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Calcium in PDB 5uwl: Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A

Protein crystallography data

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl 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) 60.07 / 2.55
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 129.962, 129.962, 142.076, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24

Other elements in 5uwl:

The structure of Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A (pdb code 5uwl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A, PDB code: 5uwl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5uwl

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Calcium binding site 1 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:40.6
occ:1.00
 O A:LEU184 2.2 32.2 1.0
O A:GLY180 2.3 39.6 1.0
OE2 A:GLU205 2.3 36.4 1.0
OD2 A:ASP202 2.3 42.0 1.0
OD1 A:ASP179 2.4 42.7 1.0
O A:SER182 2.5 42.0 1.0
CG A:ASP202 3.3 43.9 1.0
C A:LEU184 3.4 34.0 1.0
C A:GLY180 3.5 42.6 1.0
CD A:GLU205 3.5 39.5 1.0
C A:SER182 3.6 42.3 1.0
CG A:ASP179 3.7 47.3 1.0
N A:GLY180 3.8 44.1 1.0
CB A:ASP202 4.0 39.3 1.0
N A:LEU184 4.0 35.5 1.0
N A:SER182 4.1 43.6 1.0
OD1 A:ASP202 4.2 46.6 1.0
C A:GLY183 4.2 33.3 1.0
C A:PRO181 4.3 48.4 1.0
CA A:LEU184 4.3 30.7 1.0
N A:ASP179 4.3 44.0 1.0
CA A:GLY180 4.3 39.9 1.0
OE1 A:GLU205 4.3 43.3 1.0
C A:ASP179 4.3 40.3 1.0
CG A:GLU205 4.3 34.9 1.0
OD2 A:ASP179 4.4 44.4 1.0
N A:LEU185 4.4 29.7 1.0
CA A:SER182 4.4 44.4 1.0
N A:PRO181 4.4 40.5 1.0
CA A:LEU185 4.5 35.5 1.0
CA A:PRO181 4.6 44.1 1.0
CA A:GLY183 4.6 33.0 1.0
N A:GLY183 4.6 39.9 1.0
CA A:ASP179 4.7 43.4 1.0
O A:GLY183 4.7 37.2 1.0
O A:PRO181 4.7 43.3 1.0
CB A:ASP179 4.8 40.7 1.0
CB A:LEU184 4.8 32.3 1.0
CB A:PHE178 5.0 42.7 1.0

Calcium binding site 2 out of 5 in 5uwl

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Calcium binding site 2 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:72.7
occ:1.00
 OD2 A:ASP128 2.3 46.3 1.0
O A:ASP203 2.5 41.2 1.0
O A:GLU205 2.6 47.9 1.0
OD1 A:ASP203 2.7 41.4 1.0
CG A:ASP128 3.0 44.2 1.0
OD1 A:ASP128 3.1 47.8 1.0
C A:ASP203 3.6 43.2 1.0
C A:GLU205 3.7 40.5 1.0
CG A:ASP203 3.7 44.1 1.0
OG1 A:THR126 3.9 42.0 1.0
CA A:ASP203 4.2 40.3 1.0
CA A:THR206 4.2 42.9 1.0
N A:THR206 4.3 40.5 1.0
CB A:ASP203 4.4 37.8 1.0
CB A:ASP128 4.5 43.2 1.0
CD1 A:TRP207 4.5 36.4 1.0
N A:GLU205 4.6 38.0 1.0
C A:ASP204 4.6 42.8 1.0
N A:ASP204 4.6 41.3 1.0
OD2 A:ASP203 4.7 50.1 1.0
CA A:GLU205 4.8 39.4 1.0
N A:TRP207 4.8 42.6 1.0
CA A:ASP204 4.8 43.8 1.0
OG1 A:THR206 4.9 47.0 1.0

