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Arsenic in PDB 6gmq: Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol, PDB code: 6gmq 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) 29.67 / 2.76
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.830, 93.830, 363.820, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 27.9

Arsenic Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol (pdb code 6gmq). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 14 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol, PDB code: 6gmq:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 14 in 6gmq

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Arsenic binding site 1 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:0.1
occ:1.00
AS A:CAS60 0.0 0.1 1.0
CE2 A:CAS60 2.0 0.7 1.0
CE1 A:CAS60 2.0 0.2 1.0
SG A:CAS60 2.3 45.8 1.0
CB A:CAS60 3.3 39.6 1.0
CA A:CAS60 3.5 31.4 1.0
CD2 A:LEU51 4.0 38.6 1.0
N A:CAS60 4.0 31.3 1.0
CB A:LYS55 4.2 38.9 1.0
CG A:LYS55 4.4 40.7 1.0
C A:GLU59 4.4 39.8 1.0
O A:GLU59 4.4 33.3 1.0
CD A:LYS55 4.7 49.5 1.0
C A:CAS60 4.8 32.6 1.0
NE2 A:GLN49 5.0 37.4 1.0

Arsenic binding site 2 out of 14 in 6gmq

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Arsenic binding site 2 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:98.9
occ:1.00
AS A:CAS89 0.0 98.9 1.0
CE1 A:CAS89 2.0 0.3 1.0
CE2 A:CAS89 2.0 89.8 1.0
SG A:CAS89 2.2 77.2 1.0
CB A:CAS89 3.0 57.9 1.0
CA A:CAS89 3.9 47.6 1.0
C A:CAS89 4.2 40.8 1.0
N A:ILE90 4.3 37.9 1.0
C A:ILE90 4.8 33.1 1.0
O A:CAS89 4.8 45.5 1.0
N A:GLU91 4.8 37.1 1.0
O A:ILE90 5.0 35.2 1.0

Arsenic binding site 3 out of 14 in 6gmq

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Arsenic binding site 3 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As112

b:82.8
occ:1.00
AS B:CAS112 0.0 82.8 1.0
CE2 B:CAS112 2.0 81.8 1.0
CE1 B:CAS112 2.0 100.0 1.0
SG B:CAS112 2.2 65.7 1.0
CB B:CAS112 2.9 54.3 1.0
CE1 B:PHE77 4.0 34.2 1.0
CG1 B:VAL73 4.0 34.3 1.0
CD1 B:LEU110 4.1 35.0 1.0
CB B:LEU110 4.3 35.7 1.0
CA B:CAS112 4.3 54.7 1.0
CZ B:PHE77 4.3 34.2 1.0
CD2 C:LEU158 4.5 36.1 1.0
C B:CAS112 4.8 55.9 1.0
CB B:SER39 4.8 69.3 1.0
N B:CAS112 4.8 41.9 1.0
CG B:LEU110 4.8 37.1 1.0
CD1 B:PHE77 4.9 34.0 1.0
CB C:LEU158 5.0 40.6 1.0
OXT B:CAS112 5.0 48.0 1.0

Arsenic binding site 4 out of 14 in 6gmq

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Arsenic binding site 4 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:96.7
occ:1.00
AS C:CAS77 0.0 96.7 1.0
CE2 C:CAS77 2.0 97.3 1.0
CE1 C:CAS77 2.0 0.1 1.0
SG C:CAS77 2.2 81.0 1.0
CB C:CAS77 3.2 71.8 1.0
CA C:CAS77 3.5 58.6 1.0
O C:THR105 4.1 65.8 1.0
C C:CAS77 4.2 54.6 1.0
N C:ASN78 4.2 37.8 1.0
CZ C:PHE148 4.4 88.3 1.0
SD K:MET45 4.5 65.2 1.0
NH1 C:ARG79 4.6 76.5 1.0
N C:CAS77 4.7 44.8 1.0
O C:GLY104 4.8 57.8 1.0
C C:THR105 4.9 68.8 1.0
CA C:GLY106 4.9 79.2 1.0

Arsenic binding site 5 out of 14 in 6gmq

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Arsenic binding site 5 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:0.4
occ:1.00
AS D:CAS60 0.0 0.4 1.0
CE1 D:CAS60 2.0 0.7 1.0
CE2 D:CAS60 2.0 0.9 1.0
SG D:CAS60 2.3 53.8 1.0
CB D:CAS60 3.2 32.9 1.0
CA D:CAS60 3.5 32.8 1.0
CD2 D:LEU51 3.7 65.5 1.0
N D:CAS60 4.1 38.0 1.0
NE2 D:GLN49 4.4 59.4 1.0
CB D:LYS55 4.4 58.5 1.0
CG D:LYS55 4.4 56.4 1.0
O D:GLU59 4.6 47.7 1.0
C D:GLU59 4.6 42.4 1.0
C D:CAS60 4.7 35.7 1.0
CD D:GLN49 4.9 53.8 1.0
O D:CAS60 4.9 36.9 1.0
CD D:LYS55 5.0 61.0 1.0

