Atomistry » Sodium » PDB 3ajn-3b1q » 3axg
Atomistry »
  Sodium »
    PDB 3ajn-3b1q »
      3axg »

Sodium in PDB 3axg: Structure of 6-Aminohexanoate-Oligomer Hydrolase

Protein crystallography data

The structure of Structure of 6-Aminohexanoate-Oligomer Hydrolase, PDB code: 3axg was solved by S.Negoro, N.Shibata, Y.Tanaka, K.Yasuhira, H.Shibata, H.Hashimoto, Y.H.Lee, S.Ohshima, R.Santa, K.Mochiji, Y.Goto, T.Ikegami, K.Nagai, D.Kato, M.Takeo, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.00
Space group I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.863, 214.446, 478.804, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of 6-Aminohexanoate-Oligomer Hydrolase (pdb code 3axg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of 6-Aminohexanoate-Oligomer Hydrolase, PDB code: 3axg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 1 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3005

b:32.7
occ:1.00
 O A:ASN35 2.2 26.1 1.0
O A:HOH1698 2.2 35.2 1.0
O A:PHE38 2.3 34.7 1.0
O A:HOH1817 2.4 33.4 1.0
C A:ASN35 3.3 25.6 1.0
C A:PHE38 3.5 35.2 1.0
CA A:ASP36 3.9 27.7 1.0
N A:ASP36 4.1 25.4 1.0
N A:PHE38 4.2 30.1 1.0
CG A:LEU40 4.3 29.4 1.0
N A:LEU40 4.3 35.4 1.0
C A:ASP36 4.3 29.5 1.0
O D:HOH2024 4.3 54.4 1.0
CA A:ASN35 4.3 25.7 1.0
CD1 A:LEU40 4.4 25.2 1.0
CA A:PHE38 4.4 32.4 1.0
N A:ASP39 4.4 36.4 1.0
CA A:ASP39 4.5 37.8 1.0
CB A:ASN35 4.6 29.4 1.0
O A:ASP36 4.6 30.7 1.0
O A:HOH1027 4.8 38.5 1.0
N A:ALA37 4.8 27.8 1.0
CB A:LEU40 4.9 29.3 1.0
O A:HOH947 4.9 31.4 1.0
C A:ASP39 5.0 37.5 1.0
CB A:PHE38 5.0 28.7 1.0

Sodium binding site 2 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 2 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na3001

b:28.2
occ:1.00
 O K:HOH1767 2.2 34.5 1.0
O K:ASN35 2.2 25.7 1.0
O K:HOH368 2.2 27.1 1.0
O K:PHE38 2.3 35.1 1.0
O K:HOH432 2.4 34.4 1.0
C K:ASN35 3.4 26.2 1.0
C K:PHE38 3.5 35.3 1.0
CD1 K:LEU40 4.1 27.1 1.0
CG K:LEU40 4.1 32.0 1.0
CA K:ASP36 4.1 28.1 1.0
N K:ASP36 4.2 27.0 1.0
N K:PHE38 4.2 32.7 1.0
N K:LEU40 4.3 33.8 1.0
CA K:ASN35 4.3 26.1 1.0
CA K:PHE38 4.4 33.8 1.0
C K:ASP36 4.4 29.4 1.0
N K:ASP39 4.4 35.6 1.0
CA K:ASP39 4.5 36.4 1.0
CB K:ASN35 4.5 28.1 1.0
O K:HOH833 4.6 40.2 1.0
O K:ASP36 4.7 29.1 1.0
O K:HOH366 4.8 24.4 1.0
CB K:LEU40 4.8 31.4 1.0
N K:ALA37 4.8 29.3 1.0
CB K:PHE38 5.0 30.4 1.0

Sodium binding site 3 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 3 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na3006

b:44.0
occ:1.00
 O L:HOH883 2.3 34.6 1.0
O L:ASN35 2.4 34.2 1.0
O L:HOH2527 2.4 48.4 1.0
O L:HOH1127 2.4 29.6 1.0
O L:PHE38 2.4 36.4 1.0
C L:ASN35 3.4 34.1 1.0
C L:PHE38 3.6 36.8 1.0
CG L:LEU40 4.1 31.5 1.0
O L:HOH2528 4.2 46.1 1.0
CA L:ASP36 4.2 37.0 1.0
N L:LEU40 4.2 34.5 1.0
N L:ASP36 4.3 34.5 1.0
CD1 L:LEU40 4.3 30.8 1.0
O K:HOH2526 4.3 39.6 1.0
CA L:ASN35 4.4 34.3 1.0
CA L:ASP39 4.4 37.2 1.0
N L:PHE38 4.4 35.8 1.0
N L:ASP39 4.4 36.0 1.0
CB L:ASN35 4.5 30.3 1.0
CA L:PHE38 4.5 36.0 1.0
C L:ASP36 4.6 37.8 1.0
O L:HOH2145 4.6 32.5 1.0
O L:HOH364 4.7 36.1 1.0
CB L:LEU40 4.7 30.2 1.0
O L:ASP36 4.8 39.2 1.0
C L:ASP39 4.9 35.7 1.0
CB L:PHE38 5.0 34.0 1.0