Calcium binding site 3 out of 5 in 5uwl

Go back to Calcium Binding Sites List in 5uwl
Calcium binding site 3 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:62.5
occ:1.00
 O A:ASP162 2.0 40.4 1.0
O A:GLY196 2.3 55.6 1.0
O A:ASN194 2.3 63.6 1.0
O A:HOH406 2.8 44.5 1.0
OD1 A:ASP198 2.8 38.8 1.0
C A:ASP162 3.2 39.0 1.0
C A:GLY196 3.4 47.6 1.0
C A:ASN194 3.5 59.4 1.0
O A:ALA161 3.9 37.7 1.0
CG A:ASP198 3.9 44.2 1.0
CA A:ASP162 4.0 38.5 1.0
N A:ILE163 4.2 38.2 1.0
O A:GLY192 4.2 61.9 1.0
C A:TYR195 4.2 49.5 1.0
N A:GLY196 4.2 44.6 1.0
CA A:ASN194 4.2 69.9 1.0
O A:TYR195 4.3 46.5 1.0
N A:GLY197 4.3 40.5 1.0
CA A:ILE163 4.3 35.6 1.0
CA A:GLY196 4.3 43.8 1.0
CA A:GLY197 4.3 36.5 1.0
O A:HOH437 4.3 46.6 1.0
N A:ASP198 4.4 33.5 1.0
N A:ASN194 4.4 67.5 1.0
OD2 A:ASP198 4.5 40.1 1.0
N A:TYR195 4.5 51.2 1.0
N A:MET164 4.6 34.5 1.0
C A:GLY197 4.6 37.5 1.0
CA A:TYR195 4.7 56.2 1.0
C A:PRO193 4.8 64.5 1.0
CH2 A:TRP113 4.8 44.6 1.0
C A:ALA161 4.8 42.0 1.0
N A:ASP162 4.9 43.4 1.0
C A:ILE163 5.0 35.9 1.0
CG A:MET164 5.0 45.0 1.0

Calcium binding site 4 out of 5 in 5uwl

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Calcium binding site 4 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:70.5
occ:1.00
 O B:ASP203 2.3 51.5 1.0
O B:GLU205 2.4 54.5 1.0
OD2 B:ASP128 2.4 59.3 1.0
OD1 B:ASP203 2.6 48.4 1.0
CG B:ASP128 3.2 51.6 1.0
OD1 B:ASP128 3.2 44.9 1.0
C B:ASP203 3.3 49.2 1.0
CG B:ASP203 3.4 52.8 1.0
C B:GLU205 3.5 53.1 1.0
CA B:ASP203 3.8 49.0 1.0
CB B:ASP203 4.0 47.8 1.0
CA B:THR206 4.1 46.5 1.0
OG1 B:THR126 4.1 47.4 1.0
N B:THR206 4.2 50.5 1.0
OD2 B:ASP203 4.2 53.4 1.0
CD1 B:TRP207 4.3 46.5 1.0
N B:GLU205 4.4 45.3 1.0
N B:ASP204 4.5 46.2 1.0
C B:ASP204 4.5 48.0 1.0
CB B:ASP128 4.6 52.2 1.0
CA B:GLU205 4.6 46.0 1.0
N B:TRP207 4.7 45.4 1.0
OG1 B:THR206 4.7 54.7 1.0
CA B:ASP204 4.9 45.2 1.0
NE1 B:TRP207 4.9 45.8 1.0
O B:ASP204 4.9 54.1 1.0
C B:THR206 4.9 45.4 1.0

Calcium binding site 5 out of 5 in 5uwl

Go back to Calcium Binding Sites List in 5uwl
Calcium binding site 5 out of 5 in the Matrix Metalloproteinase-13 Complexed with Selective Inhibitor Compound (S)-17A


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)-17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:70.1
occ:1.00
 O B:GLY196 2.2 43.0 1.0
O B:ASP162 2.3 49.4 1.0
O B:ASN194 2.7 47.7 1.0
OD1 B:ASP198 2.7 46.8 1.0
C B:ASP162 3.3 52.1 1.0
C B:GLY196 3.4 46.1 1.0
C B:TYR195 3.7 46.0 1.0
C B:ASN194 3.8 46.1 1.0
CG B:ASP198 3.8 48.6 1.0
N B:GLY196 3.8 43.3 1.0
O B:TYR195 3.9 47.8 1.0
CA B:TYR195 4.0 44.9 1.0
N B:ASP198 4.1 44.4 1.0
CA B:GLY196 4.1 41.2 1.0
N B:ILE163 4.2 48.7 1.0
CA B:ASP162 4.2 52.1 1.0
O B:ALA161 4.3 57.0 1.0
N B:GLY197 4.3 45.8 1.0
CA B:ILE163 4.3 40.1 1.0
N B:TYR195 4.4 46.6 1.0
OD2 B:ASP198 4.5 49.2 1.0
CA B:GLY197 4.5 42.0 1.0
CH2 B:TRP113 4.5 60.1 1.0
C B:GLY197 4.5 42.0 1.0
O B:GLY192 4.7 57.4 1.0
N B:MET164 4.7 46.9 1.0
CA B:ASP198 4.8 41.2 1.0
CB B:ASP198 4.9 44.8 1.0
CA B:ASN194 5.0 51.8 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 12:15:20 2024

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