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Sodium in PDB 3wa3: Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition

Enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition

All present enzymatic activity of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition:
1.4.3.21;

Protein crystallography data

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition, PDB code: 3wa3 was solved by T.Murakawa, H.Hayashi, T.Sunami, K.Kurihara, T.Tamada, R.Kuroki, M.Suzuki, K.Tanizawa, T.Okajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 191.607, 63.036, 158.006, 90.00, 117.44, 90.00
R / Rfree (%) 18.1 / 21

Other elements in 3wa3:

The structure of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition (pdb code 3wa3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition, PDB code: 3wa3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wa3

Go back to Sodium Binding Sites List in 3wa3
Sodium binding site 1 out of 2 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:12.4
occ:1.00
OD1 A:ASP581 2.4 18.4 1.0
OD1 A:ASP440 2.4 16.0 1.0
O A:MET441 2.5 14.4 1.0
O A:ILE582 2.6 14.8 1.0
O A:HOH1108 2.7 15.3 1.0
N A:ILE582 3.2 14.6 1.0
N A:MET441 3.5 14.7 1.0
C A:ILE582 3.5 15.0 1.0
CG A:ASP581 3.6 21.1 1.0
C A:MET441 3.6 15.3 1.0
CG A:ASP440 3.7 17.1 1.0
C A:ASP581 3.7 17.0 1.0
CD1 A:PHE446 3.7 22.1 1.0
NH2 A:ARG49 3.8 22.7 1.0
CA A:ILE582 3.9 13.4 1.0
C A:ASP440 3.9 14.7 1.0
CA A:ASP581 4.0 14.9 1.0
CA A:MET441 4.0 13.5 1.0
CE1 A:PHE446 4.2 24.1 1.0
CA A:ASP440 4.3 13.2 1.0
CB A:ASP581 4.4 16.5 1.0
OD2 A:ASP440 4.4 18.3 1.0
OD2 A:ASP581 4.5 25.1 1.0
CB A:MET441 4.5 11.9 1.0
O A:ASP581 4.5 16.2 1.0
O A:ASP440 4.6 13.7 1.0
CB A:ASP440 4.6 13.6 1.0
N A:VAL583 4.7 13.3 1.0
CG2 A:VAL583 4.7 15.8 1.0
N A:ALA442 4.7 13.6 1.0
CB A:TYR546 4.8 20.3 1.0
CG A:PHE446 4.9 20.9 1.0
O A:PHE446 4.9 20.4 1.0
CG1 A:ILE582 5.0 15.9 1.0

Sodium binding site 2 out of 2 in 3wa3

Go back to Sodium Binding Sites List in 3wa3
Sodium binding site 2 out of 2 in the Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis in N2 Condition within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:11.1
occ:1.00
OD1 B:ASP581 2.4 17.8 1.0
OD1 B:ASP440 2.4 14.3 1.0
O B:MET441 2.5 13.9 1.0
O B:ILE582 2.5 13.1 1.0
O B:HOH1116 2.7 14.3 1.0
N B:ILE582 3.2 13.8 1.0
N B:MET441 3.4 14.7 1.0
C B:ILE582 3.4 12.9 1.0
C B:MET441 3.5 14.2 1.0
CG B:ASP581 3.6 21.5 1.0
CG B:ASP440 3.7 14.5 1.0
C B:ASP581 3.8 17.0 1.0
NH2 B:ARG49 3.8 22.9 1.0
CD1 B:PHE446 3.8 22.2 1.0
CA B:ILE582 3.9 13.4 1.0
C B:ASP440 3.9 13.5 1.0
CA B:MET441 4.0 12.5 1.0
CA B:ASP581 4.0 15.7 1.0
CE1 B:PHE446 4.2 19.6 1.0
CA B:ASP440 4.3 12.1 1.0
CB B:ASP581 4.4 16.6 1.0
OD2 B:ASP440 4.5 14.6 1.0
CB B:MET441 4.5 14.8 1.0
OD2 B:ASP581 4.6 21.9 1.0
O B:ASP440 4.6 12.6 1.0
N B:VAL583 4.6 12.7 1.0
O B:ASP581 4.6 14.9 1.0
CB B:ASP440 4.6 12.4 1.0
N B:ALA442 4.7 12.6 1.0
CG2 B:VAL583 4.8 15.4 1.0
CB B:TYR546 4.8 16.6 1.0
CG B:PHE446 4.9 20.1 1.0
CG1 B:ILE582 4.9 16.7 1.0
O B:PHE446 5.0 17.1 1.0

Reference:

T.Murakawa, H.Hayashi, T.Sunami, K.Kurihara, T.Tamada, R.Kuroki, M.Suzuki, K.Tanizawa, T.Okajima. High-Resolution Crystal Structure of Copper Amine Oxidase From Arthrobacter Globiformis: Assignment of Bound Diatomic Molecules As O2 Acta Crystallogr.,Sect.D V. 69 2483 2013.
ISSN: ISSN 0907-4449
PubMed: 24311589
DOI: 10.1107/S0907444913023196
Page generated: Tue Dec 15 06:29:36 2020

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