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Sodium in PDB 1w4n: Agao Covalent Complex with Tranylcypromine

Enzymatic activity of Agao Covalent Complex with Tranylcypromine

All present enzymatic activity of Agao Covalent Complex with Tranylcypromine:
1.4.3.6;

Protein crystallography data

The structure of Agao Covalent Complex with Tranylcypromine, PDB code: 1w4n was solved by A.P.Duff, D.M.Trambaiolo, D.B.Langley, G.A.Juda, E.M.Shepard, D.M.Dooley, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.28 / 1.65
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.113, 63.001, 184.490, 90.00, 112.04, 90.00
R / Rfree (%) 17.1 / 19.9

Other elements in 1w4n:

The structure of Agao Covalent Complex with Tranylcypromine also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Agao Covalent Complex with Tranylcypromine (pdb code 1w4n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Agao Covalent Complex with Tranylcypromine, PDB code: 1w4n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1w4n

Go back to Sodium Binding Sites List in 1w4n
Sodium binding site 1 out of 2 in the Agao Covalent Complex with Tranylcypromine


Mono view


Stereo pair view

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

b:32.0
occ:1.00
OD1 A:ASP440 2.3 8.7 1.0
O A:MET441 2.4 10.3 1.0
OD1 A:ASP581 2.4 12.2 1.0
O A:ILE582 2.5 8.7 1.0
O A:HOH2337 2.6 24.9 1.0
H A:ILE582 2.8 9.7 1.0
HD1 A:PHE446 3.1 13.0 1.0
H A:MET441 3.2 9.4 1.0
N A:ILE582 3.2 9.8 1.0
N A:MET441 3.4 9.6 1.0
C A:MET441 3.4 12.1 1.0
C A:ILE582 3.4 9.2 1.0
HH21 A:ARG49 3.5 37.2 1.0
CG A:ASP440 3.6 11.3 1.0
HA A:ASP581 3.6 10.5 1.0
CG A:ASP581 3.6 15.7 1.0
C A:ASP581 3.8 10.7 1.0
C A:ASP440 3.8 7.6 1.0
HB2 A:MET441 3.8 10.4 1.0
HA A:ASP440 3.9 8.8 1.0
CA A:MET441 3.9 10.4 1.0
CA A:ILE582 3.9 8.7 1.0
HH22 A:ARG49 4.0 37.2 1.0
CD1 A:PHE446 4.0 13.7 1.0
HG21 A:VAL583 4.0 9.1 1.0
HB2 A:TYR546 4.0 11.5 1.0
NH2 A:ARG49 4.1 35.4 1.0
HE1 A:PHE446 4.1 13.9 1.0
CA A:ASP581 4.1 11.2 1.0
CA A:ASP440 4.3 9.0 1.0
OD2 A:ASP440 4.3 9.4 1.0
CB A:MET441 4.4 10.6 1.0
HG13 A:ILE582 4.4 12.5 1.0
OD2 A:ASP581 4.5 16.9 1.0
CE1 A:PHE446 4.5 11.9 1.0
CB A:ASP581 4.5 11.2 1.0
O A:ASP440 4.5 9.7 1.0
HA A:ILE582 4.5 9.6 1.0
HA A:PHE446 4.5 10.0 1.0
HB2 A:ALA442 4.5 10.7 1.0
HA A:VAL583 4.5 8.3 1.0
CB A:ASP440 4.5 9.5 1.0
HA A:ALA442 4.5 10.9 1.0
N A:VAL583 4.6 8.3 1.0
N A:ALA442 4.6 11.2 1.0
HG22 A:VAL583 4.6 9.1 1.0
O A:ASP581 4.7 10.4 1.0
HG12 A:ILE582 4.7 12.5 1.0
HB3 A:ASN273 4.7 11.2 1.0
CG2 A:VAL583 4.8 9.9 1.0
HA A:MET441 4.8 10.6 1.0
HB3 A:PHE446 4.8 10.3 1.0
O A:PHE446 4.9 9.8 1.0
CB A:TYR546 4.9 10.1 1.0
CG1 A:ILE582 4.9 12.2 1.0
HB2 A:ASN273 4.9 11.2 1.0
HB3 A:TYR546 5.0 11.5 1.0

