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Calcium in PDB 5uwk: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A, PDB code: 5uwk was solved by A.B.Taylor, X.Cao, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.65 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.784, 57.155, 120.564, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.9

Other elements in 5uwk:

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A (pdb code 5uwk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A, PDB code: 5uwk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5uwk

Go back to Calcium Binding Sites List in 5uwk
Calcium binding site 1 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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 Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:17.2
occ:1.00
 O A:GLY180 2.2 20.4 1.0
OE2 A:GLU205 2.2 25.8 1.0
O A:LEU184 2.3 18.7 1.0
OD2 A:ASP202 2.3 15.7 1.0
OD1 A:ASP179 2.4 20.9 1.0
O A:SER182 2.4 23.7 1.0
CD A:GLU205 3.4 21.6 1.0
C A:GLY180 3.4 21.0 1.0
C A:LEU184 3.5 16.5 1.0
CG A:ASP202 3.5 14.9 1.0
CG A:ASP179 3.5 20.7 1.0
C A:SER182 3.5 24.3 1.0
N A:SER182 3.8 24.8 1.0
N A:LEU184 3.9 17.6 1.0
C A:PRO181 4.0 25.2 1.0
CG A:GLU205 4.1 19.4 1.0
N A:GLY180 4.1 19.3 1.0
OD2 A:ASP179 4.1 21.9 1.0
CA A:LEU184 4.2 17.1 1.0
C A:GLY183 4.2 21.6 1.0
C A:ASP179 4.2 20.9 1.0
CA A:SER182 4.3 26.5 1.0
N A:ASP179 4.3 17.8 1.0
OD1 A:ASP202 4.3 12.9 1.0
CB A:ASP202 4.3 12.8 1.0
N A:PRO181 4.3 24.2 1.0
OE1 A:GLU205 4.3 22.7 1.0
CA A:PRO181 4.3 24.7 1.0
CA A:GLY180 4.4 20.3 1.0
N A:GLY183 4.5 25.3 1.0
CB A:LEU184 4.5 18.4 1.0
O A:PRO181 4.6 27.4 1.0
N A:LEU185 4.6 15.3 1.0
CA A:ASP179 4.6 18.9 1.0
CA A:GLY183 4.6 21.4 1.0
O A:GLY183 4.6 22.9 1.0
O A:ASP179 4.6 22.3 1.0
CB A:ASP179 4.6 20.6 1.0
O A:HOH494 4.7 30.8 1.0
O A:HOH433 4.8 32.2 1.0
CA A:LEU185 4.8 15.5 1.0

Calcium binding site 2 out of 6 in 5uwk

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Calcium binding site 2 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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 Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:19.6
occ:1.00
 O A:HOH427 2.3 20.8 1.0
O A:HOH512 2.3 27.6 1.0
OD1 A:ASP203 2.4 21.1 1.0
OD2 A:ASP128 2.4 19.5 1.0
O A:GLU205 2.4 17.1 1.0
O A:ASP203 2.6 19.2 1.0
OD1 A:ASP128 2.8 23.6 1.0
CG A:ASP128 2.9 20.2 1.0
C A:ASP203 3.5 16.1 1.0
CG A:ASP203 3.5 18.2 1.0
C A:GLU205 3.6 15.9 1.0
CA A:ASP203 3.9 13.3 1.0
OG1 A:THR126 4.0 14.5 1.0
CB A:ASP203 4.1 16.6 1.0
CD1 A:TRP207 4.2 16.8 1.0
CA A:THR206 4.2 17.6 1.0
N A:THR206 4.3 19.1 1.0
N A:GLU205 4.4 14.4 1.0
CB A:ASP128 4.4 16.4 1.0
N A:ASP204 4.6 16.1 1.0
OD2 A:ASP203 4.6 16.2 1.0
NE1 A:TRP207 4.7 15.3 1.0
CA A:GLU205 4.7 18.4 1.0
C A:ASP204 4.7 13.8 1.0
N A:TRP207 4.7 16.0 1.0
CA A:ASP204 4.8 14.3 1.0
CD A:PRO127 5.0 15.5 1.0
OG1 A:THR206 5.0 23.5 1.0
C A:THR206 5.0 16.6 1.0

