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Arsenic in PDB 4bkt: Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide

Protein crystallography data

The structure of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide, PDB code: 4bkt was solved by I.Van Molle, D.M.Dias, M.Baud, C.Galdeano, C.F.G.C.Geraldes, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 2.35
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.180, 93.180, 364.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.02 / 22.75

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide (pdb code 4bkt). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide, PDB code: 4bkt:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 4bkt

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Arsenic binding site 1 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:75.8
occ:0.51
 AS A:CAS89 0.0 75.8 0.5
CE1 A:CAS89 2.0 77.5 0.5
CE2 A:CAS89 2.0 78.5 0.5
SG A:CAS89 2.2 72.5 1.0
CB A:CAS89 3.0 66.3 1.0
C A:CAS89 3.8 55.1 1.0
CA A:CAS89 3.8 57.6 1.0
N A:ILE90 3.9 47.1 1.0
C A:ILE90 4.1 47.6 1.0
O A:ILE90 4.2 47.3 1.0
O A:CAS89 4.2 54.4 1.0
N A:GLU91 4.2 44.3 1.0
CG A:GLU91 4.3 71.4 1.0
OE2 A:GLU91 4.5 0.5 1.0
CA A:ILE90 4.5 44.0 1.0
CA A:GLU91 4.6 46.8 1.0
CD A:GLU91 4.8 0.3 1.0
O A:HOH2062 4.8 50.0 1.0

Arsenic binding site 2 out of 8 in 4bkt

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Arsenic binding site 2 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:67.3
occ:0.63
 AS C:CAS77 0.0 67.3 0.6
CE2 C:CAS77 2.0 67.7 0.6
CE1 C:CAS77 2.0 71.1 0.6
SG C:CAS77 2.2 64.1 1.0
CB C:CAS77 3.3 55.5 1.0
CA C:CAS77 3.7 48.1 1.0
CA C:GLY106 4.0 55.6 1.0
N C:GLY106 4.1 56.6 1.0
O C:THR105 4.2 55.0 1.0
C C:THR105 4.2 58.5 1.0
C C:CAS77 4.3 47.0 1.0
N C:ASN78 4.4 41.8 1.0
CZ C:PHE148 4.5 72.8 1.0
SD K:MET45 4.6 77.8 1.0
N C:CAS77 4.9 45.7 1.0
O C:PHE76 5.0 47.4 1.0

Arsenic binding site 3 out of 8 in 4bkt

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Arsenic binding site 3 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:90.8
occ:0.41
 AS D:CAS89 0.0 90.8 0.4
CE1 D:CAS89 2.0 86.7 0.4
CE2 D:CAS89 2.0 91.5 0.4
SG D:CAS89 2.3 87.9 1.0
CB D:CAS89 3.0 83.1 1.0
CA D:CAS89 3.7 75.4 1.0
O D:HOH2025 4.3 56.0 1.0
C D:CAS89 4.4 72.6 1.0
N D:ILE90 4.5 65.3 1.0
O D:LEU88 4.6 76.6 1.0
N D:CAS89 4.9 74.1 1.0
O D:ILE90 4.9 68.6 1.0

Arsenic binding site 4 out of 8 in 4bkt

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Arsenic binding site 4 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:62.2
occ:0.57
 AS F:CAS77 0.0 62.2 0.6
CE1 F:CAS77 2.0 62.7 0.6
CE2 F:CAS77 2.0 65.2 0.6
SG F:CAS77 2.2 59.1 1.0
CB F:CAS77 3.2 51.2 1.0
CA F:CAS77 3.5 45.2 1.0
CE H:MET45 3.7 84.9 1.0
CA F:GLY106 3.9 48.6 1.0
N F:GLY106 4.0 49.2 1.0
C F:THR105 4.0 49.9 1.0
O F:THR105 4.1 45.0 1.0
C F:CAS77 4.2 43.9 1.0
N F:ASN78 4.4 38.7 1.0
CZ H:PHE109 4.6 64.1 1.0
CE2 F:PHE148 4.7 69.1 1.0
O F:PHE76 4.8 46.0 1.0
N F:CAS77 4.8 43.8 1.0
CA F:THR105 4.9 48.7 1.0

