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Calcium in PDB 1xud: Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xud was solved by C.K.Engel, K.U.Wendt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.022, 36.475, 95.060, 90.00, 130.41, 90.00
R / Rfree (%) 16.8 / 20.3

Other elements in 1xud:

The structure of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor (pdb code 1xud). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor, PDB code: 1xud:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1xud

Go back to Calcium Binding Sites List in 1xud
Calcium binding site 1 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1264

b:8.8
occ:1.00
 O A:LEU184 2.4 9.1 1.0
OD2 A:ASP202 2.4 6.1 1.0
O A:GLY180 2.4 10.5 1.0
OD1 A:ASP179 2.5 9.5 1.0
O A:SER182 2.6 11.4 1.0
OE2 A:GLU205 2.6 18.0 1.0
CG A:ASP202 3.5 7.5 1.0
CD A:GLU205 3.5 14.8 1.0
C A:LEU184 3.5 9.8 1.0
C A:SER182 3.6 14.7 1.0
C A:GLY180 3.6 11.8 1.0
CG A:ASP179 3.7 11.4 1.0
N A:LEU184 3.9 10.3 1.0
N A:SER182 3.9 14.1 1.0
CG A:GLU205 4.0 12.1 1.0
C A:PRO181 4.1 14.1 1.0
C A:GLY183 4.1 11.5 1.0
N A:GLY180 4.2 10.8 1.0
CA A:LEU184 4.2 10.5 1.0
N A:ASP179 4.3 8.6 1.0
CB A:ASP202 4.3 6.7 1.0
C A:ASP179 4.3 10.7 1.0
OD2 A:ASP179 4.3 11.0 1.0
CA A:SER182 4.3 15.7 1.0
OD1 A:ASP202 4.3 5.0 1.0
CA A:PRO181 4.4 14.2 1.0
N A:GLY183 4.4 13.3 1.0
OE1 A:GLU205 4.5 17.1 1.0
N A:PRO181 4.5 12.1 1.0
CA A:GLY180 4.5 10.7 1.0
CA A:GLY183 4.5 11.9 1.0
CB A:LEU184 4.6 13.0 1.0
O A:HOH2158 4.6 22.3 1.0
N A:LEU185 4.6 7.6 1.0
CA A:ASP179 4.6 9.4 1.0
O A:GLY183 4.6 10.4 1.0
O A:PRO181 4.6 14.5 1.0
O A:ASP179 4.7 11.2 1.0
CA A:LEU185 4.7 8.8 1.0
CB A:ASP179 4.7 10.2 1.0

Calcium binding site 2 out of 4 in 1xud

Go back to Calcium Binding Sites List in 1xud
Calcium binding site 2 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1265

b:20.0
occ:1.00
 O A:ASN194 2.5 13.2 1.0
O A:GLY196 2.5 9.3 1.0
O A:ASP162 2.5 9.1 1.0
OD1 A:ASP198 2.6 6.9 1.0
O A:HOH2098 2.7 15.6 1.0
O A:HOH2110 2.9 13.1 1.0
CG A:ASP198 3.5 8.2 1.0
C A:ASP162 3.6 7.2 1.0
C A:GLY196 3.6 9.4 1.0
C A:ASN194 3.7 14.2 1.0
C A:TYR195 3.7 11.3 1.0
N A:GLY196 3.8 10.2 1.0
OD2 A:ASP198 3.9 8.2 1.0
O A:TYR195 4.0 8.9 1.0
O A:HOH2120 4.0 14.6 1.0
CA A:TYR195 4.0 13.0 1.0
O A:ALA161 4.1 8.6 1.0
N A:ASP198 4.1 5.0 1.0
CA A:GLY196 4.3 9.5 1.0
CA A:ASP162 4.3 7.0 1.0
N A:TYR195 4.3 12.9 1.0
N A:ILE163 4.5 5.7 1.0
N A:GLY197 4.5 8.0 1.0
C A:GLY197 4.6 6.4 1.0
N A:MET164 4.6 6.6 1.0
CB A:ASP198 4.6 7.1 1.0
CA A:GLY197 4.6 7.9 1.0
CA A:ILE163 4.6 6.1 1.0
CA A:ASP198 4.7 6.3 1.0
O A:HOH2071 4.7 14.7 1.0
CG A:MET164 4.7 8.0 1.0
CA A:ASN194 4.8 13.8 1.0
O A:HOH2245 4.8 27.6 1.0
CH2 A:TRP113 4.8 7.9 1.0
O A:GLY192 4.8 9.9 1.0

