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Sodium in PDB 3of5: Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4

Enzymatic activity of Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4

All present enzymatic activity of Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4, PDB code: 3of5 was solved by J.S.Brunzelle, T.Skarina, E.Gordon, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.22 / 1.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.278, 93.177, 62.732, 90.00, 95.78, 90.00
R / Rfree (%) 16.9 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 (pdb code 3of5). 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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4, PDB code: 3of5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3of5

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Sodium binding site 1 out of 5 in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4


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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na600

b:50.8
occ:1.00
 O A:HOH429 2.2 35.7 1.0
O A:HOH339 2.2 35.9 1.0
O A:HOH290 2.5 39.8 1.0
O A:HIS126 2.6 15.3 1.0
C A:HIS126 3.7 15.8 1.0
O B:HOH282 4.2 32.0 1.0
O A:HOH312 4.3 38.6 1.0
CA A:HIS126 4.4 13.2 1.0
CB A:HIS126 4.5 14.9 1.0
OD2 A:ASP131 4.7 16.2 1.0
N A:THR127 4.7 12.8 1.0
CA A:THR127 4.9 10.8 1.0

Sodium binding site 2 out of 5 in 3of5

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Sodium binding site 2 out of 5 in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4


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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:35.8
occ:1.00
 OD1 A:ASN105 2.2 28.7 1.0
O A:HOH366 2.2 33.2 1.0
O A:ASP102 2.2 15.8 1.0
O A:HOH325 2.6 27.3 1.0
CG A:ASN105 2.9 38.6 1.0
ND2 A:ASN105 3.1 38.8 1.0
C A:ASP102 3.4 14.6 1.0
O A:HOH365 4.0 24.3 1.0
CA A:ASP102 4.0 13.2 1.0
O A:HOH369 4.0 36.0 1.0
CB A:ASP102 4.2 15.5 1.0
CB A:ASN105 4.2 21.4 1.0
N A:LYS103 4.5 11.8 1.0
N A:ASN105 4.6 14.1 1.0
CA A:LYS103 4.7 11.7 1.0
CA A:ASN105 4.9 15.4 1.0
CG A:ASP102 4.9 23.8 1.0
C A:LYS103 5.0 14.5 1.0

Sodium binding site 3 out of 5 in 3of5

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Sodium binding site 3 out of 5 in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4


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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na600

b:10.2
occ:1.00
 O B:ASP102 2.3 16.2 1.0
O B:HOH467 2.3 22.3 1.0
OD1 B:ASN105 2.4 18.4 1.0
OD1 B:ASP102 2.4 22.0 1.0
O B:HOH357 2.5 21.0 1.0
CG B:ASP102 3.3 24.2 1.0
C B:ASP102 3.3 17.0 1.0
CG B:ASN105 3.4 20.3 1.0
ND2 B:ASN105 3.8 19.8 1.0
CA B:ASP102 3.8 13.2 1.0
OD2 B:ASP102 4.0 26.4 1.0
CB B:ASP102 4.2 15.6 1.0
O B:HOH444 4.2 22.8 1.0
O B:HOH353 4.4 42.9 1.0
N B:LYS103 4.5 15.4 1.0
CB B:ASN105 4.7 17.9 1.0
NE2 B:GLN106 4.8 26.9 0.5
N B:ASN105 4.9 17.1 1.0
CA B:LYS103 4.9 15.0 1.0

Sodium binding site 4 out of 5 in 3of5

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Sodium binding site 4 out of 5 in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4


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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:14.6
occ:1.00
 OD1 B:ASN165 2.3 16.9 1.0
OD1 B:ASN162 2.3 18.1 1.0
O B:HOH337 2.4 21.4 1.0
O B:ASN162 2.4 11.6 1.0
O B:HOH360 2.4 17.6 1.0
C B:ASN162 3.3 12.2 1.0
CG B:ASN162 3.5 20.1 1.0
CG B:ASN165 3.5 16.3 1.0
CA B:ASN162 3.7 8.2 1.0
CA B:ASN165 3.9 11.0 1.0
O B:HOH404 4.0 23.5 1.0
N B:ASN165 4.1 10.8 1.0
CB B:ASN162 4.2 10.1 1.0
CB B:ASN165 4.3 9.6 1.0
ND2 B:ASN165 4.5 15.3 1.0
N B:ARG163 4.5 10.8 1.0
ND2 B:ASN162 4.5 25.7 1.0
O B:HOH243 4.6 36.3 1.0
O B:HOH427 4.6 47.4 1.0
O B:HOH409 4.6 29.0 1.0
O B:HOH324 4.8 14.6 1.0
O B:LEU161 4.9 11.0 1.0
CA B:ARG163 5.0 12.4 1.0

Sodium binding site 5 out of 5 in 3of5

Go back to Sodium Binding Sites List in 3of5
Sodium binding site 5 out of 5 in the Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4


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 A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:23.6
occ:1.00
 O B:HIS126 2.2 20.9 1.0
O B:HOH652 2.3 42.8 1.0
O B:HOH306 2.3 38.2 1.0
O B:HOH370 2.3 35.8 1.0
O B:HOH276 2.5 27.3 1.0
C B:HIS126 3.4 20.5 1.0
CA B:HIS126 4.2 19.0 1.0
O B:HOH289 4.3 44.2 1.0
N B:THR127 4.3 15.6 1.0
OD2 B:ASP131 4.4 18.9 1.0
CB B:HIS126 4.4 21.1 1.0
O A:HOH432 4.4 47.5 1.0
CA B:THR127 4.5 14.8 1.0
O B:HOH260 4.6 54.1 1.0
O A:HOH315 4.7 48.6 1.0
CG2 B:THR127 4.8 18.0 1.0
CD2 B:HIS126 4.9 26.2 1.0

Reference:

J.S.Brunzelle, T.Skarina, E.Gordon, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases. Crystal Structure of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4 To Be Published.
Page generated: Mon Oct 7 11:59:12 2024

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