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Arsenic in PDB 5dal: Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione

Enzymatic activity of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione

All present enzymatic activity of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione, PDB code: 5dal was solved by L.J.Parker, M.W.Parker, C.J.Morton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.550, 90.220, 68.670, 90.00, 98.01, 90.00
R / Rfree (%) 18 / 21.3

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione (pdb code 5dal). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione, PDB code: 5dal:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 5dal

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Arsenic binding site 1 out of 4 in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As302

b:32.1
occ:0.60
 AS1 A:5AU302 0.0 32.1 0.6
HSG A:GSH303 1.8 30.7 0.4
C32 A:5AU302 2.1 26.3 0.6
S10 A:5AU302 2.3 33.4 0.6
S12 A:5AU302 2.4 28.9 0.6
HB23 A:GSH303 2.5 27.3 0.4
SG2 A:GSH303 2.7 25.6 0.4
H13A A:5AU302 3.0 24.9 0.6
C37 A:5AU302 3.0 29.9 0.6
CB2 A:GSH303 3.0 22.8 0.4
C33 A:5AU302 3.1 26.9 0.6
H37 A:5AU302 3.1 35.9 0.6
H09A A:5AU302 3.2 33.7 0.6
H33 A:5AU302 3.2 32.3 0.6
HH A:TYR108 3.2 29.8 1.0
OH A:TYR108 3.3 24.8 1.0
C13 A:5AU302 3.4 20.8 0.6
C09 A:5AU302 3.4 28.1 0.6
HB22 A:GSH303 3.5 27.3 0.4
CZ A:TYR108 3.6 22.9 1.0
O A:HOH415 3.6 32.2 1.0
HE2 A:TYR108 3.9 27.7 1.0
CE2 A:TYR108 3.9 23.1 1.0
H08 A:5AU302 3.9 29.4 0.6
H13 A:5AU302 4.0 24.9 0.6
O A:HOH470 4.1 21.0 1.0
H09 A:5AU302 4.2 33.7 0.6
CA2 A:GSH303 4.2 21.1 0.4
HA2 A:GSH303 4.3 25.3 0.4
O A:HOH584 4.3 23.8 1.0
CE1 A:TYR108 4.3 24.6 1.0
C36 A:5AU302 4.3 26.9 0.6
C34 A:5AU302 4.4 26.4 0.6
C08 A:5AU302 4.4 24.5 0.6
HH A:TYR7 4.5 21.6 1.0
C14 A:5AU302 4.5 23.8 0.6
HE1 A:TYR108 4.5 29.6 1.0
H A:GLY205 4.6 27.6 1.0
HN27 A:5AU302 4.6 25.9 0.6
OH A:TYR7 4.8 18.0 1.0
CD2 A:TYR108 4.8 21.7 1.0
HA3 A:GLY205 4.9 30.0 1.0
C35 A:5AU302 4.9 32.3 0.6

Arsenic binding site 2 out of 4 in 5dal

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Arsenic binding site 2 out of 4 in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As304

b:26.9
occ:0.60
 AS7 A:PA0304 0.0 26.9 0.6
C1 A:PA0304 2.0 34.1 0.6
SG A:CYS101 2.6 29.6 1.0
C2 A:PA0304 2.9 36.8 0.6
H2 A:PA0304 2.9 44.2 0.6
O43 A:5AU302 3.0 26.5 0.6
HB2 A:CYS101 3.0 24.6 1.0
HG A:CYS101 3.1 35.6 1.0
C6 A:PA0304 3.1 27.7 0.6
H6 A:PA0304 3.2 33.2 0.6
HA A:CYS101 3.3 23.5 1.0
CB A:CYS101 3.3 20.5 1.0
HH21 A:ARG13 3.4 25.5 1.0
O A:HOH564 3.5 36.2 1.0
H41 A:5AU302 3.6 25.7 0.6
C42 A:5AU302 3.7 21.8 0.6
CA A:CYS101 3.8 19.6 1.0
HH22 A:ARG13 3.8 25.5 1.0
NH2 A:ARG13 4.0 21.3 1.0
H41A A:5AU302 4.0 25.7 0.6
C41 A:5AU302 4.0 21.4 0.6
HG B:CYS101 4.1 31.1 1.0
HB3 A:CYS101 4.2 24.6 1.0
C3 A:PA0304 4.2 39.2 0.6
O A:HOH460 4.3 31.6 1.0
C5 A:PA0304 4.4 33.5 0.6
OE2 A:GLU97 4.4 13.9 0.5
HD12 A:ILE104 4.5 23.7 1.0
O44 A:5AU302 4.6 19.7 0.6
C A:CYS101 4.7 18.8 1.0
HB A:ILE104 4.7 25.3 1.0
O A:CYS101 4.7 20.5 1.0
C4 A:PA0304 4.8 34.6 0.6
HD13 A:ILE104 4.9 23.7 1.0
N A:CYS101 4.9 16.1 1.0
HG23 A:ILE104 5.0 26.5 1.0

