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Sodium in PDB 6lon: Crystal Structure of Hpsg

Protein crystallography data

The structure of Crystal Structure of Hpsg, PDB code: 6lon was solved by J.Liu, Y.Zhang, Z.Yuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.25 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.917, 219.401, 213.141, 90.00, 98.04, 90.00
R / Rfree (%) 14.3 / 17.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hpsg (pdb code 6lon). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Hpsg, PDB code: 6lon:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6lon

Go back to Sodium Binding Sites List in 6lon
Sodium binding site 1 out of 4 in the Crystal Structure of Hpsg


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 Hpsg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na916

b:20.7
occ:1.00
O B:THR472 2.3 18.4 1.0
O B:SER570 2.4 17.0 1.0
O B:LEU568 2.4 15.8 1.0
O B:HOH1067 2.4 19.9 1.0
O B:HOH1322 2.6 24.8 1.0
HA B:HIS569 3.4 22.2 1.0
HB B:THR472 3.4 17.5 1.0
C B:THR472 3.4 19.1 1.0
HD12 B:ILE573 3.5 26.0 1.0
HA B:TYR473 3.5 19.7 1.0
C B:SER570 3.6 18.1 1.0
C B:LEU568 3.6 18.4 1.0
HD11 B:ILE573 3.7 26.0 1.0
C B:HIS569 3.9 19.2 1.0
N B:SER570 4.0 19.2 1.0
HG23 B:THR474 4.0 19.8 1.0
CA B:HIS569 4.0 18.6 1.0
HD12 B:LEU568 4.0 15.4 1.0
CD1 B:ILE573 4.0 21.6 1.0
O B:HOH1075 4.0 34.2 1.0
HG13 B:ILE573 4.1 26.6 1.0
H B:SER570 4.1 23.1 1.0
CB B:THR472 4.2 14.6 1.0
N B:HIS569 4.3 15.7 1.0
O B:GLU571 4.3 20.0 1.0
HA B:GLU571 4.3 27.5 1.0
H B:THR474 4.3 22.1 1.0
CA B:THR472 4.3 16.5 1.0
CA B:TYR473 4.3 16.5 1.0
N B:TYR473 4.3 19.9 1.0
HA B:THR472 4.4 19.8 1.0
CA B:SER570 4.4 17.2 1.0
OG1 B:THR474 4.4 15.4 1.0
O B:HIS569 4.5 18.2 1.0
C B:GLU571 4.5 16.9 1.0
HA B:LEU568 4.5 20.7 1.0
HB2 B:SER570 4.5 24.2 1.0
HG B:LEU568 4.5 21.8 1.0
N B:GLU571 4.6 25.3 1.0
CG1 B:ILE573 4.6 22.2 1.0
CA B:GLU571 4.7 22.9 1.0
CA B:LEU568 4.7 17.3 1.0
N B:THR474 4.7 18.4 1.0
OD1 B:ASP578 4.7 19.2 1.0
HG1 B:THR472 4.7 21.9 1.0
CG2 B:THR474 4.8 16.6 1.0
HG21 B:THR474 4.8 19.8 1.0
CD1 B:LEU568 4.8 12.9 1.0
HD13 B:ILE573 4.9 26.0 1.0
HD11 B:LEU568 4.9 15.4 1.0
C B:TYR473 4.9 12.8 1.0
HG1 B:THR474 5.0 18.5 1.0

Sodium binding site 2 out of 4 in 6lon

Go back to Sodium Binding Sites List in 6lon
Sodium binding site 2 out of 4 in the Crystal Structure of Hpsg


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 Hpsg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na916

