Atomistry » Sodium » PDB 5yt7-5zo8 » 5yu1
Atomistry »
  Sodium »
    PDB 5yt7-5zo8 »
      5yu1 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy