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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 05:54:02 2024

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