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Calcium in PDB 5b5o: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.75 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.409, 36.060, 95.948, 90.00, 131.09, 90.00
R / Rfree (%) 16.4 / 18.5

Other elements in 5b5o:

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine (pdb code 5b5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5b5o

Go back to Calcium Binding Sites List in 5b5o
Calcium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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 Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:10.7
occ:1.00
OE2 A:GLU205 2.2 20.5 1.0
O A:GLY180 2.3 11.6 1.0
O A:LEU184 2.3 12.7 1.0
OD2 A:ASP202 2.3 9.6 1.0
OD1 A:ASP179 2.3 11.3 1.0
O A:SER182 2.4 16.2 1.0
C A:LEU184 3.4 12.2 1.0
CG A:ASP202 3.5 9.0 1.0
CD A:GLU205 3.5 15.9 1.0
CG A:ASP179 3.5 13.2 1.0
C A:GLY180 3.5 12.2 1.0
C A:SER182 3.5 17.0 1.0
N A:LEU184 3.8 12.8 1.0
N A:SER182 3.9 17.3 1.0
C A:PRO181 4.0 18.5 1.0
OD2 A:ASP179 4.0 14.4 1.0
CA A:LEU184 4.1 13.6 1.0
N A:GLY180 4.1 11.3 1.0
CB A:ASP202 4.2 7.5 1.0
CG A:GLU205 4.2 13.9 1.0
C A:GLY183 4.3 14.8 1.0
CA A:SER182 4.3 18.1 0.5
C A:ASP179 4.3 13.1 1.0
CA A:SER182 4.3 17.9 0.5
OD1 A:ASP202 4.3 8.4 1.0
N A:ASP179 4.3 11.0 1.0
O A:PRO181 4.3 22.5 1.0
OE1 A:GLU205 4.4 14.4 1.0
CA A:PRO181 4.4 15.4 1.0
CB A:LEU184 4.4 14.5 1.0
N A:PRO181 4.4 14.4 1.0
CA A:GLY180 4.4 11.7 1.0
N A:GLY183 4.5 17.2 1.0
N A:LEU185 4.5 11.4 1.0
CA A:GLY183 4.6 15.1 1.0
CA A:ASP179 4.6 12.2 1.0
CB A:ASP179 4.7 13.0 1.0
O A:ASP179 4.7 13.7 1.0
CA A:LEU185 4.8 9.7 1.0
O A:GLY183 4.9 15.7 1.0

Calcium binding site 2 out of 4 in 5b5o

Go back to Calcium Binding Sites List in 5b5o
Calcium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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 Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:8.4
occ:1.00
O A:GLY196 2.3 7.9 1.0
O A:HOH425 2.3 10.8 1.0
O A:ASN194 2.3 11.5 1.0
O A:HOH483 2.4 10.5 1.0
O A:ASP162 2.4 8.6 1.0
OD1 A:ASP198 2.4 7.5 1.0
CG A:ASP198 3.4 7.0 1.0
C A:GLY196 3.5 8.1 1.0
C A:ASP162 3.5 8.0 1.0
C A:ASN194 3.5 11.7 1.0
OD2 A:ASP198 3.9 8.7 1.0
C A:TYR195 3.9 8.8 0.5
O A:TYR195 4.0 7.0 0.5
C A:TYR195 4.0 10.5 0.5
N A:GLY196 4.0 9.1 1.0
O A:ALA161 4.2 9.9 1.0
N A:ASP198 4.2 7.0 1.0
O A:TYR195 4.3 9.7 0.5
CA A:GLY196 4.3 8.5 1.0
CA A:ASP162 4.3 8.6 1.0
CA A:TYR195 4.3 10.6 0.5
O A:HOH421 4.3 19.6 1.0
CA A:TYR195 4.4 12.1 0.5
O A:HOH614 4.4 24.4 1.0
N A:TYR195 4.4 11.5 0.5
O A:GLY192 4.4 12.1 1.0
N A:TYR195 4.4 12.6 0.5
N A:GLY197 4.5 7.2 1.0
N A:ILE163 4.5 7.8 1.0
CA A:ASN194 4.5 14.6 1.0
N A:ASN194 4.5 13.5 1.0
CA A:GLY197 4.6 7.7 1.0
CB A:ASP198 4.6 7.6 1.0
C A:GLY197 4.7 6.1 1.0
O A:HOH424 4.7 14.0 1.0
N A:MET164 4.7 7.0 1.0
CA A:ILE163 4.7 6.9 1.0
CG A:MET164 4.7 8.1 1.0
CA A:ASP198 4.8 7.0 1.0
C A:PRO193 4.8 12.8 1.0
CH2 A:TRP113 4.9 13.2 1.0

Calcium binding site 3 out of 4 in 5b5o

Go back to Calcium Binding Sites List in 5b5o
Calcium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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 Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:10.7
occ:1.00
OE2 B:GLU205 2.3 16.1 1.0
OD2 B:ASP202 2.3 9.7 1.0
O B:LEU184 2.3 12.6 1.0
O B:GLY180 2.3 12.4 1.0
O B:SER182 2.3 14.4 1.0
OD1 B:ASP179 2.4 10.7 1.0
CG B:ASP202 3.4 8.1 1.0
C B:LEU184 3.4 11.1 1.0
C B:SER182 3.5 15.8 1.0
CD B:GLU205 3.5 13.9 1.0
C B:GLY180 3.5 13.3 1.0
CG B:ASP179 3.5 12.2 1.0
N B:SER182 3.8 15.4 1.0
N B:LEU184 3.9 11.1 1.0
C B:PRO181 4.0 15.5 1.0
OD2 B:ASP179 4.1 15.4 1.0
N B:GLY180 4.1 12.7 1.0
CA B:LEU184 4.1 11.2 1.0
CB B:ASP202 4.2 8.1 1.0
CA B:SER182 4.2 16.8 1.0
OE1 B:GLU205 4.3 14.6 1.0
C B:GLY183 4.3 12.2 1.0
N B:ASP179 4.3 11.4 1.0
OD1 B:ASP202 4.3 8.8 1.0
C B:ASP179 4.3 13.5 1.0
CA B:PRO181 4.4 14.2 1.0
CG B:GLU205 4.4 13.4 1.0
N B:PRO181 4.4 14.5 1.0
CA B:GLY180 4.4 13.3 1.0
O B:PRO181 4.4 17.1 1.0
N B:GLY183 4.5 14.2 1.0
N B:LEU185 4.5 9.8 1.0
CB B:LEU184 4.5 12.3 1.0
CA B:ASP179 4.6 11.9 1.0
CA B:GLY183 4.6 13.9 1.0
CB B:ASP179 4.7 13.0 1.0
CA B:LEU185 4.7 9.6 1.0
O B:ASP179 4.8 13.9 1.0
O B:GLY183 4.8 14.1 1.0

Calcium binding site 4 out of 4 in 5b5o

Go back to Calcium Binding Sites List in 5b5o
Calcium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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 Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:8.9
occ:1.00
O B:GLY196 2.3 9.6 1.0
O B:ASP162 2.3 8.3 1.0
O B:ASN194 2.3 10.5 1.0
O B:HOH460 2.4 10.4 1.0
O B:HOH441 2.4 10.7 1.0
OD1 B:ASP198 2.4 8.8 1.0
CG B:ASP198 3.4 8.8 1.0
C B:GLY196 3.5 9.1 1.0
C B:ASP162 3.5 8.9 1.0
C B:ASN194 3.5 11.1 1.0
C B:TYR195 3.8 10.0 1.0
O B:HOH418 3.9 15.0 1.0
OD2 B:ASP198 3.9 9.4 1.0
N B:GLY196 3.9 10.6 1.0
O B:TYR195 4.0 9.9 1.0
O B:ALA161 4.2 8.7 1.0
N B:ASP198 4.2 8.6 1.0
CA B:GLY196 4.2 10.5 1.0
CA B:ASP162 4.3 8.8 1.0
O B:HOH576 4.3 29.8 1.0
N B:TYR195 4.4 11.2 1.0
CA B:TYR195 4.4 11.3 1.0
O B:HOH581 4.4 40.6 1.0
CA B:ASN194 4.4 12.7 1.0
O B:GLY192 4.4 11.8 1.0
N B:ILE163 4.5 7.5 1.0
N B:GLY197 4.5 8.7 1.0
N B:ASN194 4.5 13.5 1.0
CB B:ASP198 4.6 8.3 1.0
CA B:ILE163 4.6 7.7 1.0
CA B:GLY197 4.6 9.1 1.0
N B:MET164 4.7 7.9 1.0
O B:HOH434 4.7 18.4 1.0
C B:GLY197 4.7 8.5 1.0
CA B:ASP198 4.8 7.9 1.0
C B:PRO193 4.8 13.9 1.0
CG B:MET164 4.9 8.6 1.0
CH2 B:TRP113 4.9 13.3 1.0
O B:PRO193 5.0 14.5 1.0

Reference:

H.Nara, A.Kaieda, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (Mmp)-13 Inhibitors with A 1,2,4-Triazol-3-Yl Moiety As A Zinc Binding Group Using A Structure-Based Design Approach J. Med. Chem. V. 60 608 2017.
ISSN: ISSN 1520-4804
PubMed: 27966948
DOI: 10.1021/ACS.JMEDCHEM.6B01007
Page generated: Sat Dec 12 05:18:17 2020

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