b:21.3
occ:1.00
O A:THR472 2.3 16.4 1.0
O A:SER570 2.3 18.2 1.0
O A:LEU568 2.4 18.8 1.0
O A:HOH1414 2.5 25.7 1.0
O A:HOH1148 2.6 19.9 1.0
HA A:HIS569 3.3 22.9 1.0
HD12 A:ILE573 3.3 27.9 1.0
C A:THR472 3.5 16.6 1.0
HA A:TYR473 3.5 22.7 1.0
HD11 A:ILE573 3.5 27.9 1.0
HB A:THR472 3.5 21.6 1.0
C A:SER570 3.5 18.1 1.0
C A:LEU568 3.6 14.4 1.0
O A:HOH1118 3.7 31.0 1.0
CD1 A:ILE573 3.9 23.2 1.0
C A:HIS569 3.9 15.4 1.0
N A:SER570 3.9 15.7 1.0
CA A:HIS569 3.9 19.1 1.0
HD12 A:LEU568 3.9 22.1 1.0
HG23 A:THR474 4.0 20.5 1.0
H A:SER570 4.0 18.9 1.0
HG13 A:ILE573 4.1 22.7 1.0
N A:HIS569 4.2 18.0 1.0
CA A:TYR473 4.3 18.9 1.0
CA A:SER570 4.3 18.6 1.0
H A:THR474 4.3 21.1 1.0
CB A:THR472 4.3 18.0 1.0
HA A:GLU571 4.3 27.1 1.0
N A:TYR473 4.3 18.0 1.0
CA A:THR472 4.4 17.0 1.0
O A:HOH1463 4.4 42.3 1.0
O A:HIS569 4.4 17.1 1.0
OG1 A:THR474 4.4 17.0 1.0
HA A:THR472 4.4 20.4 1.0
HB2 A:SER570 4.5 19.1 1.0
O A:GLU571 4.5 25.2 1.0
HA A:LEU568 4.5 24.0 1.0
HG A:LEU568 4.5 20.7 1.0
CG1 A:ILE573 4.5 18.9 1.0
N A:GLU571 4.5 19.6 1.0
C A:GLU571 4.6 20.8 1.0
HD13 A:ILE573 4.7 27.9 1.0
CA A:LEU568 4.7 20.0 1.0
CA A:GLU571 4.7 22.6 1.0
N A:THR474 4.7 17.6 1.0
HG1 A:THR472 4.7 22.8 1.0
CD1 A:LEU568 4.7 18.4 1.0
CG2 A:THR474 4.8 17.1 1.0
OD1 A:ASP578 4.8 19.3 1.0
HG21 A:THR474 4.8 20.5 1.0
HD11 A:LEU568 4.9 22.1 1.0
C A:TYR473 4.9 18.5 1.0
HG1 A:THR474 4.9 20.4 1.0
CB A:SER570 5.0 16.0 1.0

Sodium binding site 3 out of 4 in 6lon

Go back to Sodium Binding Sites List in 6lon
Sodium binding site 3 out of 4 in the Crystal Structure of Hpsg


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 Hpsg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na912

b:24.1
occ:1.00
O C:SER570 2.3 21.7 1.0
O C:THR472 2.3 18.8 1.0
O C:HOH1344 2.4 24.5 1.0
O C:LEU568 2.4 19.8 1.0
O C:HOH1102 2.5 22.3 1.0
HA C:HIS569 3.3 21.0 1.0
HD12 C:ILE573 3.4 22.4 1.0
HB C:THR472 3.4 22.5 1.0
C C:THR472 3.5 16.2 1.0
C C:SER570 3.5 19.8 1.0
HA C:TYR473 3.5 21.1 1.0
C C:LEU568 3.6 16.7 1.0
HD11 C:ILE573 3.8 22.4 1.0
C C:HIS569 3.9 17.6 1.0
N C:SER570 3.9 18.4 1.0
CA C:HIS569 3.9 17.5 1.0
CD1 C:ILE573 4.0 18.7 1.0
HD12 C:LEU568 4.1 21.0 1.0
H C:SER570 4.1 22.1 1.0
HG13 C:ILE573 4.1 29.4 1.0
HG23 C:THR474 4.2 25.0 1.0
N C:HIS569 4.2 16.7 1.0
HA C:GLU571 4.2 29.3 1.0
CB C:THR472 4.3 18.8 1.0
CA C:SER570 4.3 21.9 1.0
CA C:TYR473 4.3 17.6 1.0
CA C:THR472 4.3 22.5 1.0
N C:TYR473 4.4 15.6 1.0
HA C:THR472 4.4 27.0 1.0
O C:HIS569 4.4 19.7 1.0
H C:THR474 4.4 25.1 1.0
O C:GLU571 4.4 24.0 1.0
N C:GLU571 4.5 22.2 1.0
HG C:LEU568 4.5 20.2 1.0
OG1 C:THR474 4.5 19.2 1.0
HA C:LEU568 4.5 24.7 1.0
C C:GLU571 4.5 22.1 1.0
HB2 C:SER570 4.6 21.8 1.0
HG1 C:THR472 4.6 28.2 1.0
CA C:GLU571 4.6 24.4 1.0
CG1 C:ILE573 4.6 24.5 1.0
CA C:LEU568 4.7 20.6 1.0
OD1 C:ASP578 4.7 19.1 1.0
N C:THR474 4.8 20.9 1.0
CD1 C:LEU568 4.8 17.5 1.0
HD13 C:ILE573 4.8 22.4 1.0
HD11 C:LEU568 4.9 21.0 1.0
OG1 C:THR472 4.9 23.6 1.0
CG2 C:THR474 4.9 20.9 1.0
C C:TYR473 4.9 20.0 1.0
HG21 C:THR474 5.0 25.0 1.0

