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Sodium in PDB 3amo: Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis

Enzymatic activity of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis

All present enzymatic activity of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis:
1.4.3.21;

Protein crystallography data

The structure of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis, PDB code: 3amo was solved by M.Kataoka, H.Oya, A.Tominaga, M.Otsu, T.Okajima, K.Tanizawa, H.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.868, 63.635, 157.558, 90.00, 116.82, 90.00
R / Rfree (%) 18.9 / 24.5

Other elements in 3amo:

The structure of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis (pdb code 3amo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis, PDB code: 3amo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3amo

Go back to Sodium Binding Sites List in 3amo
Sodium binding site 1 out of 2 in the Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:15.7
occ:1.00
 OD1 A:ASP440 2.3 21.2 1.0
OD1 A:ASP581 2.4 29.5 1.0
O A:MET441 2.5 20.9 1.0
O A:ILE582 2.5 22.8 1.0
O A:HOH753 2.7 20.5 1.0
N A:ILE582 3.3 23.5 1.0
N A:MET441 3.4 16.5 1.0
C A:ILE582 3.5 22.1 1.0
C A:MET441 3.5 20.4 1.0
CG A:ASP581 3.6 29.1 1.0
CG A:ASP440 3.6 22.4 1.0
CD1 A:PHE446 3.7 27.5 1.0
C A:ASP440 3.8 17.5 1.0
C A:ASP581 3.8 24.5 1.0
NH2 A:ARG49 3.9 27.9 1.0
CA A:ILE582 3.9 23.4 1.0
CA A:MET441 4.0 19.1 1.0
CA A:ASP581 4.1 26.3 1.0
CE1 A:PHE446 4.2 31.7 1.0
CA A:ASP440 4.3 18.6 1.0
OD2 A:ASP440 4.4 26.6 1.0
OD2 A:ASP581 4.4 29.6 1.0
CB A:ASP581 4.5 26.9 1.0
O A:ASP440 4.5 17.9 1.0
CB A:ASP440 4.5 19.1 1.0
CB A:MET441 4.5 18.1 1.0
O A:ASP581 4.6 24.4 1.0
N A:VAL583 4.6 21.4 1.0
N A:ALA442 4.7 21.6 1.0
CB A:TYR546 4.7 23.1 1.0
O A:PHE446 4.8 24.6 1.0
CG2 A:VAL583 4.8 21.2 1.0
CG A:PHE446 4.8 29.7 1.0

Sodium binding site 2 out of 2 in 3amo

Go back to Sodium Binding Sites List in 3amo
Sodium binding site 2 out of 2 in the Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Time-Resolved X-Ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase From Arthrobacter Globiformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:11.9
occ:1.00
 OD1 B:ASP581 2.3 22.8 1.0
O B:MET441 2.5 19.2 1.0
O B:ILE582 2.5 19.0 1.0
OD1 B:ASP440 2.5 21.0 1.0
O B:HOH723 2.8 15.1 1.0
N B:ILE582 3.1 18.6 1.0
N B:MET441 3.4 14.7 1.0
C B:ILE582 3.4 17.6 1.0
C B:MET441 3.5 18.1 1.0
CG B:ASP581 3.5 24.5 1.0
C B:ASP581 3.7 20.6 1.0
CD1 B:PHE446 3.7 26.1 1.0
CG B:ASP440 3.7 14.9 1.0
NH2 B:ARG49 3.7 19.6 1.0
CA B:ILE582 3.8 19.1 1.0
C B:ASP440 3.9 13.9 1.0
CA B:MET441 4.0 15.5 1.0
CA B:ASP581 4.0 21.9 1.0
CE1 B:PHE446 4.1 26.2 1.0
CA B:ASP440 4.4 15.1 1.0
CB B:ASP581 4.4 22.1 1.0
OD2 B:ASP581 4.4 22.4 1.0
O B:ASP440 4.5 15.2 1.0
O B:ASP581 4.5 21.5 1.0
OD2 B:ASP440 4.5 18.5 1.0
CB B:MET441 4.5 15.3 1.0
N B:VAL583 4.6 17.5 1.0
CB B:ASP440 4.7 14.6 1.0
N B:ALA442 4.7 17.6 1.0
CB B:TYR546 4.7 19.5 1.0
CG2 B:VAL583 4.8 11.7 1.0
CG B:PHE446 4.8 25.3 1.0
O B:PHE446 4.9 22.7 1.0
CZ B:ARG49 5.0 28.8 1.0

Reference:

M.Kataoka, H.Oya, A.Tominaga, M.Otsu, T.Okajima, K.Tanizawa, H.Yamaguchi. Detection of the Reaction Intermediates Catalyzed By A Copper Amine Oxidase. J.Synchrotron Radiat. V. 18 58 2011.
ISSN: ISSN 0909-0495
PubMed: 21169693
DOI: 10.1107/S0909049510034989
Page generated: Mon Oct 7 05:50:29 2024

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