Atomistry » Arsenic » PDB 5yvb-6i5n » 6gmn
Atomistry »
  Arsenic »
    PDB 5yvb-6i5n »
      6gmn »

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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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

Go back to Arsenic Binding Sites List in 6gmn
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: Wed Jul 10 13:17:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy