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Sodium in PDB 5ey5: Lbcats

Protein crystallography data

The structure of Lbcats, PDB code: 5ey5 was solved by F.Busch, C.Rajendran, S.Schlee, K.Heyn, R.Merkl, R.Sterner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.26 / 1.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.963, 162.996, 78.058, 90.00, 93.78, 90.00
R / Rfree (%) 17.8 / 23.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Lbcats (pdb code 5ey5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Lbcats, PDB code: 5ey5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5ey5

Go back to Sodium Binding Sites List in 5ey5
Sodium binding site 1 out of 3 in the Lbcats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lbcats within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:44.4
occ:1.00
 O B:HOH638 2.2 37.9 1.0
O B:TYR303 2.3 29.0 1.0
O B:GLY305 2.3 30.7 1.0
OG1 B:THR267 2.4 34.3 1.0
O B:HOH653 2.5 36.3 1.0
O B:GLY229 3.2 40.0 1.0
CB B:THR267 3.4 33.8 1.0
C B:TYR303 3.5 28.3 1.0
C B:GLY305 3.5 34.5 1.0
C B:PRO304 3.9 33.2 1.0
C B:GLY229 4.0 36.9 1.0
O B:ALA265 4.0 35.9 1.0
N B:GLY305 4.1 29.8 1.0
O B:PRO304 4.1 32.1 1.0
CG2 B:THR267 4.3 35.5 1.0
CA B:PRO304 4.3 31.9 1.0
N B:PRO304 4.3 28.9 1.0
CA B:GLY305 4.4 32.2 1.0
CA B:TYR303 4.4 28.4 1.0
CB B:TYR303 4.4 28.2 1.0
CB B:VAL306 4.5 32.1 1.0
N B:VAL306 4.5 29.4 1.0
N B:THR267 4.5 28.4 1.0
CA B:GLY229 4.6 34.2 1.0
CA B:THR267 4.6 31.8 1.0
CA B:VAL306 4.6 31.5 1.0
N B:TYR303 4.6 30.9 1.0
O B:LEU301 4.7 43.8 1.0
OE2 B:GLU253 4.8 50.9 1.0
CD2 B:TYR303 4.8 25.1 1.0
N B:GLY230 4.9 30.3 1.0
C B:ALA265 5.0 31.4 1.0

Sodium binding site 2 out of 3 in 5ey5

Go back to Sodium Binding Sites List in 5ey5
Sodium binding site 2 out of 3 in the Lbcats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lbcats within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:61.7
occ:1.00
 O D:PRO52 2.6 30.5 1.0
O D:GLY50 2.9 32.1 1.0
O B:GLY50 3.6 35.9 1.0
C D:PRO52 3.8 29.5 1.0
O B:PRO52 3.9 30.5 1.0
O B:HOH667 4.0 39.5 1.0
O D:HOH683 4.0 41.6 1.0
N D:PRO52 4.0 29.9 1.0
C D:GLY50 4.0 33.0 1.0
C D:ARG51 4.0 27.7 1.0
CD D:PRO52 4.2 26.6 1.0
O D:ARG51 4.3 31.2 1.0
CA D:PRO52 4.5 29.1 1.0
CA D:ARG51 4.6 28.0 1.0
O D:HOH635 4.7 43.7 1.0
C B:GLY50 4.7 33.4 1.0
CG D:PRO52 4.7 33.9 1.0
N D:ARG51 4.7 27.6 1.0
N D:THR53 4.8 31.3 1.0
CA D:GLY50 4.9 31.5 1.0
CA D:THR53 4.9 32.5 1.0

Sodium binding site 3 out of 3 in 5ey5

Go back to Sodium Binding Sites List in 5ey5
Sodium binding site 3 out of 3 in the Lbcats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lbcats within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:52.7
occ:1.00
 O D:HOH629 2.1 49.7 1.0
O D:TYR303 2.4 56.7 1.0
O D:GLY305 2.5 41.7 1.0
OG1 D:THR267 2.6 42.3 1.0
O D:GLY229 3.2 44.8 1.0
C D:TYR303 3.5 57.3 1.0
CB D:THR267 3.6 42.6 1.0
C D:GLY305 3.6 39.8 1.0
O D:ALA265 3.7 48.3 1.0
C D:GLY229 4.0 41.9 1.0
N D:GLY305 4.2 39.9 1.0
C D:PRO304 4.2 46.0 1.0
CA D:TYR303 4.3 52.1 1.0
N D:TYR303 4.3 54.0 1.0
CB D:TYR303 4.3 50.5 1.0
O D:HOH664 4.4 47.1 1.0
CA D:GLY305 4.4 41.8 1.0
O D:PRO304 4.4 44.6 1.0
O D:LEU301 4.4 60.0 1.0
CG2 D:THR267 4.5 43.2 1.0
CA D:GLY229 4.5 39.4 1.0
N D:PRO304 4.5 59.0 1.0
N D:THR267 4.5 49.1 1.0
N D:VAL306 4.6 34.7 1.0
CA D:PRO304 4.6 57.8 1.0
CB D:VAL306 4.7 40.1 1.0
C D:ALA265 4.7 46.5 1.0
CA D:THR267 4.7 45.7 1.0
CD2 D:TYR303 4.7 41.9 1.0
CA D:VAL306 4.8 41.3 1.0
N D:GLY230 4.9 34.3 1.0
CG D:TYR303 5.0 45.3 1.0

Reference:

R.Merkl, S.Schlee, K.Heyn. Lbcats To Be Published.
Page generated: Mon Oct 7 20:53:48 2024

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