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Sodium in PDB 5yu1: 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: 5yu1 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) 31.42 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.362, 64.537, 106.308, 90.00, 104.17, 90.00
R / Rfree (%) 16.6 / 19.9

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 5yu1). 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: 5yu1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5yu1

Go back to Sodium Binding Sites List in 5yu1
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:21.9
occ:1.00
 OD1 A:ASP300 2.8 16.6 1.0
O A:SER301 3.0 18.3 1.0
O A:GLY234 3.0 18.9 1.0
O A:ALA232 3.2 14.7 1.0
O A:HOH542 3.3 19.8 1.0
O A:HOH657 3.4 17.0 1.0
CA A:GLY265 3.5 13.3 1.0
N A:GLU266 3.7 16.4 1.0
C A:SER301 3.8 16.1 1.0
N A:SER301 3.9 14.2 1.0
C A:ALA232 4.0 13.0 1.0
CG A:ASP300 4.0 18.4 1.0
C A:GLY265 4.0 15.4 1.0
CB A:ALA235 4.1 15.8 1.0
C A:GLY234 4.1 18.1 1.0
CB A:ALA232 4.3 13.6 1.0
CG2 A:THR302 4.3 21.4 1.0
CG A:GLU266 4.5 17.6 1.0
C A:ASP300 4.5 13.6 1.0
C A:VAL233 4.5 12.0 1.0
CA A:SER301 4.5 15.0 1.0
O A:GLU264 4.6 19.6 1.0
O A:VAL233 4.6 12.5 1.0
N A:VAL233 4.6 14.3 1.0
N A:THR302 4.6 14.1 1.0
OD2 A:ASP300 4.7 17.9 1.0
CA A:ASP300 4.7 14.2 1.0
N A:GLY265 4.7 14.8 1.0
N A:GLY234 4.8 12.3 1.0
CA A:ALA232 4.8 9.8 1.0
CA A:ALA235 4.8 17.1 1.0
CA A:VAL233 4.8 13.1 1.0
CA A:GLU266 4.8 15.8 1.0
N A:ALA235 4.9 13.8 1.0
CA A:THR302 4.9 15.4 1.0
CB A:GLU266 5.0 17.7 1.0
CB A:ASP300 5.0 15.2 1.0
OE2 A:GLU266 5.0 23.5 1.0

Sodium binding site 2 out of 4 in 5yu1

Go back to Sodium Binding Sites List in 5yu1
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:26.3
occ:1.00
 OD1 B:ASP300 2.7 23.6 1.0
O B:SER301 2.9 17.5 1.0
O B:ALA232 3.1 15.9 1.0
O B:GLY234 3.1 20.6 1.0
O B:HOH604 3.3 20.5 1.0
O B:HOH545 3.4 18.9 1.0
CA B:GLY265 3.5 17.2 1.0
C B:SER301 3.8 17.1 1.0
N B:GLU266 3.8 17.5 1.0
N B:SER301 3.8 14.4 1.0
C B:ALA232 3.9 15.6 1.0
CG B:ASP300 3.9 20.9 1.0
C B:GLY265 4.1 19.8 1.0
CB B:ALA235 4.1 18.7 1.0
CB B:ALA232 4.2 15.2 1.0
C B:GLY234 4.2 17.2 1.0
CA B:SER301 4.4 15.3 1.0
C B:ASP300 4.4 16.5 1.0
CG2 B:THR302 4.5 23.2 1.0
CG B:GLU266 4.5 18.7 1.0
O B:GLU264 4.5 20.3 1.0
C B:VAL233 4.6 15.3 1.0
N B:VAL233 4.6 14.6 1.0
OD2 B:ASP300 4.6 21.1 1.0
N B:THR302 4.6 16.7 1.0
CA B:ASP300 4.6 15.0 1.0
O B:VAL233 4.6 15.8 1.0
N B:GLY265 4.7 17.7 1.0
CA B:ALA232 4.7 15.3 1.0
N B:GLY234 4.8 15.0 1.0
CA B:ALA235 4.8 15.7 1.0
CA B:VAL233 4.8 13.3 1.0
CB B:ASP300 4.9 17.2 1.0
CA B:THR302 4.9 15.6 1.0
N B:ALA235 4.9 14.8 1.0
CA B:GLU266 5.0 18.0 1.0

