Sodium in PDB 7wnp: Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution.

Enzymatic activity of Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution.

All present enzymatic activity of Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution.:
1.4.3.21;

Protein crystallography data

The structure of Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution., PDB code: 7wnp 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) N/A / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.206, 61.979, 92.447, 90, 112.06, 90
R / Rfree (%) 18.9 / 23.5

Other elements in 7wnp:

The structure of Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution. also contains other interesting chemical elements:

Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution. (pdb code 7wnp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution., PDB code: 7wnp:

Sodium binding site 1 out of 1 in 7wnp

Go back to Sodium Binding Sites List in 7wnp
Sodium binding site 1 out of 1 in the Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallographic Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 Determined By Both X-Ray and Neutron Diffraction Data at 1.72 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na702

b:14.1
occ:1.00
OD1 X:ASP440 2.3 13.7 1.0
OD1 X:ASP581 2.3 15.0 1.0
O X:MET441 2.4 13.3 1.0
O X:ILE582 2.5 10.9 1.0
O X:DOD1099 2.7 15.5 1.0
D X:ILE582 2.7 14.4 0.1
H X:ILE582 2.8 14.4 0.9
D2 X:DOD1099 3.0 14.8 1.0
HD1 X:PHE446 3.0 17.6 1.0
D X:MET441 3.1 11.4 0.1
H X:MET441 3.1 11.3 0.9
N X:ILE582 3.2 14.1 1.0
DH21 X:ARG49 3.2 17.6 1.0
D1 X:DOD1099 3.3 16.1 1.0
N X:MET441 3.4 11.6 1.0
C X:ILE582 3.4 11.1 1.0
C X:MET441 3.4 13.1 1.0
HA X:ASP581 3.5 13.9 1.0
CG X:ASP440 3.5 14.2 1.0
CG X:ASP581 3.5 18.7 1.0
C X:ASP581 3.7 13.6 1.0
HB2 X:TYR546 3.7 15.8 1.0
DH22 X:ARG49 3.8 17.7 1.0
C X:ASP440 3.8 10.7 1.0
HB2 X:MET441 3.9 8.3 1.0
NH2 X:ARG49 3.9 16.7 1.0
CA X:ILE582 3.9 13.8 1.0
HA X:ASP440 3.9 11.9 1.0
CA X:MET441 3.9 13.3 1.0
CD1 X:PHE446 4.0 17.5 1.0
HE1 X:PHE446 4.0 18.3 1.0
CA X:ASP581 4.0 13.7 1.0
HG21 X:VAL583 4.0 15.8 1.0
CA X:ASP440 4.3 11.3 1.0
OD2 X:ASP440 4.3 14.6 1.0
CB X:ASP581 4.4 16.9 1.0
OD2 X:ASP581 4.4 19.3 1.0
CE1 X:PHE446 4.4 18.6 1.0
HB3 X:ASN273 4.5 16.7 1.0
O X:ASP440 4.5 11.0 1.0
HG12 X:ILE582 4.5 13.2 1.0
CB X:MET441 4.5 11.4 1.0
CB X:ASP440 4.5 11.2 1.0
HA X:PHE446 4.5 17.6 1.0
HA X:ILE582 4.5 15.5 1.0
HG22 X:VAL583 4.5 15.4 1.0
HB2 X:ALA442 4.5 17.1 1.0
HA X:VAL583 4.6 14.0 1.0
HA X:ALA442 4.6 14.8 1.0
O X:ASP581 4.6 13.1 1.0
N X:VAL583 4.6 11.7 1.0
HG13 X:ILE582 4.6 14.7 1.0
N X:ALA442 4.6 11.3 1.0
CB X:TYR546 4.7 13.3 1.0
HB3 X:PHE446 4.7 18.3 1.0
HB3 X:TYR546 4.8 16.9 1.0
CG2 X:VAL583 4.8 13.8 1.0
HA X:MET441 4.9 12.9 1.0
O X:PHE446 4.9 17.4 1.0
HB2 X:ASN273 4.9 15.7 1.0
HB3 X:ASP581 5.0 22.4 1.0
CG1 X:ILE582 5.0 14.6 1.0

Reference:

T.Murakawa, K.Kurihara, M.Adachi, K.Kusaka, K.Tanizawa, T.Okajima. Re-Evaluation of Protein Neutron Crystallography with and Without X-Ray/Neutron Joint Refinement. Iucrj V. 9 342 2022.
ISSN: ESSN 2052-2525
PubMed: 35546796
DOI: 10.1107/S2052252522003657
Page generated: Fri Apr 7 16:55:41 2023

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