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Arsenic in PDB 8gdt: Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain

Enzymatic activity of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain

All present enzymatic activity of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain:
2.7.11.30;

Protein crystallography data

The structure of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain, PDB code: 8gdt was solved by S.E.White, T.A.Schwartze, A.P.Hinck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.25 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.042, 128.387, 29.654, 90, 90, 90
R / Rfree (%) 21.8 / 23

Other elements in 8gdt:

The structure of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain (pdb code 8gdt). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain, PDB code: 8gdt:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 8gdt

Go back to Arsenic Binding Sites List in 8gdt
Arsenic binding site 1 out of 3 in the Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As202

b:26.2
occ:0.80
 AS A:CAC202 0.0 26.2 0.8
O1 A:CAC202 1.7 32.1 0.8
O2 A:CAC202 1.7 23.7 0.8
C1 A:CAC202 1.9 30.4 0.8
C2 A:CAC202 1.9 27.8 0.8
H13 A:CAC202 2.4 30.4 0.8
H12 A:CAC202 2.4 30.4 0.8
H11 A:CAC202 2.4 30.4 0.8
H22 A:CAC202 2.5 27.8 0.8
H23 A:CAC202 2.5 27.8 0.8
H21 A:CAC202 2.5 27.8 0.8
HD1 A:HIS102 3.2 19.0 0.0
O A:CYS101 3.5 14.5 1.0
O A:HOH308 3.7 59.4 1.0
HA A:HIS102 3.9 13.3 1.0
O A:HOH310 3.9 21.9 1.0
ND1 A:HIS102 4.1 19.0 1.0
HE1 A:TYR108 4.2 18.1 1.0
HH21 B:ARG95 4.3 21.8 1.0
HB2 A:HIS102 4.4 14.9 1.0
HZ A:PHE53 4.5 16.9 1.0
HB A:VAL100 4.6 13.0 1.0
HH A:TYR108 4.6 20.0 0.0
C A:CYS101 4.6 13.0 1.0
HH12 B:ARG95 4.6 29.3 1.0
CA A:HIS102 4.7 13.3 1.0
O A:HOH372 4.8 51.6 1.0
OE2 A:GLU82 4.8 22.7 1.0
CE1 A:TYR108 4.8 18.1 1.0
HG21 A:VAL100 4.8 13.9 1.0
CB A:HIS102 4.9 14.9 1.0
CG A:HIS102 4.9 15.7 1.0

Arsenic binding site 2 out of 3 in 8gdt

Go back to Arsenic Binding Sites List in 8gdt
Arsenic binding site 2 out of 3 in the Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As203

b:55.5
occ:0.50
 AS A:CAC203 0.0 55.5 0.5
O1 A:CAC203 1.7 36.4 0.5
O2 A:CAC203 1.7 43.6 0.5
C2 A:CAC203 1.9 38.0 0.5
C1 A:CAC203 2.0 15.1 0.5
H22 A:CAC203 2.4 38.0 0.5
H23 A:CAC203 2.4 38.0 0.5
H21 A:CAC203 2.5 38.0 0.5
H11 A:CAC203 2.5 15.1 0.5
H13 A:CAC203 2.5 15.1 0.5
H12 A:CAC203 2.5 15.1 0.5
HA A:ASP115 3.3 15.8 1.0
HB2 A:SER118 3.4 17.8 1.0
O A:HOH320 3.9 16.4 1.0
H A:SER118 4.0 14.9 1.0
CA A:ASP115 4.2 15.8 1.0
O A:HOH368 4.3 37.5 1.0
N A:SER118 4.3 14.9 1.0
CB A:SER118 4.3 17.8 1.0
HA A:SER118 4.3 16.6 1.0
HB3 A:ALA117 4.3 17.2 1.0
HB2 A:ASP115 4.4 16.3 1.0
O A:ASP115 4.5 15.3 1.0
CA A:SER118 4.5 16.6 1.0
O A:HOH373 4.5 29.8 1.0
C A:ASP115 4.6 13.0 1.0
O A:GLU114 4.7 16.9 1.0
CB A:ASP115 4.7 16.3 1.0
H A:ALA117 4.7 14.3 1.0
HG A:SER118 4.7 20.1 0.0
HB3 A:ASP115 4.8 16.3 1.0
HB3 A:SER118 4.8 17.8 1.0
C A:ALA117 4.9 16.9 1.0

