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

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B), PDB code: 6gfz 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)	49.01 / 2.30
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.609, 93.609, 364.511, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.5

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) 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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) (pdb code 6gfz). 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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B), PDB code: 6gfz:
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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:69.9 occ:1.00 AS A:CAS60 0.0 69.9 1.0 CE2 A:CAS60 2.0 78.2 1.0 CE1 A:CAS60 2.0 67.3 1.0 SG A:CAS60 2.3 54.9 1.0 CB A:CAS60 3.2 41.9 1.0 CA A:CAS60 3.4 38.6 1.0 CD2 A:LEU51 3.6 45.8 1.0 N A:CAS60 4.1 37.4 1.0 O A:GLU59 4.5 38.6 1.0 C A:GLU59 4.6 37.8 1.0 NE2 A:GLN49 4.6 53.1 1.0 CB A:LYS55 4.7 43.6 1.0 C A:CAS60 4.7 39.0 1.0 CG A:LYS55 4.7 47.7 1.0 CD A:GLN49 4.9 54.3 1.0 CG A:LEU51 4.9 46.8 1.0 O A:CAS60 5.0 39.6 1.0 CA A:LEU51 5.0 47.6 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:92.4 occ:1.00 AS A:CAS89 0.0 92.4 1.0 CE1 A:CAS89 2.0 95.5 1.0 CE2 A:CAS89 2.0 88.3 1.0 SG A:CAS89 2.2 78.2 1.0 CB A:CAS89 3.0 69.7 1.0 CA A:CAS89 3.4 62.3 1.0 N A:ILE90 4.0 53.4 1.0 C A:CAS89 4.0 56.6 1.0 O A:HOH261 4.2 54.1 1.0 O A:ILE90 4.7 54.7 1.0 N A:CAS89 4.8 59.6 1.0 C A:ILE90 4.8 55.5 1.0 O A:CAS89 4.9 55.0 1.0 O A:LEU88 4.9 60.6 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:73.8 occ:1.00 AS C:CAS77 0.0 73.8 1.0 CE1 C:CAS77 2.0 65.8 1.0 CE2 C:CAS77 2.0 74.2 1.0 SG C:CAS77 2.2 56.3 1.0 CB C:CAS77 3.1 44.3 1.0 CA C:CAS77 3.6 38.1 1.0 CA C:GLY106 4.2 45.9 1.0 CE K:MET45 4.2 1.0 1.0 O C:THR105 4.3 39.2 1.0 C C:CAS77 4.4 36.6 1.0 N C:GLY106 4.4 42.3 1.0 C C:THR105 4.5 42.0 1.0 N C:ASN78 4.6 35.5 1.0 CZ K:PHE109 4.6 46.9 1.0 CZ C:PHE148 4.7 70.4 1.0 N C:CAS77 4.8 38.0 1.0 CE2 C:PHE148 4.8 68.7 1.0 SD K:MET45 4.9 99.6 1.0 O C:PHE76 4.9 38.6 1.0 O C:GLY104 4.9 53.0 1.0 NH2 C:ARG79 5.0 73.6 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:65.1 occ:1.00 AS D:CAS60 0.0 65.1 1.0 CE1 D:CAS60 2.0 67.6 1.0 CE2 D:CAS60 2.0 75.4 1.0 SG D:CAS60 2.2 61.0 1.0 CB D:CAS60 3.1 51.4 1.0 CA D:CAS60 3.3 45.8 1.0 N D:CAS60 3.9 43.7 1.0 CD2 D:LEU51 4.1 63.6 1.0 NE2 D:GLN49 4.4 57.6 1.0 O D:GLU59 4.4 47.3 1.0 C D:GLU59 4.4 45.3 1.0 C D:CAS60 4.5 45.2 1.0 CG D:LYS55 4.7 62.8 1.0 CB D:LYS55 4.8 61.2 1.0 O D:CAS60 4.8 45.1 1.0 CD D:GLN49 4.8 57.4 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.3 occ:1.00 