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Sodium in PDB 5wqj: Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1

Protein crystallography data

The structure of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1, PDB code: 5wqj was solved by Y.Suwanai, S.Toma-Fukai, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.26 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.355, 150.360, 54.307, 90.00, 110.09, 90.00
R / Rfree (%) 14 / 17.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 (pdb code 5wqj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1, PDB code: 5wqj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5wqj

Go back to Sodium Binding Sites List in 5wqj
Sodium binding site 1 out of 5 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


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 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:6.6
occ:1.00
 O A:SER250 2.2 7.0 1.0
O A:ASP273 2.3 6.5 1.0
O A:HIS74 2.4 6.9 1.0
OD1 A:ASP273 2.4 6.2 1.0
O A:ASP73 2.6 7.4 1.0
C A:HIS74 3.0 6.7 1.0
SD A:MET75 3.2 6.8 1.0
C A:ASP273 3.2 5.0 1.0
C A:SER250 3.3 5.7 1.0
CG A:ASP273 3.3 5.3 1.0
N A:MET75 3.6 6.2 1.0
CA A:MET75 3.7 5.7 1.0
C A:ASP73 3.8 7.1 1.0
CA A:ASP273 3.9 5.2 1.0
CA A:HIS74 3.9 7.3 1.0
O A:HOH482 4.0 6.4 1.0
NH1 A:ARG112 4.0 8.2 1.0
CB A:HIS74 4.1 6.7 1.0
OD2 A:ASP273 4.1 7.1 1.0
CA A:GLY251 4.1 6.6 1.0
CB A:ASP273 4.1 5.5 1.0
N A:GLY251 4.1 5.9 1.0
CG A:MET75 4.2 6.8 1.0
CA A:SER250 4.3 6.1 1.0
N A:HIS74 4.3 7.0 1.0
N A:GLY274 4.3 5.0 1.0
NH2 A:ARG112 4.3 8.7 1.0
CB A:SER250 4.4 8.6 1.0
CE A:MET75 4.5 8.7 1.0
CZ A:ARG112 4.6 7.1 1.0
CB A:MET75 4.6 6.1 1.0
CA A:GLY274 4.6 5.9 1.0
C A:MET75 4.8 6.5 1.0
C A:GLY274 4.8 5.4 1.0
O A:GLY274 4.9 6.0 1.0
C A:GLY251 4.9 6.5 1.0

Sodium binding site 2 out of 5 in 5wqj

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Sodium binding site 2 out of 5 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


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 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:18.5
occ:1.00
 O A:ARG197 2.4 20.9 1.0
O A:HOH572 2.4 34.4 1.0
O A:GLU195 2.4 15.6 1.0
O A:HOH517 2.5 15.6 1.0
O A:ILE200 2.5 14.2 1.0
C A:ARG197 3.4 20.3 1.0
C A:GLU195 3.5 15.0 1.0
C A:ILE200 3.7 12.7 1.0
CB A:GLU195 3.9 10.4 1.0
N A:ILE200 4.0 13.8 1.0
CA A:ASP198 4.0 20.6 1.0
CA A:GLU195 4.0 13.4 1.0
N A:ASP198 4.0 20.7 1.0
N A:GLU195 4.1 14.7 1.0
N A:ARG197 4.2 16.7 1.0
N A:GLY199 4.3 18.4 1.0
CA A:ILE200 4.4 12.2 1.0
C A:PRO196 4.4 15.1 1.0
OE2 A:GLU201 4.4 24.3 1.0
CA A:ARG197 4.4 17.8 1.0
OE1 A:GLU201 4.4 23.8 1.0
C A:ASP198 4.5 19.0 1.0
N A:PRO196 4.5 14.3 1.0
CB A:ILE200 4.6 10.8 1.0
O A:PRO196 4.6 19.9 1.0
CD A:GLU201 4.7 21.8 1.0
N A:GLU201 4.8 13.3 1.0
CA A:PRO196 4.8 14.8 1.0
C A:GLY199 5.0 15.1 1.0

Sodium binding site 3 out of 5 in 5wqj

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Sodium binding site 3 out of 5 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:13.9
occ:1.00
 N A:SER147 3.1 11.0 1.0
O A:HOH510 3.2 19.1 1.0
O A:HOH427 3.2 19.5 1.0
NH1 A:ARG46 3.3 13.8 1.0
CG A:ARG46 3.6 10.7 1.0
CD A:ARG46 3.7 15.8 1.0
CA A:LYS146 3.8 13.1 1.0
CB A:SER147 3.8 9.5 1.0
CB A:LYS146 3.8 14.8 1.0
C A:LYS146 4.0 12.1 1.0
CG A:LYS146 4.0 19.7 1.0
CA A:SER147 4.1 8.9 1.0
CD A:LYS146 4.3 19.1 1.0
CZ A:ARG46 4.3 14.2 1.0
NE A:ARG46 4.4 14.3 1.0
CD2 A:PHE49 4.5 9.3 1.0
O A:SER147 4.8 13.1 1.0
CE2 A:PHE49 4.9 9.4 1.0
O A:ARG46 4.9 10.5 1.0
C A:SER147 5.0 10.7 1.0
CB A:GLU50 5.0 10.6 1.0