Arsenic binding site 6 out of 14 in 6gmq

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Arsenic binding site 6 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:0.6
occ:1.00
AS D:CAS89 0.0 0.6 1.0
CE2 D:CAS89 2.0 0.1 1.0
CE1 D:CAS89 2.0 1.0 1.0
SG D:CAS89 2.2 88.5 1.0
CB D:CAS89 3.1 87.3 1.0
CA D:CAS89 4.0 84.7 1.0
N D:ILE90 4.3 77.0 1.0
C D:CAS89 4.4 76.8 1.0
C D:ILE90 4.7 58.9 1.0
O D:ILE90 4.7 54.2 1.0
CG D:GLU91 4.8 88.2 1.0
N D:GLU91 4.8 64.8 1.0

Arsenic binding site 7 out of 14 in 6gmq

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Arsenic binding site 7 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As112

b:87.2
occ:1.00
AS E:CAS112 0.0 87.2 1.0
CE2 E:CAS112 2.0 93.7 1.0
CE1 E:CAS112 2.0 96.7 1.0
SG E:CAS112 2.2 77.1 1.0
CB E:CAS112 2.8 56.1 1.0
CE1 E:PHE77 4.0 46.3 1.0
CD1 E:LEU110 4.1 38.5 1.0
CB E:LEU110 4.1 38.9 1.0
CA E:CAS112 4.2 62.0 1.0
OXT E:CAS112 4.4 52.7 1.0
C E:CAS112 4.5 59.9 1.0
CD2 F:LEU158 4.5 40.3 1.0
CZ E:PHE77 4.6 39.5 1.0
N E:CAS112 4.7 47.5 1.0
CB E:SER39 4.7 64.7 1.0
CG E:LEU110 4.8 38.8 1.0
CG1 E:VAL73 4.8 37.5 1.0
CB F:LEU158 4.8 38.0 1.0
CD1 E:PHE77 4.8 49.5 1.0
O E:LEU110 4.9 51.4 1.0
CD2 E:TYR76 4.9 37.9 1.0
CA E:ALA107 4.9 49.1 1.0

Arsenic binding site 8 out of 14 in 6gmq

Go back to Arsenic Binding Sites List in 6gmq
Arsenic binding site 8 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:0.9
occ:1.00
AS F:CAS77 0.0 0.9 1.0
CE2 F:CAS77 2.0 0.4 1.0
CE1 F:CAS77 2.0 0.1 1.0
SG F:CAS77 2.2 99.6 1.0
CB F:CAS77 3.3 92.4 1.0
CA F:CAS77 3.6 77.1 1.0
N F:ASN78 4.1 56.9 1.0
C F:CAS77 4.1 63.8 1.0
O F:THR105 4.2 69.6 1.0
CE H:MET45 4.3 83.9 1.0
O F:GLY104 4.6 63.0 1.0
CZ F:PHE148 4.8 0.6 1.0
N F:CAS77 4.9 66.7 1.0
C F:THR105 4.9 80.7 1.0
CA F:GLY106 4.9 87.4 1.0
NE F:ARG79 4.9 81.5 1.0
O F:PHE76 5.0 64.2 1.0

Arsenic binding site 9 out of 14 in 6gmq

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Arsenic binding site 9 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:77.3
occ:1.00
AS G:CAS60 0.0 77.3 1.0
CE2 G:CAS60 2.0 79.6 1.0
CE1 G:CAS60 2.0 90.8 1.0
SG G:CAS60 2.2 58.9 1.0
CB G:CAS60 3.3 46.7 1.0
CA G:CAS60 3.6 45.1 1.0
CD2 G:LEU51 3.7 54.0 1.0
NE2 G:GLN49 4.1 56.0 1.0
N G:CAS60 4.2 42.1 1.0
CB G:LYS55 4.6 54.9 1.0
CG G:LYS55 4.7 52.2 1.0
CD G:GLN49 4.7 62.8 1.0
C G:GLU59 4.8 47.8 1.0
O G:GLU59 4.8 54.2 1.0

Arsenic binding site 10 out of 14 in 6gmq

Go back to Arsenic Binding Sites List in 6gmq
Arsenic binding site 10 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:90.3
occ:1.00
AS G:CAS89 0.0 90.3 1.0
CE2 G:CAS89 2.0 97.7 1.0
CE1 G:CAS89 2.0 92.9 1.0
SG G:CAS89 2.2 64.4 1.0
CB G:CAS89 2.9 50.5 1.0
CA G:CAS89 3.7 42.6 1.0
N G:ILE90 4.1 31.0 1.0
C G:CAS89 4.1 42.0 1.0
O G:ILE90 4.7 42.5 1.0
C G:ILE90 4.7 42.6 1.0
OE2 G:GLU91 4.8 56.6 1.0
O G:CAS89 5.0 39.0 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 13:18:43 2024

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