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Arsenic in PDB 6gmn: Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate, PDB code: 6gmn was solved by I.Van Molle, X.Lucas, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 1.94
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.710, 93.710, 364.860, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.4

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate (pdb code 6gmn). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 10 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate, PDB code: 6gmn:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 10 in 6gmn

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Arsenic binding site 1 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:0.6
occ:0.90
 AS A:CAS60 0.0 0.6 0.9
CE2 A:CAS60 2.0 0.1 0.9
CE1 A:CAS60 2.0 0.5 0.9
SG A:CAS60 2.3 39.2 0.9
CB A:CAS60 3.2 27.9 0.9
CA A:CAS60 3.5 30.9 0.9
CD2 A:LEU51 3.7 32.2 1.0
N A:CAS60 4.2 26.7 0.9
CB A:LYS55 4.2 43.4 1.0
CG A:LYS55 4.4 39.2 1.0
O A:GLU59 4.5 36.0 1.0
C A:GLU59 4.6 26.7 1.0
C A:CAS60 4.7 28.8 0.9
CA A:LEU51 4.8 33.4 1.0
NE2 A:GLN49 4.8 39.0 1.0
CB A:LEU51 4.8 35.0 1.0
N A:ASP52 4.8 38.0 1.0
CG A:LEU51 4.9 28.1 1.0
O A:CAS60 5.0 30.8 0.9

Arsenic binding site 2 out of 10 in 6gmn

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Arsenic binding site 2 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:85.9
occ:0.88
 AS C:CAS77 0.0 85.9 0.9
CE2 C:CAS77 2.0 85.2 0.9
CE1 C:CAS77 2.0 0.0 0.9
SG C:CAS77 2.2 71.4 0.9
CB C:CAS77 3.1 51.9 0.9
CA C:CAS77 3.4 37.4 0.9
C C:CAS77 3.9 32.6 0.9
O C:THR105 4.1 46.0 1.0
N C:ASN78 4.1 36.2 1.0
CA C:GLY106 4.3 45.6 1.0
C C:THR105 4.3 50.4 1.0
N C:GLY106 4.3 43.1 1.0
CZ C:PHE148 4.6 89.7 1.0
N C:CAS77 4.7 35.6 0.9
CG C:ARG79 4.8 65.6 1.0
NH1 C:ARG79 4.8 76.7 1.0
O C:CAS77 4.8 33.6 0.9
O C:GLY104 4.9 65.6 1.0
O C:PHE76 4.9 48.5 1.0

Arsenic binding site 3 out of 10 in 6gmn

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Arsenic binding site 3 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:79.7
occ:0.93
 AS D:CAS60 0.0 79.7 0.9
CE1 D:CAS60 2.0 92.0 0.9
CE2 D:CAS60 2.0 85.6 0.9
SG D:CAS60 2.3 46.8 0.9
CB D:CAS60 3.2 37.0 0.9
CA D:CAS60 3.5 31.9 0.9
CD2 D:LEU51 4.1 36.7 1.0
N D:CAS60 4.2 31.1 0.9
O D:GLU59 4.5 42.5 1.0
CB D:LYS55 4.5 50.5 1.0
CG D:LYS55 4.5 46.8 1.0
NE2 D:GLN49 4.6 43.7 1.0
C D:GLU59 4.6 33.5 1.0
C D:CAS60 4.7 26.5 0.9
O D:CAS60 4.9 35.9 0.9
CD D:GLN49 4.9 39.7 1.0

Arsenic binding site 4 out of 10 in 6gmn

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Arsenic binding site 4 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:0.8
occ:0.88
 AS D:CAS89 0.0 0.8 0.9
CE1 D:CAS89 2.0 0.0 0.9
CE2 D:CAS89 2.0 0.6 0.9
SG D:CAS89 2.2 73.0 0.9
CB D:CAS89 3.1 58.9 0.9
CA D:CAS89 3.6 54.7 0.9
N D:ILE90 4.0 54.2 1.0
C D:CAS89 4.0 50.4 0.9
O D:HOH231 4.2 56.1 1.0
O D:ILE90 4.6 56.4 1.0
C D:ILE90 4.7 48.5 1.0
N D:CAS89 4.9 49.5 0.9
CA D:ILE90 4.9 53.5 1.0
O D:CAS89 5.0 44.2 0.9

Arsenic binding site 5 out of 10 in 6gmn

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Arsenic binding site 5 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:82.6
occ:0.85
 AS F:CAS77 0.0 82.6 0.8
CE2 F:CAS77 2.0 68.1 0.8
CE1 F:CAS77 2.0 94.5 0.8
SG F:CAS77 2.2 55.8 0.8
CB F:CAS77 3.1 37.1 0.8
CA F:CAS77 3.7 40.9 0.8
NH2 F:ARG79 3.8 0.2 1.0
C F:CAS77 4.3 36.3 0.8
CE2 F:PHE148 4.5 82.2 1.0
N F:ASN78 4.6 39.8 1.0
O F:THR105 4.6 44.4 1.0
CG F:ARG79 4.7 65.8 1.0
CE H:MET45 4.7 90.0 1.0
CA F:GLY106 4.7 49.6 1.0
C F:THR105 4.8 50.1 1.0
N F:GLY106 4.8 41.8 1.0

