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Sodium in PDB 1rjo: Agao + Xe

Enzymatic activity of Agao + Xe

All present enzymatic activity of Agao + Xe:
1.4.3.6;

Protein crystallography data

The structure of Agao + Xe, PDB code: 1rjo was solved by J.M.Guss, D.M.Trambaiolo, A.P.Duff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.30 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.009, 63.189, 92.149, 90.00, 112.09, 90.00
R / Rfree (%) 15.7 / 17.8

Other elements in 1rjo:

The structure of Agao + Xe also contains other interesting chemical elements:

Xenon (Xe) 7 atoms
Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Agao + Xe (pdb code 1rjo). 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 Agao + Xe, PDB code: 1rjo:

Sodium binding site 1 out of 1 in 1rjo

Go back to Sodium Binding Sites List in 1rjo
Sodium binding site 1 out of 1 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:26.2
occ:1.00
O A:MET441 2.3 13.4 1.0
OD1 A:ASP440 2.4 13.8 1.0
OD1 A:ASP581 2.4 16.2 1.0
O A:ILE582 2.5 12.6 1.0
O A:HOH1219 2.7 22.1 1.0
N A:ILE582 3.3 13.0 1.0
N A:MET441 3.4 14.1 1.0
C A:MET441 3.4 12.9 1.0
C A:ILE582 3.5 12.2 1.0
CG A:ASP581 3.6 18.6 1.0
CG A:ASP440 3.6 15.1 1.0
C A:ASP440 3.8 13.8 1.0
C A:ASP581 3.9 12.7 1.0
CA A:MET441 3.9 13.2 1.0
CD1 A:PHE446 3.9 20.1 1.0
CA A:ILE582 3.9 12.5 1.0
CA A:ASP581 4.1 14.5 1.0
NH2 A:ARG49 4.1 17.9 1.0
CA A:ASP440 4.3 13.5 1.0
CE1 A:PHE446 4.4 21.3 1.0
OD2 A:ASP440 4.4 15.4 1.0
CB A:MET441 4.4 13.7 1.0
O A:ASP440 4.4 13.0 1.0
OD2 A:ASP581 4.5 20.2 1.0
CB A:ASP581 4.5 16.3 1.0
CB A:ASP440 4.6 13.3 1.0
N A:ALA442 4.6 12.7 1.0
N A:VAL583 4.6 11.9 1.0
O A:ASP581 4.7 12.9 1.0
CG2 A:VAL583 4.8 14.6 1.0
O A:PHE446 4.9 17.0 1.0
CB A:TYR546 4.9 16.4 1.0
CG1 A:ILE582 4.9 17.7 1.0

Reference:

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. Using Xenon As A Probe For Dioxygen-Binding Sites in Copper Amine Oxidases J.Mol.Biol. V. 344 599 2004.
ISSN: ISSN 0022-2836
PubMed: 15533431
DOI: 10.1016/J.JMB.2004.09.075
Page generated: Tue Dec 15 05:35:02 2020

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