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Sodium in PDB 9e9g: 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: 9e9g 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) 42.22 / 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 (%) 16 / 18.2

Other elements in 9e9g:

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) 2 atoms
Chlorine (Cl) 2 atoms

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 9e9g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium 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: 9e9g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 9e9g

Go back to Sodium Binding Sites List in 9e9g
Sodium binding site 1 out of 5 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
A:Na208

b:36.3
occ:0.62
 CL A:CL207 2.1 42.4 0.4
O A:HOH403 2.3 37.9 0.4
O A:HOH371 2.4 33.6 0.5
O A:HOH412 2.4 39.1 0.5
O A:GLU131 2.5 26.9 1.0
O A:LYS128 2.7 50.8 1.0
H A:GLU131 3.3 35.4 1.0
C A:GLU131 3.5 24.4 1.0
H A:LYS128 3.8 51.8 1.0
C A:LYS128 3.9 50.5 1.0
N A:GLU131 3.9 29.4 1.0
H A:GLY130 3.9 53.2 1.0
HA A:THR132 3.9 26.7 1.0
O A:HOH419 4.0 63.0 0.7
HA A:PRO129 4.0 62.7 1.0
N A:GLY130 4.3 44.2 1.0
CA A:GLU131 4.3 26.1 1.0
N A:THR132 4.3 21.2 1.0
O A:HOH388 4.4 34.7 0.3
NA A:NA210 4.5 33.4 0.8
N A:LYS128 4.5 43.0 1.0
HB2 A:LYS128 4.6 68.6 1.0
CA A:THR132 4.6 22.1 1.0
CA A:PRO129 4.6 52.2 1.0
C A:PRO129 4.6 46.5 1.0
N A:PRO129 4.7 53.0 1.0
O A:HOH405 4.7 44.4 0.4
OG1 A:THR132 4.8 29.9 1.0
HA A:GLU131 4.8 31.5 1.0
CA A:LYS128 4.8 49.9 1.0
C A:GLY130 4.8 33.2 1.0

Sodium binding site 2 out of 5 in 9e9g

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Sodium binding site 2 out of 5 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 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:Na209

b:43.2
occ:0.40
 OE1 A:GLU78 2.5 29.8 1.0
HO3 B:GOL201 2.9 50.3 0.8
O B:HOH388 2.9 35.1 0.3
O A:HOH426 2.9 33.1 0.7
HH12 B:ARG38 3.1 29.2 1.0
O3 B:GOL201 3.1 41.8 0.8
HH11 B:ARG38 3.1 29.2 1.0
HB2 A:GLU78 3.2 24.6 1.0
HD2 B:PRO94 3.4 21.9 1.0
NH1 B:ARG38 3.4 24.2 1.0
HO2 B:GOL201 3.5 36.6 0.8
CD A:GLU78 3.6 31.8 1.0
O B:HOH301 3.8 56.8 0.8
HB2 B:PRO94 3.8 21.2 1.0
H31 B:GOL201 3.8 46.4 0.8
O2 B:GOL201 3.9 30.4 0.8
O B:HOH365 3.9 57.8 0.8
C3 B:GOL201 3.9 38.6 0.8
CB A:GLU78 4.0 20.4 1.0
HB3 A:GLU78 4.1 24.6 1.0
O B:PRO94 4.2 20.3 1.0
HG2 B:PRO94 4.2 22.4 1.0
CD B:PRO94 4.2 18.1 1.0
OE2 A:GLU78 4.3 40.5 1.0
CG A:GLU78 4.4 26.5 1.0
C2 B:GOL201 4.5 33.6 0.8
CB B:PRO94 4.5 17.6 1.0
CG B:PRO94 4.6 18.6 1.0
HB3 B:TYR93 4.7 20.9 1.0
HD2 B:ARG95 4.7 28.3 1.0
CZ B:ARG38 4.7 23.6 1.0
H32 B:GOL201 4.8 46.4 0.8
HB2 B:ARG95 4.8 24.8 1.0
O A:HOH320 4.8 26.9 0.7
HD3 B:PRO94 4.8 21.9 1.0
O A:HOH330 4.9 17.1 0.8
C B:PRO94 5.0 18.3 1.0
N B:PRO94 5.0 16.4 1.0
HG3 A:GLU78 5.0 32.0 1.0
H12 B:GOL201 5.0 38.4 0.8

Sodium binding site 3 out of 5 in 9e9g

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Sodium binding site 3 out of 5 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 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:Na210

