Sodium 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

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

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:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na305 b:17.3 occ:1.00 O A:GLU205 2.4 13.1 1.0 OD2 A:ASP128 2.6 21.4 1.0 OD1 A:ASP203 2.9 13.1 1.0 O A:ASP203 3.0 10.9 1.0 CG A:ASP128 3.3 18.2 1.0 OD1 A:ASP128 3.4 22.3 1.0 C A:GLU205 3.6 10.3 1.0 C A:ASP203 3.6 9.1 1.0 O A:HOH432 3.7 30.2 1.0 OG1 A:THR126 3.8 9.2 1.0 CG A:ASP203 3.9 11.9 1.0 CA A:ASP203 4.1 8.7 1.0 N A:GLU205 4.3 10.2 1.0 CD1 A:TRP207 4.3 8.0 1.0 CA A:THR206 4.4 11.5 1.0 N A:THR206 4.4 10.6 1.0 CB A:ASP203 4.5 10.2 1.0 CD A:PRO127 4.5 8.5 1.0 N A:ASP204 4.5 8.5 1.0 C A:ASP204 4.6 10.2 1.0 CA A:GLU205 4.6 10.9 1.0 CB A:ASP128 4.6 12.8 1.0 CA A:ASP204 4.8 9.2 1.0 O A:HOH405 4.8 39.8 1.0 N A:TRP207 4.8 8.7 1.0 OD2 A:ASP203 4.9 12.8 1.0 NE1 A:TRP207 4.9 9.2 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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 B:Na305 b:11.0 occ:1.00 O B:GLU205 2.3 11.3 1.0 OD2 B:ASP128 2.5 18.6 1.0 O B:HOH536 2.5 21.2 1.0 OD1 B:ASP203 2.8 12.3 1.0 O B:ASP203 2.9 13.2 1.0 CG B:ASP128 3.2 18.1 1.0 OD1 B:ASP128 3.3 24.2 1.0 C B:GLU205 3.5 9.2 1.0 C B:ASP203 3.6 10.4 1.0 CG B:ASP203 3.9 10.4 1.0 OG1 B:THR126 4.0 8.6 1.0 CA B:ASP203 4.0 9.9 1.0 CA B:THR206 4.2 9.4 1.0 CD1 B:TRP207 4.2 8.6 1.0 N B:THR206 4.3 9.1 1.0 N B:GLU205 4.3 10.2 1.0 CB B:ASP203 4.4 10.9 1.0 N B:ASP204 4.5 8.6 1.0 O B:HOH476 4.6 30.1 1.0 CB B:ASP128 4.6 12.8 1.0 C B:ASP204 4.6 10.4 1.0 CA B:GLU205 4.6 9.8 1.0 CA B:ASP204 4.7 10.2 1.0 N B:TRP207 4.7 9.1 1.0 CD B:PRO127 4.7 8.2 1.0 NE1 B:TRP207 4.8 9.1 1.0 OD2 B:ASP203 4.9 13.2 1.0 OG1 B:THR206 4.9 13.7 1.0 C B:THR206 5.0 9.8 1.0

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