Calcium binding site 3 out of 6 in 5uwk

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Calcium binding site 3 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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 Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:16.0
occ:1.00
 O A:GLY196 2.2 17.3 1.0
O A:HOH466 2.3 16.3 1.0
O A:ASN194 2.3 16.6 1.0
O A:ASP162 2.4 16.0 1.0
OD1 A:ASP198 2.4 14.1 1.0
O A:HOH416 2.4 16.4 1.0
CG A:ASP198 3.4 15.8 1.0
C A:GLY196 3.4 17.0 1.0
C A:ASP162 3.5 15.5 1.0
C A:ASN194 3.6 18.6 1.0
OD2 A:ASP198 3.8 16.0 1.0
C A:TYR195 3.8 15.6 1.0
N A:GLY196 3.9 15.4 1.0
O A:TYR195 4.1 16.5 1.0
N A:ASP198 4.2 15.2 1.0
O A:HOH425 4.2 21.6 1.0
CA A:GLY196 4.2 17.7 1.0
O A:ALA161 4.2 16.4 1.0
CA A:TYR195 4.3 17.8 1.0
CA A:ASP162 4.3 15.1 1.0
O A:HOH548 4.4 52.4 1.0
O A:GLY192 4.4 18.9 1.0
N A:TYR195 4.4 18.0 1.0
N A:ASN194 4.4 21.3 1.0
N A:GLY197 4.4 16.1 1.0
CA A:ASN194 4.5 19.2 1.0
N A:ILE163 4.5 15.3 1.0
CB A:ASP198 4.6 12.2 1.0
CA A:GLY197 4.6 14.6 1.0
C A:GLY197 4.7 14.3 1.0
CA A:ILE163 4.7 14.2 1.0
N A:MET164 4.7 13.3 1.0
O A:HOH411 4.7 22.1 1.0
CA A:ASP198 4.8 15.0 1.0
C A:PRO193 4.8 19.6 1.0
CG A:MET164 4.8 15.4 1.0
CH2 A:TRP113 4.8 21.0 1.0

Calcium binding site 4 out of 6 in 5uwk

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Calcium binding site 4 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


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 Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:19.9
occ:1.00
 O B:GLY180 2.3 23.1 1.0
OE2 B:GLU205 2.3 26.1 1.0
O B:LEU184 2.3 23.3 1.0
OD2 B:ASP202 2.4 18.5 1.0
OD1 B:ASP179 2.4 20.5 1.0
O B:SER182 2.4 29.2 1.0
C B:LEU184 3.4 22.0 1.0
CD B:GLU205 3.5 22.8 1.0
C B:GLY180 3.5 23.6 1.0
CG B:ASP179 3.5 22.7 1.0
CG B:ASP202 3.5 18.1 1.0
C B:SER182 3.6 32.0 1.0
N B:LEU184 3.8 21.9 1.0
N B:SER182 3.9 33.0 1.0
CA B:LEU184 4.0 19.2 1.0
C B:PRO181 4.0 34.9 1.0
CG B:GLU205 4.1 19.7 1.0
OD2 B:ASP179 4.1 23.9 1.0
N B:GLY180 4.1 21.9 1.0
C B:GLY183 4.2 26.1 1.0
C B:ASP179 4.2 21.3 1.0
CA B:SER182 4.3 33.8 1.0
N B:ASP179 4.3 20.1 1.0
CB B:ASP202 4.3 15.6 1.0
O B:PRO181 4.4 36.8 1.0
OD1 B:ASP202 4.4 17.7 1.0
N B:PRO181 4.4 26.9 1.0
CA B:GLY180 4.4 22.3 1.0
CB B:LEU184 4.5 22.8 1.0
CA B:PRO181 4.5 27.2 1.0
OE1 B:GLU205 4.5 22.9 1.0
N B:GLY183 4.6 28.4 1.0
N B:LEU185 4.6 19.8 1.0
O B:GLY183 4.6 27.0 1.0
CA B:ASP179 4.6 21.4 1.0
O B:ASP179 4.6 22.6 1.0
CB B:ASP179 4.7 22.5 1.0
CA B:GLY183 4.7 27.2 1.0