b:33.4
occ:0.84
 H A:PHE133 2.3 22.7 1.0
HA A:THR132 2.6 26.7 1.0
CL A:CL207 2.6 42.4 0.4
O A:LYS126 2.7 26.8 1.0
OE2 A:GLU125 2.7 33.1 1.0
HG3 A:GLU125 2.9 32.1 1.0
HG2 A:GLU125 3.0 32.1 1.0
N A:PHE133 3.1 18.8 1.0
HG23 A:THR132 3.1 31.1 1.0
CG A:GLU125 3.3 26.6 1.0
HA A:LYS127 3.3 40.7 1.0
CD A:GLU125 3.4 32.3 1.0
CA A:THR132 3.5 22.1 1.0
HD3 A:LYS127 3.6 53.5 1.0
HB3 A:PHE133 3.7 24.4 1.0
O A:PHE133 3.7 17.6 1.0
C A:LYS126 3.7 24.8 1.0
C A:THR132 3.8 20.3 1.0
H A:LYS128 3.8 51.8 1.0
CG2 A:THR132 3.8 25.8 1.0
HG22 A:THR132 3.9 31.1 1.0
O A:GLU131 3.9 26.9 1.0
H A:LYS126 4.0 23.6 1.0
CA A:PHE133 4.1 17.1 1.0
CA A:LYS127 4.2 33.8 1.0
CB A:THR132 4.2 24.4 1.0
CB A:PHE133 4.3 20.2 1.0
C A:PHE133 4.3 16.1 1.0
HB2 A:LYS128 4.3 68.6 1.0
N A:LYS127 4.4 29.6 1.0
N A:LYS128 4.4 43.0 1.0
HB2 A:PHE133 4.4 24.4 1.0
N A:LYS126 4.4 19.6 1.0
NA A:NA208 4.5 36.3 0.6
CD A:LYS127 4.5 44.5 1.0
N A:THR132 4.5 21.2 1.0
O A:HOH371 4.5 33.6 0.5
HD2 A:LYS127 4.6 53.5 1.0
C A:GLU131 4.6 24.4 1.0
HG21 A:THR132 4.7 31.1 1.0
OE1 A:GLU125 4.7 38.8 1.0
OG1 A:THR132 4.7 29.9 1.0
C A:LYS127 4.7 39.0 1.0
CB A:GLU125 4.7 23.4 1.0
CA A:LYS126 4.8 23.4 1.0
O A:HOH307 4.8 28.4 0.5
HZ2 A:LYS127 4.8 56.3 1.0
HZ3 A:LYS127 4.9 56.3 1.0
HG2 A:LYS128 4.9 82.2 1.0
HA A:PHE133 4.9 20.6 1.0
O A:THR132 5.0 20.6 1.0
HA A:GLU125 5.0 23.9 1.0
O A:LYS128 5.0 50.8 1.0

Sodium binding site 4 out of 5 in 9e9g

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Sodium binding site 4 out of 5 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 4 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:Na211

b:84.1
occ:0.58
 O A:HOH317 1.6 36.1 0.4
O A:HOH418 1.7 42.1 0.4
OD2 A:ASP110 3.1 23.9 1.0
HB3 A:ASP110 3.8 26.9 1.0
CG A:ASP110 4.1 23.2 1.0
HZ A:PHE111 4.3 38.9 1.0
HD2 A:LYS128 4.4 95.0 1.0
CB A:ASP110 4.5 22.3 1.0
HD3 A:LYS128 4.5 95.0 1.0
HE1 A:PHE111 4.6 39.6 1.0
CZ A:PHE111 4.6 32.3 1.0
O A:HOH329 4.8 35.3 0.6
HB2 A:ASP110 4.8 26.9 1.0
CE1 A:PHE111 4.8 32.9 1.0
CD A:LYS128 4.9 79.1 1.0

Sodium binding site 5 out of 5 in 9e9g

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Sodium binding site 5 out of 5 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 5 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:Na204

b:36.0
occ:0.91
 H B:PHE75 2.1 25.1 1.0
O B:ARG38 2.7 28.2 1.0
HA B:GLU74 2.8 34.8 1.0
N B:PHE75 2.9 20.8 1.0
HD2 B:PHE75 3.0 31.7 1.0
HB2 B:PHE75 3.1 25.4 1.0
HG2 B:ARG38 3.2 29.9 1.0
O B:HOH312 3.2 50.5 1.0
HA B:HIS39 3.3 37.5 0.3
HG3 B:GLU74 3.3 51.0 1.0
HD2 B:HIS39 3.4 46.7 0.3
HA B:HIS39 3.4 34.7 0.7
HH12 B:ARG60 3.5 40.2 0.5
O B:HOH372 3.5 33.0 0.2
CA B:GLU74 3.6 28.9 1.0
CD2 B:PHE75 3.7 26.3 1.0
C B:GLU74 3.7 22.5 1.0
CB B:PHE75 3.8 21.1 1.0
C B:ARG38 3.8 26.7 1.0
CA B:PHE75 3.9 19.2 1.0
NH1 B:ARG60 4.1 33.4 0.5
CG B:GLU74 4.1 42.4 1.0
CG B:ARG38 4.1 24.8 1.0
HG2 B:GLU74 4.1 51.0 1.0
CG B:PHE75 4.2 23.0 1.0
HH11 B:ARG60 4.2 40.2 0.5
CD2 B:HIS39 4.2 38.8 0.3
CA B:HIS39 4.2 31.1 0.3
HE B:ARG38 4.3 26.4 1.0
CB B:GLU74 4.3 36.8 1.0
CA B:HIS39 4.3 28.9 0.7
O B:PHE75 4.4 21.1 1.0
HG3 B:ARG38 4.4 29.9 1.0
O B:HOH349 4.5 59.9 1.0
O B:GLY73 4.5 40.0 1.0
N B:HIS39 4.5 29.1 1.0
HB2 B:GLU74 4.5 44.2 1.0
HB3 B:PHE75 4.6 25.4 1.0
HA B:PHE75 4.7 23.1 1.0
C B:PHE75 4.7 19.3 1.0
N B:GLU74 4.7 31.1 1.0
HD2 B:HIS39 4.8 41.7 0.7
NE B:ARG38 4.8 21.9 1.0
CE2 B:PHE75 4.8 25.7 1.0
HB3 B:ARG38 4.8 28.5 1.0
CB B:ARG38 4.9 23.7 1.0
HE2 B:PHE75 4.9 30.9 1.0
CA B:ARG38 4.9 22.8 1.0
O B:HIS39 4.9 32.0 1.0
HH22 B:ARG60 4.9 39.5 0.5
CD B:ARG38 4.9 21.8 1.0
O B:GLU74 4.9 22.2 1.0
HD3 B:ARG38 5.0 26.2 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.
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