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Sodium in PDB 1sed: Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis

Protein crystallography data

The structure of Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis, PDB code: 1sed was solved by Y.Kim, A.Joachimiak, E.Evdokimova, A.Savchenko, A.Edwards, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.784, 64.550, 64.503, 111.37, 107.19, 107.13
R / Rfree (%) 18.9 / 20.9

Other elements in 1sed:

The structure of Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis (pdb code 1sed). 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 Protein of Unknown Function Yhal From Bacillus Subtilis, PDB code: 1sed:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1sed

Go back to Sodium Binding Sites List in 1sed
Sodium binding site 1 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis


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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:37.6
occ:0.95
O A:GLY77 2.8 31.0 1.0
O A:HOH875 3.1 53.9 1.0
C2 A:GOL802 3.1 62.2 0.9
C3 A:GOL802 3.2 61.8 0.9
C1 A:GOL802 3.2 63.2 0.9
O3 A:GOL801 3.3 59.0 0.9
C2 A:GOL801 3.3 60.1 0.9
O A:HOH874 3.5 51.9 1.0
O3 A:GOL802 3.5 59.5 0.9
C3 A:GOL801 3.6 60.1 0.9
C1 A:GOL801 3.7 61.1 0.9
O1 A:GOL802 3.7 62.8 0.8
C A:GLY77 4.0 32.9 1.0
O1 A:GOL801 4.0 62.1 0.9
O2 A:GOL802 4.4 62.4 0.9
O2 A:GOL801 4.5 57.2 0.9
CA A:GLN78 4.7 32.5 1.0
CA A:GLY77 4.8 30.2 1.0
N A:GLN78 4.9 31.8 1.0

Sodium binding site 2 out of 3 in 1sed

Go back to Sodium Binding Sites List in 1sed
Sodium binding site 2 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis


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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:32.6
occ:0.95
O B:GLY77 2.7 32.7 1.0
O B:HOH869 2.9 56.5 1.0
O3 B:GOL803 3.1 58.7 0.9
O B:HOH880 3.1 53.7 1.0
O1 B:GOL804 3.1 62.0 0.9
C1 B:GOL804 3.2 63.1 0.9
C3 B:GOL804 3.3 61.6 0.9
C2 B:GOL803 3.3 60.8 0.9
C2 B:GOL804 3.4 61.9 0.9
C1 B:GOL803 3.6 61.3 0.9
O B:HOH882 3.7 58.5 1.0
C3 B:GOL803 3.7 60.3 0.9
O3 B:GOL804 3.7 60.8 0.9
O1 B:GOL803 3.9 62.5 0.9
C B:GLY77 3.9 34.8 1.0
O2 B:GOL803 4.6 59.6 0.9
CA B:GLN78 4.7 32.3 1.0
O2 B:GOL804 4.8 63.4 0.8
CA B:GLY77 4.8 30.6 1.0
N B:GLN78 4.8 32.7 1.0

Sodium binding site 3 out of 3 in 1sed

Go back to Sodium Binding Sites List in 1sed
Sodium binding site 3 out of 3 in the Crystal Structure of Protein of Unknown Function Yhal From Bacillus Subtilis


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 Protein of Unknown Function Yhal From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na506

b:35.3
occ:0.95
O C:GLY77 2.8 29.4 1.0
C2 C:GOL806 3.1 65.6 0.9
C2 C:GOL805 3.2 59.5 0.9
O3 C:GOL805 3.2 56.5 0.9
C1 C:GOL806 3.3 66.1 0.9
O C:HOH807 3.3 51.4 1.0
O C:HOH822 3.4 56.9 1.0
O3 C:GOL806 3.4 63.6 0.9
C3 C:GOL805 3.5 58.9 0.9
C1 C:GOL805 3.6 60.6 0.9
C3 C:GOL806 3.6 64.8 0.9
O1 C:GOL806 3.7 65.5 0.9
C C:GLY77 4.0 33.1 1.0
O1 C:GOL805 4.0 61.7 0.9
O2 C:GOL806 4.3 65.9 0.8
O2 C:GOL805 4.5 57.1 0.9
CA C:GLN78 4.7 33.1 1.0
N C:GLN78 4.9 31.1 1.0
CA C:GLY77 4.9 29.9 1.0

Reference:

Y.Kim, A.Joachimiak, E.Evdokimova, A.Savchenko, A.Edwards. The Crystal Structure of the Hypothetical Protein Yhai, APC1180 From Bacillus Subtilis To Be Published.
Page generated: Tue Dec 15 05:35:52 2020

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