Arsenic binding site 5 out of 8 in 4bkt

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Arsenic binding site 5 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:70.5
occ:0.37
 AS G:CAS89 0.0 70.5 0.4
CE1 G:CAS89 2.0 68.5 0.4
CE2 G:CAS89 2.0 71.7 0.4
SG G:CAS89 2.3 68.4 1.0
CB G:CAS89 3.1 63.0 1.0
CA G:CAS89 3.7 57.0 1.0
O G:HOH2022 3.9 54.2 1.0
N G:ILE90 4.1 52.2 1.0
C G:CAS89 4.2 58.2 1.0
O G:ILE90 4.6 52.4 1.0
C G:ILE90 4.8 53.0 1.0

Arsenic binding site 6 out of 8 in 4bkt

Go back to Arsenic Binding Sites List in 4bkt
Arsenic binding site 6 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:61.5
occ:0.60
 AS I:CAS77 0.0 61.5 0.6
CE1 I:CAS77 2.0 61.8 0.6
CE2 I:CAS77 2.0 63.1 0.6
SG I:CAS77 2.3 57.6 1.0
CB I:CAS77 3.2 48.5 1.0
CA I:CAS77 3.6 42.8 1.0
CA I:GLY106 3.6 48.7 1.0
N I:GLY106 3.8 48.1 1.0
C I:THR105 4.1 51.5 1.0
O I:THR105 4.1 48.3 1.0
C I:CAS77 4.2 43.3 1.0
N I:ASN78 4.4 38.5 1.0
CE2 I:PHE148 4.7 56.4 1.0
O I:PHE76 4.8 46.3 1.0
N I:CAS77 4.9 40.9 1.0

Arsenic binding site 7 out of 8 in 4bkt

Go back to Arsenic Binding Sites List in 4bkt
Arsenic binding site 7 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As89

b:57.1
occ:0.46
 AS J:CAS89 0.0 57.1 0.5
CE2 J:CAS89 2.0 58.5 0.5
CE1 J:CAS89 2.0 56.0 0.5
SG J:CAS89 2.2 54.7 1.0
CB J:CAS89 3.2 49.5 1.0
O J:HOH2055 3.5 58.5 1.0
CA J:CAS89 3.8 44.5 1.0
O J:HOH2056 4.1 45.4 1.0
C J:CAS89 4.2 45.2 1.0
N J:ILE90 4.3 40.2 1.0
O J:ILE90 4.6 42.6 1.0
C J:ILE90 4.8 41.3 1.0
OE2 J:GLU91 4.9 46.2 1.0

Arsenic binding site 8 out of 8 in 4bkt

Go back to Arsenic Binding Sites List in 4bkt
Arsenic binding site 8 out of 8 in the Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Von Hippel Lindau Protein:Elonginb:Elonginc Complex, in Complex with (2S,4R)-N-Methyl-1-[2-(3-Methyl-1,2-Oxazol-5-Yl)Ethanoyl]-4- Oxidanyl-Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:As77

b:68.6
occ:1.00
 AS L:CAS77 0.0 68.6 1.0
CE2 L:CAS77 2.0 68.7 1.0
CE1 L:CAS77 2.0 70.8 1.0
SG L:CAS77 2.3 59.4 1.0
CB L:CAS77 3.3 49.5 1.0
CA L:CAS77 3.5 41.2 1.0
CA L:GLY106 3.8 37.4 1.0
N L:GLY106 3.9 38.4 1.0
O L:THR105 4.0 38.2 1.0
C L:THR105 4.1 42.0 1.0
C L:CAS77 4.1 39.0 1.0
N L:ASN78 4.2 35.1 1.0
CE2 L:PHE148 4.7 49.1 1.0
N L:CAS77 4.8 39.7 1.0
O L:PHE76 4.8 37.9 1.0
O L:CAS77 4.9 36.4 1.0
CA L:THR105 5.0 41.1 1.0

Reference:

D.M.Dias, I.Van Molle, M.G.J.Baud, C.Galdeano, C.F.G.C.Geraldes, A.Ciulli. Is uc(Nmr) Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions? Acs Med.Chem.Lett. V. 5 23 2014.
ISSN: ISSN 1948-5875
PubMed: 24436777
DOI: 10.1021/ML400296C
Page generated: Sun Jul 6 23:37:15 2025

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