Calcium binding site 3 out of 4 in 1xud

Go back to Calcium Binding Sites List in 1xud
Calcium binding site 3 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1264

b:14.0
occ:1.00
 O B:LEU184 2.4 14.4 1.0
O B:GLY180 2.5 13.7 1.0
OD2 B:ASP202 2.5 7.4 1.0
OD1 B:ASP179 2.6 14.8 1.0
OE1 B:GLU205 2.6 23.9 1.0
O B:SER182 2.6 20.7 1.0
C B:SER182 3.5 21.5 1.0
CG B:ASP202 3.5 8.7 1.0
C B:LEU184 3.6 13.5 1.0
CD B:GLU205 3.6 17.7 1.0
C B:GLY180 3.7 15.4 1.0
CG B:ASP179 3.7 16.4 1.0
N B:LEU184 3.8 14.2 1.0
N B:SER182 3.9 19.7 1.0
CG B:GLU205 4.0 14.9 1.0
C B:PRO181 4.1 18.3 1.0
C B:GLY183 4.1 15.8 1.0
N B:GLY180 4.2 14.3 1.0
CA B:LEU184 4.2 15.1 1.0
CB B:ASP202 4.2 6.7 1.0
CA B:SER182 4.3 21.6 1.0
N B:ASP179 4.3 11.7 1.0
C B:ASP179 4.3 15.0 1.0
OD2 B:ASP179 4.3 17.5 1.0
N B:GLY183 4.4 19.3 1.0
OD1 B:ASP202 4.4 5.7 1.0
CA B:PRO181 4.5 17.4 1.0
CB B:LEU184 4.5 15.5 1.0
O B:PRO181 4.5 20.4 1.0
CA B:GLY183 4.5 17.7 1.0
N B:PRO181 4.5 16.4 1.0
CA B:GLY180 4.6 15.3 1.0
OE2 B:GLU205 4.6 16.0 1.0
CA B:ASP179 4.6 14.0 1.0
O B:GLY183 4.6 17.0 1.0
N B:LEU185 4.6 12.2 1.0
O B:ASP179 4.7 15.4 1.0
CB B:ASP179 4.8 15.1 1.0
CA B:LEU185 4.8 11.5 1.0

Calcium binding site 4 out of 4 in 1xud

Go back to Calcium Binding Sites List in 1xud
Calcium binding site 4 out of 4 in the Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Matrix Metalloproteinase-13 Complexed with Non-Zinc Binding Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1265

b:18.6
occ:1.00
 O B:ASP162 2.5 10.7 1.0
O B:GLY196 2.6 12.9 1.0
OD1 B:ASP198 2.6 10.9 1.0
O B:ASN194 2.6 20.1 1.0
O B:HOH3074 2.7 17.7 1.0
O B:HOH3128 2.8 35.9 1.0
CG B:ASP198 3.4 9.7 1.0
C B:ASP162 3.6 10.6 1.0
C B:GLY196 3.6 11.5 1.0
C B:ASN194 3.7 20.0 1.0
C B:TYR195 3.8 15.0 1.0
OD2 B:ASP198 3.8 9.4 1.0
O B:TYR195 3.9 13.4 1.0
O B:ALA161 4.0 11.1 1.0
N B:GLY196 4.0 13.0 1.0
N B:ASP198 4.1 8.8 1.0
O B:HOH3176 4.1 35.0 1.0
O B:HOH3021 4.1 8.7 1.0
CA B:ASP162 4.3 11.2 1.0
CA B:TYR195 4.3 15.7 1.0
CA B:GLY196 4.3 10.8 1.0
N B:ILE163 4.5 9.4 1.0
N B:TYR195 4.5 17.8 1.0
N B:GLY197 4.5 11.0 1.0
CB B:ASP198 4.6 7.9 1.0
O B:GLY192 4.6 19.9 1.0
N B:MET164 4.6 7.7 1.0
C B:GLY197 4.6 10.6 1.0
CA B:ILE163 4.6 8.2 1.0
CA B:GLY197 4.6 10.6 1.0
CA B:ASP198 4.7 8.5 1.0
N B:ASN194 4.8 23.0 1.0
CA B:ASN194 4.8 22.6 1.0
O B:HOH3070 4.8 16.8 1.0
CG B:MET164 4.9 6.9 1.0
C B:PRO193 4.9 22.8 1.0
C B:ALA161 5.0 12.0 1.0

Reference:

C.K.Engel, B.Pirard, S.Schimanski, R.Kirsch, J.Habermann, O.Klingler, V.Schlotte, K.U.Weithmann, K.U.Wendt. Structural Basis For the Highly Selective Inhibition of Mmp-13. Chem.Biol. V. 12 181 2005.
ISSN: ISSN 1074-5521
PubMed: 15734640
DOI: 10.1016/J.CHEMBIOL.2004.11.014
Page generated: Tue Jul 8 03:36:43 2025

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