Sodium in PDB 6l9c: Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4

Enzymatic activity of Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4

All present enzymatic activity of Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4:
1.4.3.21;

Protein crystallography data

The structure of Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4, PDB code: 6l9c was solved by T.Murakawa, K.Kurihara, M.Shoji, C.Shibazaki, T.Sunami, T.Tamada, N.Yano, T.Yamada, K.Kusaka, M.Suzuki, Y.Shigeta, R.Kuroki, H.Hayashi, Y.Yano, K.Tanizawa, M.Adachi, T.Okajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.548, 61.779, 92.332, 90.00, 112.13, 90.00
R / Rfree (%) 18 / 21

Other elements in 6l9c:

The structure of Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 also contains other interesting chemical elements:

Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 (pdb code 6l9c). 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 Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4, PDB code: 6l9c:

Sodium binding site 1 out of 1 in 6l9c

Go back to Sodium Binding Sites List in 6l9c
Sodium binding site 1 out of 1 in the Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Neutron Structure of Copper Amine Oxidase From Arthrobacter Glibiformis at Pd 7.4 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na702

b:19.2
occ:1.00
OD1 X:ASP440 2.3 18.9 1.0
OD1 X:ASP581 2.3 20.3 1.0
O X:MET441 2.3 18.9 1.0
O X:ILE582 2.4 18.0 1.0
D X:ILE582 2.6 20.2 0.1
H X:ILE582 2.7 20.5 0.9
O X:HOH1185 2.7 19.8 1.0
HD1 X:PHE446 3.1 21.5 1.0
D2 X:HOH1185 3.1 22.9 1.0
D X:MET441 3.1 13.2 0.1
N X:ILE582 3.1 18.8 1.0
H X:MET441 3.2 12.8 0.9
DH21 X:ARG49 3.2 22.1 1.0
N X:MET441 3.3 17.6 1.0
C X:ILE582 3.4 17.1 1.0
C X:MET441 3.4 18.4 1.0
D1 X:HOH1185 3.4 20.6 0.8
HA X:ASP581 3.5 18.8 1.0
CG X:ASP440 3.6 18.9 1.0
CG X:ASP581 3.6 22.3 1.0
C X:ASP581 3.7 18.6 1.0
C X:ASP440 3.8 17.5 1.0
HB2 X:TYR546 3.8 25.7 1.0
HB2 X:MET441 3.8 14.9 1.0
DH22 X:ARG49 3.9 22.7 0.9
CA X:ILE582 3.9 18.6 1.0
HH21 X:ARG49 3.9 22.6 0.1
CA X:MET441 3.9 17.7 1.0
HA X:ASP440 3.9 20.0 1.0
NH2 X:ARG49 3.9 21.2 1.0
HG22 X:VAL583 4.0 21.7 1.0
CA X:ASP581 4.0 18.8 1.0
CD1 X:PHE446 4.0 22.8 1.0
HE1 X:PHE446 4.1 24.7 1.0
CA X:ASP440 4.3 17.4 1.0
OD2 X:ASP440 4.4 19.8 1.0
CB X:ASP581 4.4 20.4 1.0
CB X:MET441 4.4 17.8 1.0
HB3 X:ASN273 4.5 19.9 1.0
O X:ASP440 4.5 18.4 1.0
OD2 X:ASP581 4.5 22.4 1.0
HA X:ALA442 4.5 21.1 1.0
HA X:ILE582 4.5 22.8 1.0
CB X:ASP440 4.5 18.6 1.0
HG13 X:ILE582 4.5 22.7 1.0
HB2 X:ALA442 4.5 27.3 1.0
HA X:PHE446 4.5 20.5 1.0
CE1 X:PHE446 4.5 25.2 1.0
HA X:VAL583 4.5 19.8 1.0
HG12 X:ILE582 4.6 19.0 1.0
N X:VAL583 4.6 18.1 1.0
HG23 X:VAL583 4.6 20.6 1.0
N X:ALA442 4.6 18.5 1.0
O X:ASP581 4.6 19.8 1.0
HB3 X:PHE446 4.7 28.7 1.0
CB X:TYR546 4.7 21.0 1.0
HB3 X:TYR546 4.8 19.6 1.0
CG2 X:VAL583 4.8 19.1 1.0
HA X:MET441 4.9 19.4 1.0
HB2 X:ASN273 4.9 20.9 1.0
CG1 X:ILE582 4.9 20.0 1.0
O X:PHE446 5.0 22.1 1.0
OD1 X:ASN448 5.0 19.8 1.0

Reference:

T.Murakawa, K.Kurihara, M.Shoji, C.Shibazaki, T.Sunami, T.Tamada, N.Yano, T.Yamada, K.Kusaka, M.Suzuki, Y.Shigeta, R.Kuroki, H.Hayashi, T.Yano, K.Tanizawa, M.Adachi, T.Okaijima. Neutron Crystallography of Copper Amine Oxidase Reveals Keto/Enolate Interconversion of the Quinone Cofactor and Unusual Proton Sharing Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1922538117
Page generated: Tue Dec 15 12:31:50 2020

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