Arsenic binding site 6 out of 10 in 6gmn

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Arsenic binding site 6 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:76.1
occ:0.90
 AS G:CAS60 0.0 76.1 0.9
CE2 G:CAS60 2.0 75.6 0.9
CE1 G:CAS60 2.0 87.4 0.9
SG G:CAS60 2.2 55.9 0.9
CB G:CAS60 3.1 42.7 0.9
CA G:CAS60 3.3 38.2 0.9
N G:CAS60 4.1 38.1 0.9
CD2 G:LEU51 4.2 42.6 1.0
NE2 G:GLN49 4.3 48.7 1.0
CB G:LYS55 4.5 45.8 1.0
C G:CAS60 4.5 43.3 0.9
CG G:LYS55 4.6 49.2 1.0
O G:GLU59 4.6 45.4 1.0
C G:GLU59 4.7 47.4 1.0
CD G:GLN49 4.8 46.6 1.0
O G:CAS60 4.8 47.2 0.9

Arsenic binding site 7 out of 10 in 6gmn

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Arsenic binding site 7 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:0.6
occ:0.97
 AS G:CAS89 0.0 0.6 1.0
CE2 G:CAS89 2.0 0.5 1.0
CE1 G:CAS89 2.0 0.7 1.0
SG G:CAS89 2.2 58.9 1.0
CB G:CAS89 3.0 36.5 1.0
CA G:CAS89 3.6 30.7 1.0
N G:ILE90 4.0 35.9 1.0
C G:CAS89 4.0 29.4 1.0
O G:HOH230 4.3 53.0 1.0
O G:ILE90 4.5 38.3 1.0
C G:ILE90 4.7 41.4 1.0
O G:CAS89 4.8 36.2 1.0

Arsenic binding site 8 out of 10 in 6gmn

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Arsenic binding site 8 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As60

b:94.8
occ:0.87
 AS J:CAS60 0.0 94.8 0.9
CE1 J:CAS60 2.0 94.3 0.9
CE2 J:CAS60 2.0 91.8 0.9
SG J:CAS60 2.3 44.6 0.9
CB J:CAS60 3.2 32.6 0.9
CA J:CAS60 3.5 30.0 0.9
CD2 J:LEU51 3.8 34.6 1.0
CG J:LYS55 4.2 41.0 1.0
N J:CAS60 4.2 28.1 0.9
CB J:LYS55 4.3 45.5 1.0
O J:GLU59 4.6 38.1 1.0
NE2 J:GLN49 4.7 34.3 1.0
C J:GLU59 4.7 32.6 1.0
C J:CAS60 4.8 33.8 0.9
CA J:LEU51 4.9 28.2 1.0
CD J:LYS55 4.9 39.2 1.0

Arsenic binding site 9 out of 10 in 6gmn

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Arsenic binding site 9 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As89

b:86.6
occ:0.94
 AS J:CAS89 0.0 86.6 0.9
CE1 J:CAS89 2.0 0.5 0.9
CE2 J:CAS89 2.0 94.1 0.9
SG J:CAS89 2.2 46.9 0.9
CB J:CAS89 3.2 31.5 0.9
O J:HOH250 3.7 57.8 1.0
CA J:CAS89 3.8 28.2 0.9
O J:HOH259 4.0 42.5 1.0
C J:CAS89 4.1 32.6 0.9
O J:HOH248 4.2 53.7 1.0
N J:ILE90 4.2 30.4 1.0
O J:HOH312 4.5 65.0 1.0
O J:ILE90 4.7 33.1 1.0
C J:ILE90 4.7 30.0 1.0
OE2 J:GLU91 4.8 42.5 1.0
O J:CAS89 5.0 30.9 0.9

Arsenic binding site 10 out of 10 in 6gmn

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Arsenic binding site 10 out of 10 in the Pvhl:Elob:Eloc in Complex with Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate


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 Methyl 4H-Furo[3,2-B]Pyrrole-5- Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:As77

b:82.6
occ:0.98
 AS L:CAS77 0.0 82.6 1.0
CE1 L:CAS77 2.0 0.6 1.0
CE2 L:CAS77 2.0 0.8 1.0
SG L:CAS77 2.2 40.0 1.0
CB L:CAS77 3.1 39.7 1.0
CA L:CAS77 3.6 31.1 1.0
CA L:GLY106 3.9 35.5 1.0
O L:THR105 4.1 32.1 1.0
N L:GLY106 4.1 32.1 1.0
C L:THR105 4.2 34.6 1.0
C L:CAS77 4.3 26.4 1.0
N L:ASN78 4.5 24.9 1.0
N L:CAS77 4.9 24.6 1.0
CE2 L:PHE148 4.9 46.4 1.0
NH2 L:ARG79 4.9 89.5 1.0
O L:PHE76 5.0 28.7 1.0

Reference:

X.Lucas, I.Van Molle, A.Ciulli. Surface Probing By Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase. J. Med. Chem. V. 61 7387 2018.
ISSN: ISSN 1520-4804
PubMed: 30040896
DOI: 10.1021/ACS.JMEDCHEM.8B00842
Page generated: Sat Dec 12 01:48:55 2020

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