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Sodium in PDB 7stt: Crystal Structure of Sulfatase From Pedobacter Yulinensis

Protein crystallography data

The structure of Crystal Structure of Sulfatase From Pedobacter Yulinensis, PDB code: 7stt was solved by A.O'malley, C.R.Schlachter, L.L.Grimes, J.J.Tomashek, A.L.Lee, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.37 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.62, 83.62, 116.052, 90, 90, 120
R / Rfree (%) 14.8 / 17.8

Other elements in 7stt:

The structure of Crystal Structure of Sulfatase From Pedobacter Yulinensis also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sulfatase From Pedobacter Yulinensis (pdb code 7stt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Sulfatase From Pedobacter Yulinensis, PDB code: 7stt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7stt

Go back to Sodium Binding Sites List in 7stt
Sodium binding site 1 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


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 Sulfatase From Pedobacter Yulinensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:22.9
occ:1.00
O A:PHE147 2.2 26.8 1.0
O A:PRO149 2.2 24.8 1.0
OD2 A:ASP145 2.3 26.1 1.0
O A:HOH1000 2.4 40.2 1.0
O A:HOH1022 2.5 46.3 1.0
OD1 A:ASP145 2.7 33.1 1.0
CG A:ASP145 2.8 25.9 1.0
C A:PRO149 3.3 24.2 1.0
C A:PHE147 3.4 23.5 1.0
N A:PRO149 4.0 26.2 1.0
C A:PHE148 4.1 25.7 1.0
N A:TYR150 4.1 22.4 1.0
CA A:TYR150 4.2 21.9 1.0
O A:HOH1013 4.2 43.5 1.0
CA A:PHE147 4.3 23.9 1.0
N A:SER151 4.3 21.1 1.0
CB A:ASP145 4.3 21.3 1.0
CA A:PRO149 4.3 25.5 1.0
N A:PHE147 4.3 22.1 1.0
N A:PHE148 4.4 23.9 1.0
O A:PHE148 4.4 25.4 1.0
CB A:PHE147 4.5 25.6 1.0
O A:HOH1144 4.5 36.2 1.0
CD A:PRO149 4.5 29.9 1.0
CA A:PHE148 4.6 23.8 1.0
CG A:PRO149 4.6 29.5 1.0
C A:TYR150 4.7 20.2 1.0

Sodium binding site 2 out of 3 in 7stt

Go back to Sodium Binding Sites List in 7stt
Sodium binding site 2 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


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 Sulfatase From Pedobacter Yulinensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:14.5
occ:1.00
O A:TYR92 2.2 16.3 1.0
OE1 A:GLU97 2.3 15.1 1.0
O A:PRO89 2.4 14.7 1.0
O A:HOH852 2.4 13.8 1.0
CD A:GLU97 3.1 15.9 1.0
OE2 A:GLU97 3.2 17.4 1.0
C A:TYR92 3.4 14.7 1.0
C A:PRO89 3.4 15.2 1.0
CA A:PRO89 3.8 14.4 1.0
CA A:VAL93 3.9 14.4 1.0
N A:VAL93 4.0 14.5 1.0
N A:THR94 4.1 14.9 1.0
CB A:PRO89 4.2 15.4 1.0
OG1 A:THR94 4.5 14.4 1.0
C A:VAL93 4.5 14.2 1.0
CG A:GLU97 4.5 15.6 1.0
CA A:TYR92 4.6 15.7 1.0
N A:TYR92 4.6 14.6 1.0
N A:THR90 4.6 15.6 1.0
CG2 A:THR94 4.7 14.4 1.0
ND1 A:HIS128 4.9 14.3 1.0

Sodium binding site 3 out of 3 in 7stt

Go back to Sodium Binding Sites List in 7stt
Sodium binding site 3 out of 3 in the Crystal Structure of Sulfatase From Pedobacter Yulinensis


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 Sulfatase From Pedobacter Yulinensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:23.7
occ:1.00
O A:THR83 2.3 13.4 1.0
O A:ASP80 2.4 15.0 1.0
OD1 A:ASP80 2.4 26.4 1.0
O A:HOH892 2.5 29.5 1.0
O A:HOH971 2.8 33.9 1.0
C A:ASP80 3.2 14.8 1.0
CA A:ASP80 3.5 15.4 1.0
CG A:ASP80 3.5 23.0 1.0
C A:THR83 3.5 13.1 1.0
CB A:ASP80 4.0 19.0 1.0
CG2 A:THR83 4.1 13.1 1.0
O A:HOH1070 4.2 34.5 1.0
N A:THR83 4.3 12.9 1.0
CA A:THR83 4.4 12.4 1.0
N A:GLU81 4.5 14.7 1.0
N A:ASP84 4.5 13.9 1.0
CA A:ASP84 4.6 14.0 1.0
OD2 A:ASP80 4.7 28.1 1.0
O A:HOH752 4.7 33.4 1.0
O A:HOH636 4.8 22.6 1.0
N A:ASP80 4.8 15.1 1.0
O A:HOH608 4.8 35.0 1.0
CB A:ASP117 4.9 17.7 1.0
CB A:THR83 4.9 12.5 1.0
CA A:GLU81 5.0 15.6 1.0

Reference:

C.R.Schlachter, A.O'malley, L.L.Grimes, J.J.Tomashek, M.Chruszcz, L.A.Lee. Purification, Characterization, and Structural Studies of A Sulfatase From Pedobacter Yulinensis . Molecules V. 27 2021.
ISSN: ESSN 1420-3049
PubMed: 35011319
DOI: 10.3390/MOLECULES27010087
Page generated: Wed Oct 9 09:01:47 2024

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