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Sodium in PDB 5yu3: Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase

Enzymatic activity of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase

All present enzymatic activity of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase:
4.3.1.12;

Protein crystallography data

The structure of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase, PDB code: 5yu3 was solved by K.J.Min, H.J.Yoon, A.Matsuura, Y.H.Kim, H.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.25 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.529, 64.783, 106.858, 90.00, 104.20, 90.00
R / Rfree (%) 16.6 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase (pdb code 5yu3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase, PDB code: 5yu3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5yu3

Go back to Sodium Binding Sites List in 5yu3
Sodium binding site 1 out of 4 in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:17.3
occ:1.00
 O A:SER301 2.7 16.5 1.0
OD1 A:ASP300 2.8 17.1 1.0
O A:ALA232 2.8 15.4 1.0
O A:GLY234 3.0 21.3 1.0
O A:HOH553 3.1 23.1 1.0
O A:HOH733 3.6 24.8 1.0
C A:ALA232 3.6 15.1 1.0
C A:SER301 3.7 13.7 1.0
N A:SER301 3.7 14.9 1.0
CA A:GLY265 3.9 16.4 1.0
N A:GLU266 4.0 16.6 1.0
CG A:ASP300 4.0 18.2 1.0
C A:GLY234 4.1 20.0 1.0
C A:VAL233 4.1 15.2 1.0
CB A:ALA232 4.2 15.3 1.0
N A:VAL233 4.2 15.3 1.0
O A:VAL233 4.2 16.2 1.0
CB A:ALA235 4.3 20.0 1.0
CA A:SER301 4.3 14.7 1.0
C A:ASP300 4.3 16.4 1.0
CA A:VAL233 4.4 15.8 1.0
C A:GLY265 4.4 18.0 1.0
N A:GLY234 4.5 16.6 1.0
CG A:GLU266 4.5 17.0 1.0
CG2 A:THR302 4.5 18.3 1.0
CA A:ALA232 4.5 14.0 1.0
CA A:ASP300 4.5 15.4 1.0
N A:THR302 4.6 15.8 1.0
OE2 A:GLU266 4.8 21.8 1.0
OD2 A:ASP300 4.8 16.8 1.0
CA A:GLY234 4.9 16.9 1.0
CA A:ALA235 4.9 19.9 1.0
N A:ALA235 4.9 17.4 1.0
CB A:ASP300 4.9 15.3 1.0
CA A:THR302 4.9 14.6 1.0

Sodium binding site 2 out of 4 in 5yu3

Go back to Sodium Binding Sites List in 5yu3
Sodium binding site 2 out of 4 in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:18.9
occ:1.00
 O B:SER301 2.7 19.5 1.0
O B:ALA232 2.8 17.3 1.0
OD1 B:ASP300 2.8 20.4 1.0
O B:GLY234 3.0 21.5 1.0
O B:HOH524 3.1 21.8 1.0
O B:HOH685 3.5 27.1 1.0
C B:ALA232 3.6 15.8 1.0
C B:SER301 3.7 18.7 1.0
N B:SER301 3.8 15.2 1.0
CA B:GLY265 3.9 21.9 1.0
N B:GLU266 4.0 18.7 1.0
CG B:ASP300 4.1 20.1 1.0
CB B:ALA232 4.1 16.0 1.0
C B:GLY234 4.1 20.9 1.0
C B:VAL233 4.2 18.6 1.0
N B:VAL233 4.2 16.3 1.0
O B:VAL233 4.3 17.8 1.0
CB B:ALA235 4.3 20.9 1.0
CA B:SER301 4.3 15.8 1.0
C B:GLY265 4.4 22.8 1.0
C B:ASP300 4.4 18.0 1.0
CA B:VAL233 4.4 17.6 1.0
CA B:ALA232 4.5 16.2 1.0
CG B:GLU266 4.5 20.3 1.0
N B:GLY234 4.5 19.0 1.0
CG2 B:THR302 4.6 21.2 1.0
CA B:ASP300 4.6 17.1 1.0
N B:THR302 4.7 15.4 1.0
OE2 B:GLU266 4.7 21.9 1.0
OD2 B:ASP300 4.8 21.3 1.0
CA B:ALA235 4.9 20.9 1.0
O B:GLU264 4.9 28.6 1.0
CA B:GLY234 4.9 16.5 1.0
N B:ALA235 4.9 19.1 1.0
CB B:ASP300 5.0 17.6 1.0