Sodium binding site 4 out of 4 in 6lon

Go back to Sodium Binding Sites List in 6lon
Sodium binding site 4 out of 4 in the Crystal Structure of Hpsg


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 Hpsg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na912

b:20.7
occ:1.00
O D:THR472 2.2 16.4 1.0
O D:LEU568 2.3 16.0 1.0
O D:SER570 2.4 18.6 1.0
O D:HOH1354 2.5 19.6 1.0
O D:HOH1195 2.5 20.8 1.0
HA D:HIS569 3.3 20.7 1.0
HD12 D:ILE573 3.4 24.7 1.0
C D:THR472 3.4 14.7 1.0
HB D:THR472 3.4 21.6 1.0
C D:LEU568 3.5 17.8 1.0
HA D:TYR473 3.5 20.3 1.0
C D:SER570 3.6 21.7 1.0
HD11 D:ILE573 3.7 24.7 1.0
C D:HIS569 3.9 17.3 1.0
CA D:HIS569 3.9 17.3 1.0
HG23 D:THR474 4.0 22.7 1.0
CD1 D:ILE573 4.0 20.6 1.0
O D:HOH1287 4.0 30.5 1.0
N D:SER570 4.0 18.1 1.0
HD12 D:LEU568 4.1 23.0 1.0
HG13 D:ILE573 4.2 25.4 1.0
H D:SER570 4.2 21.8 1.0
N D:HIS569 4.2 15.7 1.0
CB D:THR472 4.2 18.1 1.0
OG1 D:THR474 4.3 17.0 1.0
CA D:THR472 4.3 15.6 1.0
CA D:TYR473 4.3 17.0 1.0
H D:THR474 4.3 17.3 1.0
N D:TYR473 4.3 15.8 1.0
HA D:GLU571 4.3 29.2 1.0
HA D:THR472 4.3 18.6 1.0
HG D:LEU568 4.4 19.8 1.0
CA D:SER570 4.4 15.4 1.0
O D:GLU571 4.4 22.2 1.0
O D:HIS569 4.5 18.3 1.0
O D:HOH1449 4.5 37.6 1.0
HA D:LEU568 4.5 18.2 1.0
C D:GLU571 4.6 20.4 1.0
N D:GLU571 4.6 20.0 1.0
HB2 D:SER570 4.6 20.1 1.0
CG1 D:ILE573 4.7 21.1 1.0
CA D:LEU568 4.7 15.2 1.0
N D:THR474 4.7 14.4 1.0
CG2 D:THR474 4.7 18.9 1.0
CA D:GLU571 4.7 24.3 1.0
HG21 D:THR474 4.7 22.7 1.0
OD1 D:ASP578 4.8 16.1 1.0
HD13 D:ILE573 4.8 24.7 1.0
HG1 D:THR474 4.8 20.4 1.0
HG1 D:THR472 4.8 25.0 1.0
CD1 D:LEU568 4.8 19.1 1.0
C D:TYR473 4.9 14.6 1.0
HD11 D:LEU568 4.9 23.0 1.0

Reference:

J.Liu, Y.Zhang, Z.Yuchi, H.Zhao, Y.Wei, L.Lin, L.Teng, J.Yin, Q.Lu, J.Chen, Y.Zheng, Y.Li, R.Xu, W.Zhai, Y.Liu, Y.Liu, E.Ang. Two Radical-Dependent Mechanisms For Anaerobic Degradation of the Globally Abundant Organosulfur Compound Dihydroxypropanesulfonate Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2003434117
Page generated: Tue Dec 15 12:32:58 2020

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