.6 18.8 1.0
CB B:ASP158 4.6 16.1 1.0
O B:ASP158 4.6 21.8 1.0
CA B:LEU164 4.8 13.1 1.0
O B:ASN162 4.8 22.3 1.0
CA B:ASN162 4.9 24.0 1.0

Calcium binding site 5 out of 6 in 1cqr

Go back to Calcium Binding Sites List in 1cqr
Calcium binding site 5 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2304

b:25.1
occ:1.00
 OD2 B:ASP107 2.3 18.0 1.0
O B:GLU184 2.3 14.1 1.0
O B:ASP182 2.4 17.9 1.0
OD1 B:ASP182 2.4 15.3 1.0
OD1 B:ASP107 2.4 16.4 1.0
O B:HOH62 2.4 28.2 1.0
O B:HOH34 2.4 12.8 1.0
CG B:ASP107 2.7 12.2 1.0
C B:ASP182 3.3 13.8 1.0
CG B:ASP182 3.4 8.9 1.0
C B:GLU184 3.5 14.0 1.0
CA B:ASP182 3.8 12.4 1.0
CB B:ASP182 4.1 7.2 1.0
OG1 B:THR105 4.1 10.3 1.0
CD1 B:TRP186 4.2 11.3 1.0
OE1 B:GLN185 4.2 40.3 1.0
CB B:ASP107 4.2 12.1 1.0
CA B:GLN185 4.3 18.3 1.0
N B:GLU184 4.3 17.6 1.0
N B:GLN185 4.3 15.9 1.0
O B:HOH32 4.3 28.3 1.0
OD2 B:ASP182 4.3 9.5 1.0
N B:ASP183 4.4 15.4 1.0
C B:ASP183 4.5 17.9 1.0
CA B:GLU184 4.6 16.0 1.0
CA B:ASP183 4.6 16.9 1.0
NE1 B:TRP186 4.7 11.4 1.0
N B:TRP186 4.8 14.7 1.0

Calcium binding site 6 out of 6 in 1cqr

Go back to Calcium Binding Sites List in 1cqr
Calcium binding site 6 out of 6 in the Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2305

b:23.4
occ:1.00
 O B:ASN175 2.3 16.4 1.0
O B:GLY173 2.3 17.9 1.0
OD1 B:ASP177 2.3 15.8 1.0
O B:ASP141 2.3 13.4 1.0
O B:HOH41 2.3 15.3 1.0
O B:HOH5 2.4 11.0 1.0
CG B:ASP177 3.4 13.1 1.0
C B:ASP141 3.4 12.5 1.0
C B:GLY173 3.5 16.5 1.0
C B:ASN175 3.5 14.1 1.0
OD2 B:ASP177 3.9 14.5 1.0
N B:ASN175 4.1 14.4 1.0
C B:ILE174 4.1 14.8 1.0
O B:ALA140 4.1 13.3 1.0
N B:GLY173 4.2 18.0 1.0
CA B:ASP141 4.2 13.2 1.0
N B:ASP177 4.2 11.4 1.0
O B:HOH78 4.2 26.2 1.0
C B:GLY176 4.3 12.3 1.0
CA B:GLY173 4.3 17.1 1.0
O B:ILE174 4.3 16.7 1.0
N B:GLY176 4.4 12.5 1.0
CA B:GLY176 4.4 11.4 1.0
N B:ILE174 4.4 15.0 1.0
O B:GLY171 4.4 14.7 1.0
CA B:ASN175 4.4 14.9 1.0
CA B:ILE174 4.4 14.5 1.0
N B:ILE142 4.5 12.3 1.0
CB B:ASP177 4.5 13.8 1.0
C B:PRO172 4.6 16.9 1.0
N B:MET143 4.7 11.7 1.0
CA B:ILE142 4.7 10.0 1.0
OE1 B:GLU139 4.7 52.1 1.0
CA B:ASP177 4.7 13.5 1.0
O B:HOH3 4.8 26.1 1.0
CG B:MET143 4.8 9.2 1.0
CH2 B:TRP92 4.8 9.7 1.0
O B:PRO172 4.9 18.6 1.0
O B:GLY176 4.9 12.5 1.0

Reference:

L.Chen, T.J.Rydel, F.Gu, C.M.Dunaway, S.Pikul, K.M.Dunham, B.L.Barnett. Crystal Structure of the Stromelysin Catalytic Domain at 2.0 A Resolution: Inhibitor-Induced Conformational Changes. J.Mol.Biol. V. 293 545 1999.
ISSN: ISSN 0022-2836
PubMed: 10543949
DOI: 10.1006/JMBI.1999.3147
Page generated: Thu Jul 11 07:07:36 2024

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