Sodium binding site 3 out of 4 in 5yu1

Go back to Sodium Binding Sites List in 5yu1
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:22.1
occ:1.00
 OD1 C:ASP300 2.8 17.0 1.0
O C:GLY234 2.9 14.8 1.0
O C:SER301 3.0 16.1 1.0
O C:ALA232 3.1 13.0 1.0
O C:HOH520 3.3 17.9 1.0
O C:HOH645 3.3 16.4 1.0
CA C:GLY265 3.6 14.4 1.0
N C:GLU266 3.6 14.3 1.0
C C:SER301 3.9 14.1 1.0
N C:SER301 3.9 10.8 1.0
C C:ALA232 3.9 11.3 1.0
CG C:ASP300 4.0 18.0 1.0
CB C:ALA235 4.0 13.8 1.0
C C:GLY265 4.0 13.7 1.0
C C:GLY234 4.0 14.2 1.0
CB C:ALA232 4.3 10.9 1.0
C C:VAL233 4.5 11.2 1.0
CA C:SER301 4.5 14.3 1.0
CG2 C:THR302 4.5 19.2 1.0
C C:ASP300 4.5 12.2 1.0
O C:GLU264 4.6 15.7 1.0
O C:VAL233 4.6 10.8 1.0
N C:VAL233 4.6 8.9 1.0
CG C:GLU266 4.6 20.0 1.0
N C:GLY234 4.7 11.9 1.0
N C:THR302 4.7 13.0 1.0
CA C:ALA235 4.7 15.3 1.0
CA C:ASP300 4.7 11.0 1.0
OD2 C:ASP300 4.7 17.5 1.0
N C:GLY265 4.8 13.3 1.0
CA C:ALA232 4.8 11.2 1.0
CA C:VAL233 4.8 11.4 1.0
N C:ALA235 4.8 12.7 1.0
CA C:GLU266 4.8 16.1 1.0
CB C:GLU266 5.0 20.0 1.0
CB C:ASP300 5.0 11.2 1.0
CA C:GLY234 5.0 9.8 1.0
CA C:THR302 5.0 14.0 1.0

Sodium binding site 4 out of 4 in 5yu1

Go back to Sodium Binding Sites List in 5yu1
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:22.5
occ:1.00
 OD1 D:ASP300 2.7 21.0 1.0
O D:SER301 2.9 17.6 1.0
O D:GLY234 3.0 15.2 1.0
O D:ALA232 3.2 17.2 1.0
O D:HOH649 3.3 16.4 1.0
O D:HOH536 3.3 21.2 1.0
CA D:GLY265 3.4 17.7 1.0
N D:GLU266 3.7 18.0 1.0
C D:SER301 3.8 18.2 1.0
CG D:ASP300 3.9 19.4 1.0
CB D:ALA235 3.9 15.4 1.0
C D:GLY265 4.0 18.9 1.0
N D:SER301 4.0 16.3 1.0
C D:ALA232 4.0 15.6 1.0
C D:GLY234 4.1 15.4 1.0
CG2 D:THR302 4.2 22.2 1.0
CB D:ALA232 4.4 15.6 1.0
O D:GLU264 4.5 19.1 1.0
OD2 D:ASP300 4.5 21.6 1.0
CA D:SER301 4.5 18.1 1.0
C D:VAL233 4.5 16.5 1.0
CG D:GLU266 4.6 18.1 1.0
O D:VAL233 4.6 15.0 1.0
N D:GLY265 4.6 15.3 1.0
C D:ASP300 4.6 18.2 1.0
N D:THR302 4.6 16.8 1.0
N D:VAL233 4.7 16.0 1.0
CA D:ALA235 4.7 17.6 1.0
CA D:ASP300 4.8 17.3 1.0
N D:GLY234 4.8 13.7 1.0
N D:ALA235 4.8 14.2 1.0
CA D:THR302 4.9 16.7 1.0
CA D:VAL233 4.9 13.9 1.0
CA D:ALA232 4.9 15.4 1.0
CA D:GLU266 4.9 20.6 1.0
CB D:ASP300 5.0 18.1 1.0
C D:GLU264 5.0 17.0 1.0
OE2 D:GLU266 5.0 22.7 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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