AS D:CAS89 0.0 0.3 1.0 CE1 D:CAS89 2.0 0.5 1.0 CE2 D:CAS89 2.0 0.6 1.0 SG D:CAS89 2.2 0.9 1.0 CB D:CAS89 3.0 0.6 1.0 CA D:CAS89 3.5 90.4 1.0 N D:ILE90 4.0 82.4 1.0 C D:CAS89 4.1 85.3 1.0 O D:ILE90 4.8 80.7 1.0 N D:CAS89 4.8 86.7 1.0 C D:ILE90 4.9 81.3 1.0 O D:LEU88 4.9 85.9 1.0 OE2 D:GLU91 4.9 0.4 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:73.8 occ:1.00 AS F:CAS77 0.0 73.8 1.0 CE1 F:CAS77 2.0 74.8 1.0 CE2 F:CAS77 2.0 74.3 1.0 SG F:CAS77 2.2 63.1 1.0 CB F:CAS77 3.2 49.3 1.0 CA F:CAS77 3.6 43.3 1.0 CA F:GLY106 4.0 53.7 1.0 O F:THR105 4.2 42.9 1.0 N F:GLY106 4.2 50.3 1.0 C F:THR105 4.3 47.4 1.0 C F:CAS77 4.3 38.9 1.0 CE H:MET45 4.5 91.9 1.0 N F:ASN78 4.5 36.3 1.0 CE2 F:PHE148 4.7 62.8 1.0 CZ F:PHE148 4.8 69.5 1.0 N F:CAS77 4.8 42.4 1.0 O F:PHE76 4.9 40.8 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:74.9 occ:1.00 AS G:CAS60 0.0 74.9 1.0 CE1 G:CAS60 2.0 75.7 1.0 CE2 G:CAS60 2.0 77.5 1.0 SG G:CAS60 2.2 71.3 1.0 CB G:CAS60 3.1 61.6 1.0 CA G:CAS60 3.3 59.0 1.0 N G:CAS60 4.0 57.3 1.0 CD2 G:LEU51 4.1 68.7 1.0 NE2 G:GLN49 4.4 65.1 1.0 C G:CAS60 4.5 56.5 1.0 C G:GLU59 4.6 60.3 1.0 O G:GLU59 4.7 60.0 1.0 CD G:GLN49 4.7 62.6 1.0 O G:CAS60 4.7 54.1 1.0 CB G:LYS55 4.8 69.4 1.0 CG G:LYS55 4.8 72.1 1.0 OE1 G:GLN49 5.0 60.3 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.4 occ:1.00 AS G:CAS89 0.0 0.4 1.0 CE2 G:CAS89 2.0 0.8 1.0 CE1 G:CAS89 2.0 0.4 1.0 SG G:CAS89 2.2 84.4 1.0 CB G:CAS89 3.0 71.5 1.0 CA G:CAS89 3.6 65.5 1.0 N G:ILE90 4.0 56.7 1.0 C G:CAS89 4.1 61.3 1.0 O G:HOH211 4.6 60.1 1.0 O G:ILE90 4.7 56.8 1.0 C G:ILE90 4.7 59.1 1.0 N G:CAS89 4.9 63.7 1.0 CA G:ILE90 5.0 58.0 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:66.1 occ:1.00 AS I:CAS77 0.0 66.1 1.0 CE1 I:CAS77 2.0 70.7 1.0 CE2 I:CAS77 2.0 61.8 1.0 SG I:CAS77 2.2 54.4 1.0 CB I:CAS77 3.1 43.6 1.0 CA I:CAS77 3.5 38.2 1.0 CA I:GLY106 3.8 39.6 1.0 N I:GLY106 4.0 38.9 1.0 O I:THR105 4.1 36.3 1.0 C I:THR105 4.1 40.0 1.0 C I:CAS77 4.2 36.6 1.0 N I:ASN78 4.3 35.2 1.0 N I:CAS77 4.8 35.2 1.0 O I:PHE76 4.9 37.8 1.0 NH1 I:ARG79 5.0 76.2 1.0

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


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 (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:63.2 occ:1.00 AS J:CAS60 0.0 63.2 1.0 CE1 J:CAS60 2.0 66.2 1.0 CE2 J:CAS60 2.0 67.7 1.0 SG J:CAS60 2.3 51.7 1.0 CB J:CAS60 3.2 43.8 1.0 CA J:CAS60 3.4 43.9 1.0 CD2 J:LEU51 3.9 47.0 1.0 N J:CAS60 4.1 41.8 1.0 NE2 J:GLN49 4.3 48.8 1.0 O J:GLU59 4.5 43.5 1.0 C J:CAS60 4.5 43.3 1.0 C J:GLU59 4.6 45.4 1.0 CB J:LYS55 4.7 46.5 1.0 CG J:LYS55 4.7 48.3 1.0 O J:CAS60 4.7 47.3 1.0 CD J:GLN49 4.8 46.3 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