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Sodium 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:

Arsenic (As) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 8gdt

Go back to Sodium Binding Sites List in 8gdt
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
B:Na202

b:30.0
occ:1.00
 H B:PHE75 2.0 19.4 1.0
O B:ARG38 2.7 27.5 1.0
HA B:GLU74 2.8 23.5 1.0
N B:PHE75 2.9 19.4 1.0
HD2 B:PHE75 3.0 22.8 1.0
HB2 B:PHE75 3.0 19.1 1.0
HG2 B:ARG38 3.1 23.2 1.0
HG3 B:GLU74 3.2 31.0 1.0
CL B:CL203 3.4 30.0 1.0
HH12 B:ARG60 3.4 32.9 0.5
HA B:HIS39 3.5 27.4 1.0
CA B:GLU74 3.6 23.5 1.0
C B:GLU74 3.7 19.8 1.0
CD2 B:PHE75 3.7 22.8 1.0
CB B:PHE75 3.7 19.1 1.0
CA B:PHE75 3.8 18.9 1.0
HG2 B:GLU74 3.9 31.0 1.0
C B:ARG38 3.9 23.1 1.0
CG B:GLU74 3.9 31.0 1.0
CG B:ARG38 4.0 23.2 1.0
NH1 B:ARG60 4.0 32.9 0.5
CG B:PHE75 4.2 20.3 1.0
HH11 B:ARG60 4.2 32.9 0.5
HG3 B:ARG38 4.2 23.2 1.0
HE B:ARG38 4.2 19.6 1.0
CB B:GLU74 4.3 30.9 1.0
O B:PHE75 4.3 19.4 1.0
CA B:HIS39 4.4 27.4 1.0
O B:GLY73 4.6 34.4 1.0
N B:HIS39 4.6 26.3 1.0
HB3 B:PHE75 4.6 19.1 1.0
C B:PHE75 4.6 18.5 1.0
HB2 B:GLU74 4.6 30.9 1.0
HA B:PHE75 4.6 18.9 1.0
HD2 B:HIS39 4.7 41.1 1.0
N B:GLU74 4.7 25.1 1.0
NE B:ARG38 4.7 19.6 1.0
CE2 B:PHE75 4.8 22.1 1.0
CB B:ARG38 4.9 25.0 1.0
CD B:ARG38 4.9 21.6 1.0
CA B:ARG38 4.9 21.5 1.0
HH21 B:ARG60 4.9 41.4 0.5
O B:HIS39 4.9 29.9 1.0
O B:GLU74 4.9 21.3 1.0
HE2 B:PHE75 4.9 22.1 1.0
HB3 B:ARG38 4.9 25.0 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: Wed Oct 9 12:02:46 2024

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