Sodium binding site 3 out of 4 in 5yu3

Go back to Sodium Binding Sites List in 5yu3
Sodium binding site 3 out of 4 in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:10.5
occ:1.00
 O C:ALA232 2.6 11.8 1.0
O C:SER301 2.7 13.7 1.0
OD1 C:ASP300 2.8 15.1 1.0
O C:GLY234 2.9 18.7 1.0
O C:HOH640 3.0 16.7 1.0
C C:ALA232 3.5 11.1 1.0
O C:HOH728 3.6 26.1 1.0
C C:SER301 3.7 13.6 1.0
N C:SER301 3.7 11.1 1.0
N C:GLU266 3.9 17.0 1.0
C C:GLY234 4.0 15.8 1.0
C C:VAL233 4.0 12.3 1.0
CG C:ASP300 4.1 17.4 1.0
O C:VAL233 4.1 12.0 1.0
CA C:GLY265 4.1 18.5 1.0
N C:VAL233 4.1 10.7 1.0
CB C:ALA232 4.2 11.3 1.0
CA C:SER301 4.3 11.3 1.0
CA C:VAL233 4.3 10.8 1.0
C C:ASP300 4.3 12.7 1.0
N C:GLY234 4.3 12.5 1.0
CB C:ALA235 4.3 16.7 1.0
CA C:ALA232 4.4 10.9 1.0
C C:GLY265 4.5 17.1 1.0
CA C:ASP300 4.5 10.6 1.0
CG C:GLU266 4.6 23.6 1.0
N C:THR302 4.7 12.2 1.0
CA C:GLY234 4.7 11.3 1.0
CG2 C:THR302 4.8 17.3 1.0
N C:ALA235 4.8 12.8 1.0
CB C:GLU266 4.9 22.1 1.0
CA C:ALA235 4.9 15.7 1.0
OD2 C:ASP300 4.9 15.6 1.0
CA C:GLU266 4.9 19.7 1.0
CB C:ASP300 4.9 10.4 1.0
CB C:SER301 4.9 12.3 1.0
OE2 C:GLU266 5.0 17.4 1.0

Sodium binding site 4 out of 4 in 5yu3

Go back to Sodium Binding Sites List in 5yu3
Sodium binding site 4 out of 4 in the Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4- Diamino Butyric Acid By Lysine Cyclodeaminase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:18.3
occ:1.00
 O D:SER301 2.7 15.1 1.0
OD1 D:ASP300 2.8 16.7 1.0
O D:ALA232 2.9 16.0 1.0
O D:GLY234 2.9 18.2 1.0
O D:HOH541 3.1 22.4 1.0
O D:HOH681 3.7 21.9 1.0
C D:ALA232 3.7 14.6 1.0
C D:SER301 3.7 17.7 1.0
N D:SER301 3.8 15.2 1.0
CA D:GLY265 3.9 16.0 1.0
N D:GLU266 3.9 18.7 1.0
CG D:ASP300 4.0 17.3 1.0
C D:GLY234 4.0 17.8 1.0
C D:VAL233 4.2 15.2 1.0
CB D:ALA235 4.2 18.5 1.0
CB D:ALA232 4.2 14.9 1.0
O D:VAL233 4.3 15.8 1.0
N D:VAL233 4.3 15.5 1.0
C D:GLY265 4.4 16.6 1.0
CA D:SER301 4.4 15.0 1.0
CG2 D:THR302 4.4 18.8 1.0
CA D:VAL233 4.5 15.8 1.0
C D:ASP300 4.5 16.2 1.0
CG D:GLU266 4.5 18.1 1.0
N D:GLY234 4.5 14.2 1.0
CA D:ALA232 4.6 14.9 1.0
CA D:ASP300 4.6 15.4 1.0
N D:THR302 4.6 16.4 1.0
OD2 D:ASP300 4.7 18.0 1.0
OE2 D:GLU266 4.8 20.7 1.0
CA D:ALA235 4.8 17.6 1.0
N D:ALA235 4.9 14.8 1.0
CA D:GLY234 4.9 13.5 1.0
O D:GLU264 4.9 17.9 1.0
CA D:THR302 4.9 14.6 1.0
CB D:ASP300 5.0 14.7 1.0

Reference:

K.Min, H.J.Yoon, A.Matsuura, Y.H.Kim, H.H.Lee. Structural Basis For Recognition of L-Lysine, L-Ornithine, and L-2,4-Diamino Butyric Acid By Lysine Cyclodeaminase. Mol. Cells V. 41 331 2018.
ISSN: ISSN 0219-1032
PubMed: 29629557
DOI: 10.14348/MOLCELLS.2018.2313
Page generated: Tue Oct 8 01:26:17 2024

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