Arsenic in PDB 6gfy: Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A), PDB code: 6gfy was solved by M.S.Gadd, A.Testa, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 2.70
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.115, 94.115, 367.972, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.8

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) (pdb code 6gfy). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 12 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A), PDB code: 6gfy:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:84.0 occ:1.00 AS A:CAS60 0.0 84.0 1.0 CE2 A:CAS60 2.0 77.2 1.0 CE1 A:CAS60 2.0 83.8 1.0 SG A:CAS60 2.3 63.9 1.0 CB A:CAS60 3.2 51.8 1.0 CA A:CAS60 3.5 46.8 1.0 CD2 A:LEU51 3.8 52.2 1.0 N A:CAS60 4.1 44.1 1.0 CB A:LYS55 4.5 43.8 1.0 CG A:LYS55 4.6 46.9 1.0 O A:GLU59 4.6 46.4 1.0 C A:GLU59 4.6 45.6 1.0 NE2 A:GLN49 4.8 49.9 1.0 C A:CAS60 4.8 45.8 1.0 CB A:LEU51 4.9 50.0 1.0 CG A:LEU51 5.0 51.3 1.0 CA A:LEU51 5.0 49.3 1.0

Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:96.7 occ:1.00 AS A:CAS89 0.0 96.7 1.0 CE2 A:CAS89 2.0 90.0 1.0 CE1 A:CAS89 2.0 96.7 1.0 SG A:CAS89 2.2 80.0 1.0 CB A:CAS89 3.1 69.0 1.0 CA A:CAS89 3.6 60.0 1.0 N A:ILE90 3.9 52.6 1.0 C A:CAS89 4.1 54.7 1.0 O A:HOH223 4.3 55.6 1.0 OE2 A:GLU91 4.4 61.2 1.0 O A:ILE90 4.6 50.3 1.0 C A:ILE90 4.7 49.6 1.0 N A:CAS89 5.0 56.1 1.0 CA A:ILE90 5.0 49.6 1.0

Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:67.6 occ:1.00 AS C:CAS77 0.0 67.6 1.0 CE1 C:CAS77 2.0 66.1 1.0 CE2 C:CAS77 2.0 68.8 1.0 SG C:CAS77 2.2 54.9 1.0 CB C:CAS77 3.1 47.5 1.0 CA C:CAS77 3.6 42.9 1.0 O C:THR105 4.3 42.2 1.0 C C:CAS77 4.4 40.4 1.0 CE K:MET45 4.5 90.8 1.0 CZ C:PHE148 4.5 57.8 1.0 CA C:GLY106 4.5 43.8 1.0 N C:ASN78 4.6 38.8 1.0 C C:THR105 4.6 44.2 1.0 N C:GLY106 4.7 44.5 1.0 CZ K:PHE109 4.8 55.9 1.0 CE2 C:PHE148 4.8 57.9 1.0 N C:CAS77 4.9 39.1 1.0 SD K:MET45 5.0 91.5 1.0 NH2 C:ARG79 5.0 62.3 1.0

Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:69.9 occ:1.00 AS D:CAS60 0.0 69.9 1.0 CE1 D:CAS60 2.0 67.3 1.0 CE2 D:CAS60 2.0 70.6 1.0 SG D:CAS60 2.3 57.5 1.0 CB D:CAS60 3.2 50.2 1.0 CA D:CAS60 3.4 46.3 1.0 N D:CAS60 4.1 45.3 1.0 CD2 D:LEU51 4.1 52.8 1.0 NE2 D:GLN49 4.5 52.5 1.0 O D:GLU59 4.6 45.9 1.0 C D:GLU59 4.6 46.4 1.0 C D:CAS60 4.7 44.3 1.0 CB D:LYS55 4.7 63.7 1.0 CG D:LYS55 4.7 66.6 1.0 O D:CAS60 4.9 45.0 1.0 CD D:GLN49 5.0 51.7 1.0

Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.7 occ:1.00 AS D:CAS89 0.0 0.7 1.0 CE2 D:CAS89 2.0 0.4 1.0 CE1 D:CAS89 2.0 0.8 1.0 SG D:CAS89 2.2 0.1 1.0 CB D:CAS89 3.1 98.6 1.0 CA D:CAS89 3.6 87.3 1.0 O D:HOH210 3.7 48.2 1.0 N D:ILE90 4.0 76.2 1.0 C D:CAS89 4.2 80.5 1.0 O D:ILE90 4.6 72.5 1.0 C D:ILE90 4.8 70.9 1.0 OE2 D:GLU91 4.8 95.4 1.0 N D:CAS89 4.9 82.2 1.0 O D:LEU88 5.0 81.8 1.0

Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:60.0 occ:1.00 AS F:CAS77 0.0 60.0 1.0 CE1 F:CAS77 2.0 59.9 1.0 CE2 F:CAS77 2.0 61.5 1.0 SG F:CAS77 2.2 49.8 1.0 CB F:CAS77 3.1 43.4 1.0 CA F:CAS77 3.7 39.3 1.0 CA F:GLY106 4.3 41.0 1.0 O F:THR105 4.3 36.8 1.0 C F:CAS77 4.4 36.9 1.0 N F:GLY106 4.5 42.2 1.0 C F:THR105 4.5 42.3 1.0 CE H:MET45 4.5 80.6 1.0 N F:ASN78 4.6 36.6 1.0 CZ F:PHE148 4.6 46.8 1.0 N F:CAS77 4.9 38.1 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:65.7 occ:1.00 AS G:CAS60 0.0 65.7 1.0 CE1 G:CAS60 2.0 66.3 1.0 CE2 G:CAS60 2.0 64.1 1.0 SG G:CAS60 2.2 56.5 1.0 CB G:CAS60 3.2 52.5 1.0 CA G:CAS60 3.5 52.1 1.0 CD2 G:LEU51 4.1 51.9 1.0 NE2 G:GLN49 4.1 51.9 1.0 N G:CAS60 4.2 53.8 1.0 CD G:GLN49 4.7 51.0 1.0 C G:CAS60 4.7 49.9 1.0 C G:GLU59 4.8 56.7 1.0 CB G:LYS55 4.8 58.4 1.0 CG G:LYS55 4.8 60.2 1.0 O G:GLU59 4.9 55.7 1.0 O G:CAS60 4.9 46.6 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.5 occ:1.00 AS G:CAS89 0.0 0.5 1.0 CE2 G:CAS89 2.0 0.2 1.0 CE1 G:CAS89 2.0 0.4 1.0 SG G:CAS89 2.2 79.8 1.0 CB G:CAS89 3.1 67.7 1.0 CA G:CAS89 3.6 59.2 1.0 N G:ILE90 4.0 52.4 1.0 C G:CAS89 4.2 56.6 1.0 O G:HOH207 4.4 35.4 1.0 C G:ILE90 4.9 48.6 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:58.8 occ:1.00 AS I:CAS77 0.0 58.8 1.0 CE1 I:CAS77 2.0 58.3 1.0 CE2 I:CAS77 2.0 59.7 1.0 SG I:CAS77 2.2 49.0 1.0 CB I:CAS77 3.1 40.8 1.0 CA I:CAS77 3.6 35.8 1.0 CA I:GLY106 4.1 36.6 1.0 O I:THR105 4.2 35.5 1.0 C I:CAS77 4.2 33.9 1.0 N I:ASN78 4.4 34.8 1.0 N I:GLY106 4.4 37.5 1.0 C I:THR105 4.4 36.6 1.0 CE2 I:PHE148 4.8 54.8 1.0 CZ I:PHE148 4.9 55.4 1.0 N I:CAS77 4.9 34.6 1.0

Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 10 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:84.8 occ:1.00 AS J:CAS60 0.0 84.8 1.0 CE2 J:CAS60 2.0 87.3 1.0 CE1 J:CAS60 2.0 85.0 1.0 SG J:CAS60 2.3 68.2 1.0 CB J:CAS60 3.3 55.0 1.0 CA J:CAS60 3.5 52.2 1.0 CD2 J:LEU51 4.0 46.8 1.0 N J:CAS60 4.2 50.7 1.0 NE2 J:GLN49 4.5 49.4 1.0 O J:GLU59 4.6 51.9 1.0 CB J:LYS55 4.6 45.3 1.0 CG J:LYS55 4.6 47.0 1.0 C J:GLU59 4.6 52.2 1.0 C J:CAS60 4.8 49.1 1.0 CD J:GLN49 5.0 48.3 1.0

A.Testa, X.Lucas, G.V.Castro, K.H.Chan, J.E.Wright, A.C.Runcie, M.S.Gadd, W.T.A.Harrison, E.J.Ko, D.Fletcher, A.Ciulli. 3-Fluoro-4-Hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition By the Vhl E3 Ubiquitin Ligase For Targeted Protein Degradation. J. Am. Chem. Soc. V. 140 9299 2018.
ISSN: ESSN 1520-5126
PubMed: 29949369
DOI: 10.1021/JACS.8B05807