Sodium binding site 2 out of 2 in 1w4n

Go back to Sodium Binding Sites List in 1w4n
Sodium binding site 2 out of 2 in the Agao Covalent Complex with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Agao Covalent Complex with Tranylcypromine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:26.4
occ:1.00
O B:MET441 2.4 6.4 1.0
OD1 B:ASP581 2.4 9.2 1.0
O B:ILE582 2.4 6.4 1.0
OD1 B:ASP440 2.5 6.6 1.0
O B:HOH2363 2.6 25.3 1.0
H B:ILE582 2.9 8.3 1.0
HD1 B:PHE446 3.1 11.6 1.0
N B:ILE582 3.2 7.8 1.0
H B:MET441 3.2 5.5 1.0
N B:MET441 3.4 4.6 1.0
C B:ILE582 3.4 5.1 1.0
C B:MET441 3.4 7.8 1.0
HA B:ASP581 3.5 9.1 1.0
HH21 B:ARG49 3.6 17.6 1.0
CG B:ASP581 3.6 15.7 1.0
CG B:ASP440 3.7 7.8 1.0
C B:ASP581 3.8 10.0 1.0
C B:ASP440 3.8 5.5 1.0
CA B:ILE582 3.9 7.8 1.0
CA B:MET441 3.9 7.8 1.0
HB2 B:MET441 3.9 7.6 1.0
HA B:ASP440 3.9 5.4 1.0
CD1 B:PHE446 4.0 10.5 1.0
HB2 B:TYR546 4.0 8.3 1.0
CA B:ASP581 4.0 8.2 1.0
HE1 B:PHE446 4.1 13.5 1.0
HH22 B:ARG49 4.1 17.6 1.0
HG21 B:VAL583 4.1 6.9 1.0
NH2 B:ARG49 4.2 15.2 1.0
CA B:ASP440 4.3 5.3 1.0
O B:ASP440 4.4 5.2 1.0
CB B:ASP581 4.4 10.3 1.0
CE1 B:PHE446 4.5 13.3 1.0
CB B:MET441 4.5 6.1 1.0
HA B:ILE582 4.5 7.0 1.0
OD2 B:ASP440 4.5 9.2 1.0
HA B:PHE446 4.5 7.7 1.0
OD2 B:ASP581 4.5 15.3 1.0
HG12 B:ILE582 4.5 8.6 1.0
HA B:ALA442 4.5 6.8 1.0
O B:ASP581 4.6 8.2 1.0
N B:VAL583 4.6 5.6 1.0
HA B:VAL583 4.6 6.7 1.0
HB1 B:ALA442 4.6 7.5 1.0
HG22 B:VAL583 4.6 6.9 1.0
HG13 B:ILE582 4.6 8.6 1.0
N B:ALA442 4.6 5.3 1.0
CB B:ASP440 4.6 4.4 1.0
HB3 B:PHE446 4.8 8.3 1.0
HA B:MET441 4.8 6.8 1.0
HB3 B:ASN273 4.8 6.6 1.0
CG2 B:VAL583 4.8 6.8 1.0
O B:PHE446 4.8 9.6 1.0
CB B:TYR546 4.9 7.6 1.0
HB3 B:TYR546 4.9 8.3 1.0
CG1 B:ILE582 4.9 8.8 1.0
OD1 B:ASN448 5.0 7.1 1.0
HB2 B:ASN273 5.0 6.6 1.0

Reference:

D.B.Langley, D.M.Trambaiolo, A.P.Duff, D.M.Dooley, H.C.Freeman, J.M.Guss. Complexes of the Copper-Containing Amine Oxidase From Arthrobacter Globiformis with the Inhibitors Benzylhydrazine and Tranylcypromine. Acta Crystallogr.,Sect.F V. 64 577 2008.
ISSN: ESSN 1744-3091
PubMed: 18607080
DOI: 10.1107/S174430910801556X
Page generated: Tue Dec 15 05:40:30 2020

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