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Sodium in PDB 4dfg: Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A

Enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A

All present enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A, PDB code: 4dfg was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.23
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.580, 85.930, 45.990, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18

Other elements in 4dfg:

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A (pdb code 4dfg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A, PDB code: 4dfg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4dfg

Go back to Sodium Binding Sites List in 4dfg
Sodium binding site 1 out of 2 in the Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.3
occ:1.00
 O A:HOH627 2.3 17.3 1.0
O A:HOH628 2.4 21.3 1.0
O A:ASP60 2.4 14.0 1.0
O A:HOH626 2.4 19.0 1.0
O A:HOH643 2.4 30.1 1.0
O A:HOH629 2.8 26.6 1.0
C A:ASP60 3.4 13.7 1.0
N A:ASP60 3.8 12.8 1.0
CA A:ASP60 4.0 13.5 1.0
O A:ARG41 4.1 15.5 1.0
O A:HOH697 4.2 34.4 0.5
OE1 A:GLN61 4.3 29.9 0.3
CB A:GLN61 4.4 16.0 0.7
CB A:GLN61 4.4 17.1 0.3
CB A:ASP60 4.4 16.2 1.0
N A:GLN61 4.4 13.7 1.0
O A:HOH696 4.4 30.3 0.5
N A:ARG41 4.5 19.6 1.0
O A:HOH670 4.6 38.4 1.0
O A:GLN61 4.6 16.8 1.0
O A:HOH685 4.6 29.4 0.5
CD1 A:ILE62 4.7 15.4 1.0
C A:TYR59 4.7 10.9 1.0
O A:PRO39 4.7 19.5 1.0
CA A:GLN61 4.7 14.4 0.3
CA A:GLN61 4.7 14.4 0.7
CD A:GLN61 4.7 25.3 0.3
C A:GLN61 4.8 13.3 1.0
CA A:GLY40 4.8 21.7 1.0
OE1 A:GLN61 4.8 29.5 0.7

Sodium binding site 2 out of 2 in 4dfg

Go back to Sodium Binding Sites List in 4dfg
Sodium binding site 2 out of 2 in the Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wild-Type Hiv-1 Protease with Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:24.9
occ:0.50
 O B:HOH1044 2.3 23.0 1.0
O B:HOH1042 2.3 25.7 0.5
O B:ASP60 2.4 16.1 1.0
O B:HOH1046 2.5 33.8 0.2
O B:HOH1045 2.6 27.2 1.0
O B:HOH1043 2.9 24.9 0.2
C B:ASP60 3.5 14.5 1.0
N B:ASP60 3.7 13.5 1.0
O B:HOH1047 3.9 37.0 1.0
CA B:ASP60 4.0 13.9 1.0
O B:ARG41 4.2 15.1 1.0
CB B:ASP60 4.3 14.6 1.0
CB B:GLN61 4.3 17.3 0.2
O B:PRO39 4.5 17.9 1.0
CD1 B:ILE62 4.5 17.2 1.0
C B:TYR59 4.6 11.1 1.0
N B:GLN61 4.6 12.9 1.0
CB B:GLN61 4.8 16.4 0.8
O B:GLN61 4.9 17.6 1.0
CA B:GLN61 4.9 13.7 0.2
C B:GLN61 4.9 14.0 1.0
CA B:TYR59 4.9 10.8 1.0
CA B:GLY40 4.9 14.4 1.0
N B:ARG41 4.9 13.4 1.0
CA B:GLN61 4.9 13.3 0.8

Reference:

A.K.Ghosh, B.D.Chapsal, M.Steffey, J.Agniswamy, Y.F.Wang, M.Amano, I.T.Weber, H.Mitsuya. Substituent Effects on P2-Cyclopentyltetrahydrofuranyl Urethanes: Design, Synthesis, and X-Ray Studies of Potent Hiv-1 Protease Inhibitors. Bioorg.Med.Chem.Lett. V. 22 2308 2012.
ISSN: ISSN 0960-894X
PubMed: 22364812
DOI: 10.1016/J.BMCL.2012.01.061
Page generated: Mon Oct 7 14:56:20 2024

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