Sodium binding site 4 out of 5 in 5wqj

Go back to Sodium Binding Sites List in 5wqj
Sodium binding site 4 out of 5 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:6.7
occ:1.00
 O B:SER250 2.2 6.6 1.0
O B:ASP273 2.3 6.2 1.0
O B:HIS74 2.4 6.5 1.0
OD1 B:ASP273 2.4 6.7 1.0
O B:ASP73 2.7 6.2 1.0
C B:HIS74 3.0 6.5 1.0
SD B:MET75 3.2 7.0 1.0
C B:SER250 3.3 5.8 1.0
C B:ASP273 3.3 4.9 1.0
CG B:ASP273 3.3 5.8 1.0
N B:MET75 3.6 6.2 1.0
CA B:MET75 3.7 6.5 1.0
C B:ASP73 3.8 5.8 1.0
CA B:ASP273 3.9 5.2 1.0
CA B:HIS74 3.9 6.8 1.0
CB B:HIS74 4.0 6.7 1.0
O B:HOH478 4.0 7.5 1.0
NH1 B:ARG112 4.1 8.0 1.0
OD2 B:ASP273 4.1 7.0 1.0
CB B:ASP273 4.1 5.5 1.0
N B:GLY251 4.1 6.0 1.0
CA B:GLY251 4.2 6.1 1.0
CG B:MET75 4.2 6.3 1.0
CA B:SER250 4.3 6.9 1.0
N B:GLY274 4.3 5.4 1.0
N B:HIS74 4.3 7.0 1.0
NH2 B:ARG112 4.3 8.6 1.0
CE B:MET75 4.5 7.5 1.0
CB B:MET75 4.5 6.7 1.0
CZ B:ARG112 4.5 7.4 1.0
CB B:SER250 4.6 7.8 1.0
CA B:GLY274 4.6 5.9 1.0
C B:MET75 4.8 6.8 1.0
C B:GLY274 4.8 5.0 1.0
O B:GLY274 4.9 5.6 1.0
C B:GLY251 5.0 6.3 1.0

Sodium binding site 5 out of 5 in 5wqj

Go back to Sodium Binding Sites List in 5wqj
Sodium binding site 5 out of 5 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:17.9
occ:1.00
 O B:GLU195 2.4 14.4 1.0
O B:HOH559 2.5 17.9 1.0
O B:ARG197 2.5 20.7 1.0
O B:ILE200 2.5 14.1 1.0
C B:GLU195 3.4 14.0 1.0
C B:ARG197 3.5 17.6 1.0
C B:ILE200 3.7 12.4 1.0
CB B:GLU195 3.9 11.9 1.0
N B:ILE200 4.0 12.7 1.0
CA B:GLU195 4.0 12.6 1.0
N B:GLU195 4.0 13.2 1.0
CA B:ASP198 4.1 20.3 1.0
N B:ARG197 4.1 17.4 1.0
N B:ASP198 4.1 19.4 1.0
N B:GLY199 4.2 19.2 1.0
CA B:ILE200 4.3 11.9 1.0
C B:PRO196 4.3 17.0 1.0
CA B:ARG197 4.4 17.9 1.0
C B:ASP198 4.5 20.4 1.0
N B:PRO196 4.5 14.8 1.0
OE2 B:GLU201 4.5 26.1 1.0
OE1 B:GLU201 4.6 30.4 1.0
CB B:ILE200 4.6 11.8 1.0
O B:PRO196 4.7 16.6 1.0
N B:GLU201 4.8 13.4 1.0
CD B:GLU201 4.8 24.6 1.0
CA B:PRO196 4.8 15.4 1.0
C B:GLY199 5.0 14.9 1.0

Reference:

K.Hanaoka, K.Sasakura, Y.Suwanai, S.Toma-Fukai, K.Shimamoto, Y.Takano, N.Shibuya, T.Terai, T.Komatsu, T.Ueno, Y.Ogasawara, Y.Tsuchiya, Y.Watanabe, H.Kimura, C.Wang, M.Uchiyama, H.Kojima, T.Okabe, Y.Urano, T.Shimizu, T.Nagano. Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-Producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-Site Cysteine Persulfide Sci Rep V. 7 40227 2017.
ISSN: ESSN 2045-2322
PubMed: 28079151
DOI: 10.1038/SREP40227
Page generated: Tue Oct 8 01:05:05 2024

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