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

Protein crystallography data

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

Other elements in 6gfy:

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

Arsenic Binding Sites:

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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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 6gfy

Go back to Arsenic Binding Sites List in 6gfy
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

Reference:

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
Page generated: Sat Dec 12 01:48:53 2020

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