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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

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:

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

Sodium Binding Sites:

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 5b5o

Go back to Sodium Binding Sites List in 5b5o
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 5b5o

Go back to Sodium Binding Sites List in 5b5o
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

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: Tue Dec 15 10:27:27 2020

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