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Sodium in PDB 5yu4: 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: 5yu4 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) 44.63 / 2.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.077, 64.755, 106.861, 90.00, 104.14, 90.00
R / Rfree (%) 16.3 / 19.8

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 5yu4). 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: 5yu4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5yu4

Go back to Sodium Binding Sites List in 5yu4
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:32.8
occ:1.00
 O A:SER301 2.8 30.3 1.0
OD1 A:ASP300 2.8 29.2 1.0
O A:HOH592 3.1 31.3 1.0
O A:ALA232 3.1 28.4 1.0
O A:GLY234 3.2 35.2 1.0
O A:HOH644 3.2 37.0 1.0
CA A:GLY265 3.6 31.5 1.0
C A:SER301 3.7 27.8 1.0
N A:SER301 3.8 27.3 1.0
N A:GLU266 3.8 33.8 1.0
C A:ALA232 3.8 27.2 1.0
CG A:ASP300 3.9 31.1 1.0
C A:GLY265 4.1 34.4 1.0
CB A:ALA235 4.2 32.3 1.0
C A:GLY234 4.2 34.0 1.0
CG2 A:THR302 4.3 30.9 1.0
CB A:ALA232 4.3 27.9 1.0
CA A:SER301 4.4 31.1 1.0
C A:VAL233 4.4 31.2 1.0
C A:ASP300 4.4 29.9 1.0
N A:VAL233 4.4 29.7 1.0
O A:VAL233 4.4 30.3 1.0
N A:THR302 4.5 30.9 1.0
CA A:VAL233 4.6 29.8 1.0
CA A:ASP300 4.6 30.2 1.0
CG A:GLU266 4.6 28.4 1.0
OD2 A:ASP300 4.7 32.3 1.0
N A:GLY234 4.7 29.3 1.0
CA A:ALA232 4.7 29.8 1.0
O A:GLU264 4.8 31.2 1.0
N A:GLY265 4.8 27.6 1.0
CA A:THR302 4.9 29.2 1.0
CA A:ALA235 4.9 39.1 1.0
CB A:ASP300 4.9 29.6 1.0
N A:ALA235 5.0 35.8 1.0
CA A:GLU266 5.0 30.6 1.0

Sodium binding site 2 out of 4 in 5yu4

Go back to Sodium Binding Sites List in 5yu4
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:35.9
occ:1.00
 OD1 B:ASP300 2.7 32.3 1.0
O B:SER301 2.8 29.1 1.0
O B:ALA232 2.9 27.9 1.0
O B:GLY234 3.2 33.9 1.0
O B:HOH528 3.2 31.6 1.0
O B:HOH629 3.4 34.4 1.0
CA B:GLY265 3.7 31.4 1.0
C B:SER301 3.7 28.6 1.0
C B:ALA232 3.7 29.8 1.0
N B:SER301 3.8 29.1 1.0
N B:GLU266 3.9 32.2 1.0
CG B:ASP300 3.9 32.6 1.0
CB B:ALA232 4.1 25.7 1.0
CB B:ALA235 4.2 34.7 1.0
C B:GLY234 4.2 31.2 1.0
C B:GLY265 4.3 33.0 1.0
CA B:SER301 4.4 28.9 1.0
N B:VAL233 4.4 31.6 1.0
C B:VAL233 4.4 28.7 1.0
C B:ASP300 4.4 30.1 1.0
O B:VAL233 4.5 30.9 1.0
CG2 B:THR302 4.5 30.4 1.0
CG B:GLU266 4.5 31.7 1.0
CA B:ALA232 4.6 31.5 1.0
CA B:ASP300 4.6 28.8 1.0
CA B:VAL233 4.6 27.9 1.0
N B:THR302 4.6 28.4 1.0
OD2 B:ASP300 4.7 32.2 1.0
N B:GLY234 4.7 31.9 1.0
O B:GLU264 4.8 34.3 1.0
N B:GLY265 4.8 29.5 1.0
OE2 B:GLU266 4.9 32.8 1.0
CB B:ASP300 4.9 28.5 1.0
CA B:THR302 4.9 28.8 1.0
CA B:ALA235 5.0 38.2 1.0