Sodium binding site 4 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 4 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na3003

b:32.1
occ:1.00
 O M:PHE38 2.2 26.2 1.0
O M:ASN35 2.3 22.9 1.0
O M:HOH1455 2.3 24.9 1.0
O M:HOH445 2.4 24.7 1.0
C M:PHE38 3.4 27.0 1.0
C M:ASN35 3.4 24.5 1.0
N M:PHE38 4.1 27.0 1.0
CG M:LEU40 4.1 26.1 1.0
CD1 M:LEU40 4.2 21.9 1.0
CA M:PHE38 4.2 25.7 1.0
CA M:ASP36 4.2 26.3 1.0
N M:ASP36 4.3 24.1 1.0
N M:LEU40 4.3 26.1 1.0
CA M:ASN35 4.4 22.9 1.0
O M:HOH2632 4.4 41.2 1.0
O M:HOH2165 4.4 46.8 1.0
N M:ASP39 4.4 28.3 1.0
C M:ASP36 4.5 27.6 1.0
CA M:ASP39 4.6 29.9 1.0
CB M:ASN35 4.6 20.9 1.0
O M:HOH477 4.7 21.5 1.0
O M:HOH398 4.7 21.2 1.0
CB M:PHE38 4.8 22.8 1.0
N M:ALA37 4.8 27.3 1.0
CB M:LEU40 4.8 23.7 1.0
O M:ASP36 4.9 29.7 1.0
C M:ASP39 5.0 28.1 1.0

Sodium binding site 5 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 5 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na3002

b:32.4
occ:1.00
 O N:HOH1382 2.2 25.7 1.0
O N:HOH402 2.2 20.8 1.0
O N:PHE38 2.3 28.0 1.0
O N:ASN35 2.3 22.1 1.0
O N:HOH2035 2.5 32.9 1.0
C N:ASN35 3.3 22.4 1.0
C N:PHE38 3.5 26.9 1.0
CD1 N:LEU40 4.0 23.7 1.0
CG N:LEU40 4.1 22.2 1.0
CA N:ASP36 4.1 25.0 1.0
N N:ASP36 4.1 23.5 1.0
N N:PHE38 4.1 27.2 1.0
CA N:ASN35 4.3 21.5 1.0
CA N:PHE38 4.3 26.1 1.0
N N:LEU40 4.4 28.1 1.0
C N:ASP36 4.4 26.7 1.0
O N:HOH531 4.4 23.0 1.0
CB N:ASN35 4.4 20.1 1.0
N N:ASP39 4.5 28.1 1.0
O N:ASP36 4.6 28.2 1.0
CA N:ASP39 4.6 30.6 1.0
O N:HOH467 4.7 26.6 1.0
CB N:LEU40 4.8 22.5 1.0
CB N:PHE38 4.8 28.9 1.0
N N:ALA37 4.9 26.9 1.0

Sodium binding site 6 out of 6 in 3axg

Go back to Sodium Binding Sites List in 3axg
Sodium binding site 6 out of 6 in the Structure of 6-Aminohexanoate-Oligomer Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of 6-Aminohexanoate-Oligomer Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na3004

b:34.6
occ:1.00
 O O:PHE38 2.3 27.9 1.0
O O:HOH821 2.3 24.5 1.0
O O:ASN35 2.4 25.8 1.0
O O:HOH1789 2.5 38.8 1.0
C O:PHE38 3.5 28.3 1.0
C O:ASN35 3.5 27.5 1.0
CA O:ASP36 4.1 29.8 1.0
N O:ASP36 4.3 27.9 1.0
N O:PHE38 4.3 28.7 1.0
N O:LEU40 4.3 29.1 1.0
CG O:LEU40 4.4 23.1 1.0
CD1 O:LEU40 4.4 22.4 1.0
C O:ASP36 4.4 29.6 1.0
N O:ASP39 4.4 29.8 1.0
CA O:PHE38 4.5 28.4 1.0
CA O:ASP39 4.5 31.2 1.0
CA O:ASN35 4.6 25.6 1.0
O O:ASP36 4.6 30.6 1.0
CB O:ASN35 4.8 25.2 1.0
CB O:LEU40 4.9 26.6 1.0
O O:HOH561 4.9 28.6 1.0
N O:ALA37 4.9 28.6 1.0
C O:ASP39 5.0 30.4 1.0

Reference:

S.Negoro, N.Shibata, Y.Tanaka, K.Yasuhira, H.Shibata, H.Hashimoto, Y.H.Lee, S.Oshima, R.Santa, K.Mochiji, Y.Goto, T.Ikegami, K.Nagai, D.Kato, M.Takeo, Y.Higuchi. Three-Dimensional Structure of Nylon Hydrolase and Mechanism of Nylon-6 Hydrolysis J.Biol.Chem. V. 287 5079 2012.
ISSN: ISSN 0021-9258
PubMed: 22187439
DOI: 10.1074/JBC.M111.321992
Page generated: Sun Aug 17 12:44:36 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy