Sodium in PDB 7ynh: Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System

Enzymatic activity of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System

All present enzymatic activity of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System:
1.4.3.21;

Protein crystallography data

The structure of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System, PDB code: 7ynh was solved by T.Murakawa, T.Okajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.51, 64.61, 158.24, 90, 116.86, 90
R / Rfree (%) 17.8 / 21

Other elements in 7ynh:

The structure of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System (pdb code 7ynh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System, PDB code: 7ynh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7ynh

Go back to Sodium Binding Sites List in 7ynh
Sodium binding site 1 out of 2 in the Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:16.9
occ:1.00
 OD1 A:ASP440 2.4 24.5 1.0
O A:MET441 2.4 23.9 1.0
OD1 A:ASP581 2.4 28.8 1.0
O A:ILE582 2.5 21.1 1.0
O A:HOH1021 2.8 23.4 1.0
N A:ILE582 3.2 21.6 1.0
C A:ILE582 3.4 18.9 1.0
C A:MET441 3.4 21.8 1.0
N A:MET441 3.5 18.9 1.0
CG A:ASP440 3.6 22.5 1.0
CG A:ASP581 3.7 28.3 1.0
NH2 A:ARG49 3.8 30.9 1.0
C A:ASP581 3.8 25.1 1.0
C A:ASP440 3.9 19.4 1.0
CA A:ILE582 3.9 20.4 1.0
CA A:MET441 4.0 19.4 1.0
CD1 A:PHE446 4.0 35.8 1.0
CA A:ASP581 4.1 24.1 1.0
CA A:ASP440 4.3 19.6 1.0
CE1 A:PHE446 4.4 32.7 1.0
OD2 A:ASP440 4.4 22.4 1.0
CB A:ASP581 4.5 27.5 1.0
O A:ASP440 4.5 19.5 1.0
OD2 A:ASP581 4.5 30.2 1.0
N A:VAL583 4.6 23.4 1.0
CB A:ASP440 4.6 19.9 1.0
N A:ALA442 4.6 18.3 1.0
O A:ASP581 4.7 22.9 1.0
CB A:MET441 4.7 26.0 1.0
CG2 A:VAL583 4.7 19.3 1.0
CB A:TYR546 4.8 29.0 1.0
CG1 A:ILE582 4.9 21.6 1.0

Sodium binding site 2 out of 2 in 7ynh

Go back to Sodium Binding Sites List in 7ynh
Sodium binding site 2 out of 2 in the Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catalytic Intermediate of Copper Amine Oxidase Determined By Serial Femtosecond X-Ray Crystallography Using A Single-Flow Liquid Jet System within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:19.1
occ:1.00
 O B:MET441 2.4 21.8 1.0
OD1 B:ASP581 2.4 26.2 1.0
OD1 B:ASP440 2.4 22.6 1.0
O B:ILE582 2.5 17.7 1.0
O B:HOH1000 2.7 24.8 1.0
N B:ILE582 3.2 21.8 1.0
N B:MET441 3.4 18.7 1.0
C B:ILE582 3.4 18.8 1.0
C B:MET441 3.5 19.2 1.0
CG B:ASP581 3.6 32.1 1.0
CG B:ASP440 3.7 25.3 1.0
C B:ASP581 3.7 21.5 1.0
NH2 B:ARG49 3.8 26.5 1.0
C B:ASP440 3.9 19.6 1.0
CA B:ILE582 3.9 18.0 1.0
CA B:MET441 4.0 20.9 1.0
CD1 B:PHE446 4.0 30.6 1.0
CA B:ASP581 4.0 26.1 1.0
CA B:ASP440 4.3 18.2 1.0
CE1 B:PHE446 4.4 31.4 1.0
CB B:ASP581 4.5 23.9 1.0
OD2 B:ASP440 4.5 25.7 1.0
O B:ASP440 4.5 18.7 1.0
OD2 B:ASP581 4.5 31.2 1.0
O B:ASP581 4.5 23.6 1.0
N B:VAL583 4.6 20.7 1.0
CB B:ASP440 4.6 21.3 1.0
N B:ALA442 4.6 19.9 1.0
CB B:MET441 4.7 18.1 1.0
CB B:TYR546 4.7 27.7 1.0
CG2 B:VAL583 4.8 23.7 1.0
CG1 B:ILE582 4.9 25.2 1.0

Reference:

T.Murakawa, M.Suzuki, K.Fukui, T.Masuda, M.Sugahara, K.Tono, T.Tanaka, S.Iwata, E.Nango, T.Yano, K.Tanizawa, T.Okajima. Serial Femtosecond X-Ray Crystallography of An Anaerobically Formed Catalytic Intermediate of Copper Amine Oxidase. Acta Crystallogr D Struct V. 78 1428 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36458614
DOI: 10.1107/S2059798322010385
Page generated: Fri Apr 7 17:15:41 2023

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