Arsenic binding site 3 out of 4 in 5dal

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Arsenic binding site 3 out of 4 in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As303

b:30.1
occ:0.58
 AS1 B:5AU303 0.0 30.1 0.6
C32 B:5AU303 2.0 30.0 0.6
HSG B:GSH304 2.3 31.8 0.4
S10 B:5AU303 2.3 31.3 0.6
S12 B:5AU303 2.4 27.7 0.6
HB22 B:GSH304 2.5 25.3 0.4
SG2 B:GSH304 2.8 26.5 0.4
C37 B:5AU303 3.0 31.7 0.6
C33 B:5AU303 3.0 30.4 0.6
H09A B:5AU303 3.0 28.2 0.6
H37 B:5AU303 3.1 38.0 0.6
CB2 B:GSH304 3.1 21.1 0.4
H13A B:5AU303 3.1 24.2 0.6
H33 B:5AU303 3.2 36.4 0.6
HH B:TYR108 3.2 27.0 1.0
OH B:TYR108 3.2 22.5 1.0
C09 B:5AU303 3.3 23.5 0.6
C13 B:5AU303 3.4 20.2 0.6
O B:HOH420 3.5 31.0 1.0
HB23 B:GSH304 3.6 25.3 0.4
CZ B:TYR108 3.6 24.1 1.0
O B:HOH418 3.7 21.1 1.0
HE2 B:TYR108 3.9 26.5 1.0
CE2 B:TYR108 3.9 22.1 1.0
H09 B:5AU303 3.9 28.2 0.6
H14 B:5AU303 4.0 24.3 0.6
O B:HOH597 4.0 20.9 1.0
H08 B:5AU303 4.1 27.3 0.6
H13 B:5AU303 4.2 24.2 0.6
HH B:TYR7 4.3 21.5 1.0
HA2 B:GSH304 4.3 24.4 0.4
CE1 B:TYR108 4.3 25.2 1.0
CA2 B:GSH304 4.3 20.3 0.4
C36 B:5AU303 4.3 39.6 0.6
C34 B:5AU303 4.3 27.6 0.6
C08 B:5AU303 4.4 22.8 0.6
C14 B:5AU303 4.4 20.3 0.6
HE1 B:TYR108 4.5 30.2 1.0
H B:GLY205 4.6 25.3 1.0
OH B:TYR7 4.7 17.9 1.0
CD2 B:TYR108 4.8 21.2 1.0
C35 B:5AU303 4.9 27.7 0.6
HN3 B:GSH304 5.0 28.3 0.4

Arsenic binding site 4 out of 4 in 5dal

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Arsenic binding site 4 out of 4 in the Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Human Glutathione Transferase Pi Complexed with A Metalloid in the Presence of Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As305

b:24.4
occ:0.60
 AS7 B:PA0305 0.0 24.4 0.6
C1 B:PA0305 2.0 29.8 0.6
SG B:CYS101 2.7 25.9 1.0
C2 B:PA0305 2.8 28.4 0.6
H2 B:PA0305 2.9 34.1 0.6
O43 B:5AU303 3.0 27.7 0.6
C6 B:PA0305 3.0 23.6 0.6
HB2 B:CYS101 3.1 21.8 1.0
HA B:CYS101 3.1 20.2 1.0
HG B:CYS101 3.2 31.1 1.0
H6 B:PA0305 3.2 28.3 0.6
CB B:CYS101 3.3 18.1 1.0
HH21 B:ARG13 3.4 24.9 1.0
H41 B:5AU303 3.5 28.1 0.6
C42 B:5AU303 3.7 18.2 0.6
CA B:CYS101 3.7 16.9 1.0
HH22 B:ARG13 3.8 24.9 1.0
NH2 B:ARG13 3.9 20.7 1.0
C41 B:5AU303 4.0 23.4 0.6
H41A B:5AU303 4.2 28.1 0.6
C3 B:PA0305 4.2 34.6 0.6
HG A:CYS101 4.2 35.6 1.0
HB3 B:CYS101 4.2 21.8 1.0
C5 B:PA0305 4.3 26.0 0.6
O B:HOH421 4.5 28.6 1.0
O44 B:5AU303 4.5 22.0 0.6
O B:CYS101 4.5 18.3 1.0
C B:CYS101 4.6 16.2 1.0
HD11 B:ILE104 4.6 25.4 1.0
OE2 B:GLU97 4.6 26.2 1.0
HB B:ILE104 4.6 19.6 1.0
C4 B:PA0305 4.8 31.4 0.6
N B:CYS101 4.9 13.1 1.0

Reference:

L.J.Parker, M.W.Parker, C.J.Morton, A.Bocedi, D.B.Ascher, J.B.Aitken, H.H.Harris, M.Lo Bello, G.Ricci. Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-Based Therapeutics To Be Published.
Page generated: Sat Dec 12 01:46:30 2020

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