Calcium binding site 5 out of 6 in 5uwk

Go back to Calcium Binding Sites List in 5uwk
Calcium binding site 5 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:23.3
occ:1.00
 O B:HOH424 2.2 22.0 1.0
O B:HOH523 2.3 28.5 1.0
O B:GLU205 2.4 20.5 1.0
OD2 B:ASP128 2.5 19.9 1.0
OD1 B:ASP203 2.5 22.8 1.0
O B:ASP203 2.7 20.0 1.0
OD1 B:ASP128 2.9 26.1 1.0
CG B:ASP128 3.0 22.7 1.0
C B:ASP203 3.5 16.4 1.0
C B:GLU205 3.6 20.7 1.0
CG B:ASP203 3.6 20.3 1.0
CA B:ASP203 3.9 16.2 1.0
OG1 B:THR126 4.0 16.3 1.0
CB B:ASP203 4.2 18.4 1.0
CA B:THR206 4.2 18.9 1.0
CD1 B:TRP207 4.2 17.7 1.0
N B:THR206 4.3 19.5 1.0
N B:GLU205 4.4 17.8 1.0
CB B:ASP128 4.5 19.9 1.0
N B:ASP204 4.5 15.9 1.0
CA B:GLU205 4.6 19.3 1.0
C B:ASP204 4.7 19.6 1.0
OD2 B:ASP203 4.7 17.7 1.0
N B:TRP207 4.7 19.0 1.0
NE1 B:TRP207 4.8 15.5 1.0
CA B:ASP204 4.8 17.6 1.0
OG1 B:THR206 5.0 26.8 1.0
CD B:PRO127 5.0 15.1 1.0
C B:THR206 5.0 19.3 1.0

Calcium binding site 6 out of 6 in 5uwk

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Calcium binding site 6 out of 6 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-10A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:16.1
occ:1.00
 O B:HOH458 2.3 16.8 1.0
O B:ASN194 2.3 21.0 1.0
O B:ASP162 2.3 16.1 1.0
O B:GLY196 2.4 16.5 1.0
OD1 B:ASP198 2.4 15.0 1.0
O B:HOH415 2.4 18.3 1.0
CG B:ASP198 3.4 14.4 1.0
C B:ASN194 3.5 21.2 1.0
C B:GLY196 3.5 17.5 1.0
C B:ASP162 3.5 15.8 1.0
C B:TYR195 3.8 19.3 1.0
OD2 B:ASP198 3.9 15.9 1.0
N B:GLY196 3.9 18.3 1.0
O B:TYR195 4.1 16.8 1.0
N B:ASP198 4.2 13.7 1.0
O B:ALA161 4.2 17.8 1.0
O B:HOH441 4.2 25.3 1.0
CA B:TYR195 4.2 21.6 1.0
CA B:GLY196 4.2 18.1 1.0
CA B:ASP162 4.3 14.1 1.0
N B:TYR195 4.3 21.5 1.0
O B:GLY192 4.4 20.3 1.0
N B:ASN194 4.4 22.9 1.0
CA B:ASN194 4.5 25.3 1.0
O B:HOH551 4.5 45.9 1.0
N B:ILE163 4.5 15.0 1.0
N B:GLY197 4.5 17.0 1.0
CB B:ASP198 4.6 14.9 1.0
O B:HOH411 4.7 19.8 1.0
CA B:GLY197 4.7 13.7 1.0
CA B:ILE163 4.7 13.6 1.0
N B:MET164 4.7 12.5 1.0
C B:GLY197 4.7 13.8 1.0
CG B:MET164 4.8 15.1 1.0
CA B:ASP198 4.8 15.4 1.0
C B:PRO193 4.8 23.7 1.0
CH2 B:TRP113 4.9 17.2 1.0
O B:PRO193 5.0 25.1 1.0

Reference:

J.Y.Choi, R.Fuerst, A.M.Knapinska, A.B.Taylor, L.Smith, X.Cao, P.J.Hart, G.B.Fields, W.R.Roush. Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J. Med. Chem. V. 60 5816 2017.
ISSN: ISSN 1520-4804
PubMed: 28653849
DOI: 10.1021/ACS.JMEDCHEM.7B00514
Page generated: Mon Jul 15 12:15:21 2024

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