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Calcium in PDB 1b8y: X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity

Enzymatic activity of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity

All present enzymatic activity of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity:
3.4.24.17;

Protein crystallography data

The structure of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity, PDB code: 1b8y was solved by A.G.Pavlovsky, M.G.Williams, Q.-Z.Ye, D.F.Ortwine, C.F.Purchase Ii, A.D.White, V.Dhanaraj, B.D.Roth, L.L.Johnson, D.Hupe, C.Humblet, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.970, 69.970, 77.670, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 21.4

Other elements in 1b8y:

The structure of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity (pdb code 1b8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity, PDB code: 1b8y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1b8y

Go back to Calcium Binding Sites List in 1b8y
Calcium binding site 1 out of 3 in the X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:14.3
occ:1.00
 O A:GLY159 2.4 13.6 1.0
OE2 A:GLU184 2.4 12.8 1.0
O A:VAL163 2.4 13.0 1.0
O A:GLY161 2.5 15.9 1.0
OD2 A:ASP181 2.5 13.7 1.0
OD1 A:ASP158 2.5 15.9 1.0
CG A:ASP181 3.4 13.1 1.0
C A:VAL163 3.5 12.9 1.0
C A:GLY159 3.6 13.0 1.0
CD A:GLU184 3.6 14.5 1.0
C A:GLY161 3.6 15.7 1.0
CG A:ASP158 3.7 19.3 1.0
N A:GLY161 3.9 13.9 1.0
CB A:ASP181 4.1 7.5 1.0
N A:VAL163 4.1 14.3 1.0
C A:PRO160 4.1 12.7 1.0
N A:GLY159 4.3 11.6 1.0
OD1 A:ASP181 4.3 13.4 1.0
OE1 A:GLU184 4.3 17.1 1.0
OD2 A:ASP158 4.3 22.1 1.0
C A:ASP158 4.3 14.7 1.0
CA A:VAL163 4.3 14.2 1.0
CA A:GLY161 4.4 14.4 1.0
N A:ASP158 4.4 14.9 1.0
CA A:PRO160 4.4 12.7 1.0
N A:PRO160 4.5 12.5 1.0
C A:ASN162 4.5 17.4 1.0
N A:LEU164 4.5 14.5 1.0
CA A:GLY159 4.5 11.2 1.0
CG A:GLU184 4.6 9.8 1.0
CA A:LEU164 4.6 12.1 1.0
O A:ASP158 4.6 16.1 1.0
O A:PRO160 4.6 14.5 1.0
N A:ASN162 4.7 16.3 1.0
CA A:ASP158 4.7 15.8 1.0
CB A:ASP158 4.8 15.5 1.0
CB A:VAL163 4.8 13.8 1.0
CA A:ASN162 4.9 18.9 1.0
O A:HOH451 4.9 18.7 1.0
O A:ASN162 5.0 19.4 1.0
CB A:ASN162 5.0 23.1 1.0

Calcium binding site 2 out of 3 in 1b8y

Go back to Calcium Binding Sites List in 1b8y
Calcium binding site 2 out of 3 in the X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.3
occ:1.00
 O A:ASP141 2.4 11.0 1.0
O A:ASN175 2.4 9.8 1.0
O A:GLY173 2.4 13.4 1.0
OD1 A:ASP177 2.5 13.7 1.0
O A:HOH404 2.5 13.3 1.0
O A:HOH403 2.6 13.9 1.0
CG A:ASP177 3.4 11.4 1.0
C A:ASP141 3.5 11.5 1.0
C A:ASN175 3.6 9.5 1.0
C A:GLY173 3.6 13.6 1.0
OD2 A:ASP177 3.7 9.9 1.0
O A:ALA140 4.0 13.3 1.0
N A:ASP177 4.1 11.4 1.0
C A:ILE174 4.2 14.6 1.0
CA A:ASP141 4.3 10.5 1.0
N A:ASN175 4.3 11.3 1.0
N A:GLY173 4.3 13.3 1.0
CA A:GLY176 4.3 9.8 1.0
C A:GLY176 4.4 11.4 1.0
O A:ILE174 4.4 15.8 1.0
N A:GLY176 4.4 9.5 1.0
O A:GLY171 4.5 12.5 1.0
CA A:GLY173 4.5 12.1 1.0
N A:ILE142 4.5 10.9 1.0
CA A:ASN175 4.5 10.5 1.0
N A:ILE174 4.6 13.1 1.0
CA A:ILE174 4.6 14.1 1.0
N A:MET143 4.6 10.7 1.0
CB A:ASP177 4.6 8.9 1.0
O A:HOH419 4.7 26.8 1.0
CA A:ILE142 4.7 10.9 1.0
C A:PRO172 4.7 13.4 1.0
CA A:ASP177 4.8 11.2 1.0
CG A:MET143 4.8 6.4 1.0
CH2 A:TRP92 5.0 11.4 1.0
C A:ALA140 5.0 12.6 1.0

Calcium binding site 3 out of 3 in 1b8y

Go back to Calcium Binding Sites List in 1b8y
Calcium binding site 3 out of 3 in the X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Non-Peptide Inhibitors: Implications For Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:40.5
occ:1.00
 O A:GLU184 2.5 17.3 1.0
O A:HOH401 2.5 24.9 1.0
OD2 A:ASP107 2.6 12.7 1.0
OD1 A:ASP182 2.6 12.9 1.0
O A:ASP182 2.7 11.2 1.0
OD1 A:ASP107 3.2 11.1 1.0
CG A:ASP107 3.3 11.7 1.0
C A:ASP182 3.3 10.8 1.0
CG A:ASP182 3.6 12.9 1.0
C A:GLU184 3.7 15.7 1.0
CA A:ASP182 3.7 8.7 1.0
O A:HOH480 3.7 39.6 1.0
O A:HOH402 3.9 30.9 1.0
OG1 A:THR105 4.0 7.1 1.0
CB A:ASP182 4.1 9.1 1.0
CD1 A:TRP186 4.3 8.8 1.0
N A:GLU184 4.3 11.9 1.0
N A:ASP183 4.3 10.2 1.0
CA A:GLN185 4.4 18.4 1.0
C A:ASP183 4.5 11.5 1.0
CA A:ASP183 4.5 10.7 1.0
N A:GLN185 4.6 17.2 1.0
OD2 A:ASP182 4.6 12.3 1.0
CA A:GLU184 4.6 12.7 1.0
CD A:PRO106 4.6 7.8 1.0
CB A:ASP107 4.7 9.6 1.0
NE1 A:TRP186 4.7 9.2 1.0
N A:TRP186 4.8 12.6 1.0

Reference:

A.G.Pavlovsky, M.G.Williams, Q.Z.Ye, D.F.Ortwine, C.F.Purchase Ii, A.D.White, V.Dhanaraj, B.D.Roth, L.L.Johnson, D.Hupe, C.Humblet, T.L.Blundell. X-Ray Structure of Human Stromelysin Catalytic Domain Complexed with Nonpeptide Inhibitors: Implications For Inhibitor Selectivity. Protein Sci. V. 8 1455 1999.
ISSN: ISSN 0961-8368
PubMed: 10422833
Page generated: Mon Jul 7 13:36:48 2025

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