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Sodium in PDB 6zpl: Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.

Enzymatic activity of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.

All present enzymatic activity of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.:
3.2.1.4;

Protein crystallography data

The structure of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions., PDB code: 6zpl was solved by A.Shahsavar, P.Stohler, G.Bourenkov, I.Zimmermann, M.Siegrist, W.Guba, E.Pinard, S.Sinning, M.A.Seeger, T.R.Schneider, R.J.P.Dawson, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.07 / 3.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 116.41, 69.71, 149.43, 90, 92.86, 90
R / Rfree (%) 27.7 / 29.1

Other elements in 6zpl:

The structure of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. (pdb code 6zpl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions., PDB code: 6zpl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6zpl

Go back to Sodium Binding Sites List in 6zpl
Sodium binding site 1 out of 2 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:44.6
occ:1.00
 O B:GLY115 2.7 65.5 1.0
O B:VAL118 3.0 63.1 1.0
HA B:TYR116 3.3 66.6 1.0
C B:GLY115 3.7 66.7 1.0
HD23 B:LEU468 4.0 57.5 1.0
HG1 B:THR472 4.1 58.9 1.0
HG12 B:VAL118 4.1 61.1 1.0
H B:VAL118 4.2 62.5 1.0
CA B:TYR116 4.2 67.0 1.0
C B:VAL118 4.2 62.9 1.0
O04 B:QET701 4.3 89.7 1.0
H05 B:QET701 4.3 90.5 1.0
N B:TYR116 4.3 67.6 1.0
OG1 B:THR472 4.3 62.9 1.0
HD1 B:TYR116 4.4 70.5 1.0
HG13 B:VAL118 4.5 62.4 1.0
HA2 B:GLY119 4.5 55.8 1.0
HA B:LEU468 4.6 56.8 1.0
HA3 B:GLY119 4.6 56.1 1.0
C B:TYR116 4.7 66.4 1.0
HA2 B:GLY115 4.7 68.3 1.0
CA B:GLY115 4.7 67.7 1.0
HA3 B:GLY115 4.8 69.5 1.0
CG1 B:VAL118 4.8 64.4 1.0
O B:TYR116 4.8 65.8 1.0
O B:LEU468 4.8 62.1 1.0
CD2 B:LEU468 4.9 62.5 1.0
HD21 B:LEU468 4.9 58.0 1.0
CA B:GLY119 5.0 61.8 1.0

Sodium binding site 2 out of 2 in 6zpl

Go back to Sodium Binding Sites List in 6zpl
Sodium binding site 2 out of 2 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor, Sybody SB_GLYT1#7 and Bound Na and Cl Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:65.0
occ:1.00
 O A:VAL118 2.2 57.7 1.0
H05 A:QET701 2.8 96.9 1.0
HA A:TYR116 3.0 52.2 1.0
O A:GLY115 3.1 59.0 1.0
O04 A:QET701 3.2 98.2 1.0
C A:VAL118 3.4 57.9 1.0
HG1 A:THR472 3.4 45.9 1.0
HA3 A:GLY119 3.4 45.3 1.0
C10 A:QET701 3.4 98.7 1.0
H A:VAL118 3.5 50.6 1.0
C19 A:QET701 3.5 98.6 1.0
O A:TYR116 3.6 60.1 1.0
OG1 A:THR472 3.8 57.0 1.0
C A:TYR116 3.8 60.4 1.0
CA A:TYR116 3.9 60.4 1.0
C09 A:QET701 3.9 98.7 1.0
H07 A:QET701 3.9 99.3 1.0
HA2 A:GLY119 4.0 44.9 1.0
CA A:GLY119 4.1 56.9 1.0
N A:GLY119 4.1 57.5 1.0
C A:GLY115 4.1 60.0 1.0
N01 A:QET701 4.1 99.6 1.0
N A:VAL118 4.1 59.5 1.0
H18 A:QET701 4.2 99.9 1.0
CA A:VAL118 4.4 58.8 1.0
HG12 A:VAL118 4.4 48.4 1.0
N A:TYR116 4.5 60.7 1.0
HG13 A:VAL118 4.6 49.6 1.0
HD23 A:LEU468 4.6 44.4 1.0
C02 A:QET701 4.6 98.9 1.0
C18 A:QET701 4.7 100.0 1.0
HD1 A:TYR116 4.7 54.3 1.0
N A:ALA117 4.7 60.9 1.0
H09 A:QET701 4.7 101.2 1.0
C01 A:QET701 4.8 99.9 1.0
O01 A:QET701 4.9 98.5 1.0
HB3 A:TYR116 5.0 55.0 1.0
CG1 A:VAL118 5.0 58.7 1.0

Reference:

A.Shahsavar, P.Stohler, G.Bourenkov, I.Zimmermann, M.Siegrist, W.Guba, E.Pinard, S.Sinning, M.A.Seeger, T.R.Schneider, R.J.P.Dawson, P.Nissen. Structural Insights Into the Inhibition of Glycine Reuptake. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33658720
DOI: 10.1038/S41586-021-03274-Z
Page generated: Tue Oct 8 15:38:39 2024

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