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Iodine in PDB 7gpw: Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824:
3.4.22.28;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824, PDB code: 7gpw was solved by R.M.Lithgo, M.Fairhead, L.Koekemoer, J.C.Aschenbrenner, B.H.Balcomb, A.S.Godoy, P.G.Marples, X.Ni, C.W.E.Tomlinson, W.Thompson, C.Wild, D.Fearon, M.A.Walsh, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.83 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.75, 62.233, 147.664, 90, 90, 90
R / Rfree (%) 19 / 21.2

Iodine Binding Sites:

The binding sites of Iodine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824 (pdb code 7gpw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824, PDB code: 7gpw:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 7gpw

Go back to Iodine Binding Sites List in 7gpw
Iodine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I201

b:28.9
occ:0.28
 I1 A:HHQ201 0.0 28.9 0.3
C3 A:HHQ201 2.0 24.0 0.3
C4 A:HHQ201 2.9 24.6 0.3
C2 A:HHQ201 2.9 24.1 0.3
OE1 A:GLN146 3.6 32.0 1.0
CE A:MET112 3.7 29.8 1.0
CB B:PRO115 3.8 27.7 1.0
CG B:PRO115 3.8 28.7 1.0
CE1 A:PHE109 4.0 38.3 1.0
C5 A:HHQ201 4.2 24.1 0.3
C1 A:HHQ201 4.2 22.8 0.3
CZ A:PHE109 4.3 37.3 1.0
SD A:MET112 4.5 32.9 1.0
CD A:ARG143 4.6 43.4 1.0
CD1 A:PHE109 4.6 36.9 1.0
N1 A:HHQ201 4.7 24.5 0.3
CE1 B:PHE4 4.7 40.8 1.0
CD A:GLN146 4.8 26.1 1.0
NH1 A:ARG143 4.9 51.8 1.0

Iodine binding site 2 out of 3 in 7gpw

Go back to Iodine Binding Sites List in 7gpw
Iodine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:25.4
occ:0.34
 I1 B:HHQ201 0.0 25.4 0.3
C3 B:HHQ201 2.1 26.6 0.3
C2 B:HHQ201 3.0 27.1 0.3
O B:ILE46 3.0 21.4 1.0
C4 B:HHQ201 3.0 27.4 0.3
O B:HOH348 3.8 23.8 1.0
C B:ILE46 3.8 22.1 1.0
O B:HOH402 4.0 26.9 1.0
O B:HOH442 4.0 27.5 0.3
CE1 B:TYR48 4.2 35.5 1.0
C5 B:HHQ201 4.3 27.6 0.3
N B:GLU21 4.3 28.6 1.0
C1 B:HHQ201 4.3 26.8 0.3
CD1 B:TYR48 4.3 33.2 1.0
CA B:ILE47 4.3 21.8 1.0
O B:HOH449 4.3 33.9 1.0
O B:ARG19 4.3 20.3 1.0
CA B:THR20 4.3 21.1 1.0
C B:THR20 4.4 24.3 1.0
N B:ILE47 4.4 22.9 1.0
O B:HOH428 4.4 24.3 1.0
CB B:ILE46 4.6 30.0 1.0
N1 B:HHQ201 4.7 27.8 0.3
CG2 B:ILE46 4.8 33.0 1.0
CA B:ILE46 4.8 25.1 1.0
C B:ILE47 5.0 24.3 1.0

Iodine binding site 3 out of 3 in 7gpw

Go back to Iodine Binding Sites List in 7gpw
Iodine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Enterovirus D68 3C Protease in Complex with Ncl-00023824 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:65.3
occ:0.44
 I1 B:HHQ202 0.0 65.3 0.4
C3 B:HHQ202 2.1 61.1 0.4
C2 B:HHQ202 3.0 60.0 0.4
C4 B:HHQ202 3.0 60.8 0.4
OH B:TYR31 3.3 33.7 1.0
O B:TYR178 3.7 22.3 1.0
CA B:PHE179 3.9 28.9 1.0
CD1 B:PHE179 4.1 23.6 1.0
C5 B:HHQ202 4.3 60.6 0.4
CE1 B:TYR31 4.3 28.3 1.0
CZ B:TYR31 4.3 30.8 1.0
CG1 B:VAL34 4.3 19.3 1.0
C1 B:HHQ202 4.3 60.1 0.4
CG2 B:ILE74 4.4 17.6 0.4
C B:PHE179 4.5 33.5 1.0
O B:PHE179 4.5 38.3 1.0
CB B:PHE179 4.6 25.7 1.0
C B:TYR178 4.7 23.7 1.0
N1 B:HHQ202 4.8 59.8 0.4
N B:PHE179 4.8 24.3 1.0
CG B:PHE179 4.8 24.6 1.0
CD1 B:ILE74 4.8 18.2 0.4
CG2 B:VAL34 4.8 22.1 1.0
CE1 B:PHE179 5.0 25.1 1.0

Reference:

R.M.Lithgo, M.Fairhead, L.Koekemoer, J.C.Aschenbrenner, B.H.Balcomb, A.S.Godoy, P.G.Marples, X.Ni, C.W.E.Tomlinson, W.Thompson, C.Wild, D.Fearon, M.A.Walsh, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Aug 12 01:10:16 2024

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