Arsenic binding site 3 out of 3 in 8gdt

Go back to Arsenic Binding Sites List in 8gdt
Arsenic binding site 3 out of 3 in the Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As204

b:55.5
occ:0.50
 AS A:CAC204 0.0 55.5 0.5
O1 A:CAC204 1.7 24.6 0.5
O2 A:CAC204 1.8 26.6 0.5
C2 A:CAC204 1.9 21.6 0.5
C1 A:CAC204 2.0 34.0 0.5
H23 A:CAC204 2.4 21.6 0.5
H21 A:CAC204 2.4 21.6 0.5
H22 A:CAC204 2.5 21.6 0.5
H11 A:CAC204 2.5 34.0 0.5
H13 A:CAC204 2.5 34.0 0.5
H12 A:CAC204 2.5 34.0 0.5
HZ3 A:LYS126 3.1 40.7 1.0
HD2 A:LYS124 3.5 50.4 1.0
OD1 A:ASP115 3.6 16.2 1.0
HA A:LEU113 3.6 17.1 1.0
HE2 A:LYS126 3.7 32.9 1.0
HE2 A:MET135 3.7 23.1 1.0
NZ A:LYS126 3.9 40.7 1.0
H A:GLU114 3.9 16.7 1.0
O A:ILE112 3.9 19.1 1.0
HA A:CYS136 3.9 13.6 0.5
HZ1 A:LYS126 4.0 40.7 1.0
HA A:CYS136 4.0 13.6 0.5
CG A:ASP115 4.0 14.2 1.0
HD21 A:LEU113 4.1 24.5 1.0
HB2 A:LYS124 4.1 24.0 1.0
OD2 A:ASP115 4.1 17.0 1.0
O A:MET135 4.1 14.1 1.0
HB3 A:MET135 4.2 14.5 1.0
HG2 A:MET135 4.2 17.8 1.0
CE A:LYS126 4.2 32.9 1.0
H A:ASP115 4.3 14.7 1.0
HE3 A:LYS126 4.4 32.9 1.0
CD A:LYS124 4.4 50.4 1.0
HD22 A:LEU113 4.5 24.5 1.0
HZ1 A:LYS124 4.5 26.4 1.0
HD3 A:LYS124 4.5 50.4 1.0
HE1 A:MET135 4.5 23.1 1.0
CE A:MET135 4.6 23.1 1.0
N A:GLU114 4.6 16.7 1.0
CA A:LEU113 4.6 17.1 1.0
HZ2 A:LYS126 4.6 40.7 1.0
C A:MET135 4.6 12.8 1.0
CD2 A:LEU113 4.7 24.5 1.0
CA A:CYS136 4.8 13.6 0.5
H A:SER137 4.8 12.3 1.0
CA A:CYS136 4.8 13.6 0.5
HB3 A:ASP115 4.8 16.3 1.0
HB2 A:GLU114 4.8 24.9 1.0
C A:ILE112 4.9 17.2 1.0
CB A:MET135 4.9 14.5 1.0
HB3 A:PHE111 4.9 21.8 1.0
CG A:MET135 4.9 17.8 1.0
CB A:LYS124 5.0 24.0 1.0

Reference:

S.E.White, T.A.Schwartze, A.P.Hinck. Heligmosomoides Polygyrus Tgf-Beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human Tgf-Beta Type II Receptor Extracellular Domain To Be Published.
Page generated: Sat Sep 28 08:35:22 2024

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