Sodium binding site 3 out of 4 in 5yu4

Go back to Sodium Binding Sites List in 5yu4
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:27.4
occ:1.00
 OD1 C:ASP300 2.7 28.8 1.0
O C:SER301 2.8 25.8 1.0
O C:ALA232 2.9 22.9 1.0
O C:HOH557 3.0 29.9 1.0
O C:GLY234 3.2 30.2 1.0
O C:HOH641 3.5 34.2 1.0
C C:ALA232 3.7 23.5 1.0
C C:SER301 3.7 24.2 1.0
N C:GLU266 3.8 22.9 1.0
CA C:GLY265 3.8 24.0 1.0
N C:SER301 3.8 22.4 1.0
CG C:ASP300 4.0 29.4 1.0
CB C:ALA235 4.2 32.7 1.0
C C:GLY234 4.2 29.3 1.0
C C:GLY265 4.2 26.2 1.0
C C:VAL233 4.3 25.9 1.0
O C:VAL233 4.3 23.6 1.0
CB C:ALA232 4.3 20.3 1.0
N C:VAL233 4.3 21.2 1.0
C C:ASP300 4.4 24.8 1.0
CA C:SER301 4.4 22.7 1.0
CA C:VAL233 4.5 21.1 1.0
CG2 C:THR302 4.6 32.0 1.0
CA C:ASP300 4.6 26.8 1.0
CG C:GLU266 4.6 26.4 1.0
CA C:ALA232 4.6 22.7 1.0
N C:THR302 4.6 24.7 1.0
N C:GLY234 4.6 22.3 1.0
OD2 C:ASP300 4.7 23.9 1.0
O C:GLU264 4.9 28.3 1.0
CA C:GLU266 4.9 26.9 1.0
CB C:ASP300 4.9 24.5 1.0
OE2 C:GLU266 4.9 28.4 1.0
CA C:ALA235 4.9 35.4 1.0
CA C:THR302 5.0 25.4 1.0
CB C:GLU266 5.0 26.9 1.0
N C:ALA235 5.0 27.2 1.0

Sodium binding site 4 out of 4 in 5yu4

Go back to Sodium Binding Sites List in 5yu4
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:30.7
occ:1.00
 OD1 D:ASP300 2.7 29.1 1.0
O D:SER301 2.8 26.1 1.0
O D:GLY234 3.2 24.9 1.0
O D:HOH544 3.2 30.0 1.0
O D:ALA232 3.2 29.1 1.0
O D:HOH621 3.4 31.3 1.0
CA D:GLY265 3.5 28.8 1.0
C D:SER301 3.7 26.3 1.0
N D:GLU266 3.8 32.6 1.0
CG D:ASP300 3.9 30.5 1.0
N D:SER301 3.9 29.4 1.0
C D:ALA232 3.9 26.3 1.0
C D:GLY265 4.1 29.0 1.0
CB D:ALA235 4.1 27.6 1.0
C D:GLY234 4.2 27.9 1.0
CG2 D:THR302 4.2 29.7 1.0
CB D:ALA232 4.4 27.3 1.0
C D:VAL233 4.4 26.6 1.0
CA D:SER301 4.4 29.0 1.0
O D:VAL233 4.5 26.4 1.0
C D:ASP300 4.5 28.8 1.0
N D:VAL233 4.5 26.4 1.0
CG D:GLU266 4.5 29.6 1.0
OD2 D:ASP300 4.6 28.4 1.0
N D:THR302 4.6 24.3 1.0
O D:GLU264 4.6 29.8 1.0
CA D:VAL233 4.7 26.9 1.0
CA D:ASP300 4.7 30.8 1.0
N D:GLY265 4.7 28.0 1.0
N D:GLY234 4.8 27.1 1.0
CA D:ALA232 4.8 26.8 1.0
CA D:ALA235 4.9 32.6 1.0
CA D:THR302 4.9 27.7 1.0
CB D:ASP300 4.9 32.1 1.0
CA D:GLU266 5.0 32.5 1.0
N D:ALA235 5.0 26.5 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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