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Chlorine 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
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6zpl

Go back to Chlorine Binding Sites List in 6zpl
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl703

b:75.0
occ:1.00
 HH B:TYR142 1.8 71.3 1.0
OH B:TYR142 2.5 69.0 1.0
OG B:SER371 2.6 66.3 1.0
HE21 B:GLN367 2.7 65.0 1.0
HG B:SER371 2.7 67.3 1.0
HB2 B:SER371 2.8 64.5 1.0
HB3 B:SER371 2.8 64.8 1.0
OG B:SER407 2.8 66.4 1.0
CB B:SER371 2.9 65.9 1.0
HG B:SER407 3.3 66.2 1.0
CZ B:TYR142 3.4 70.0 1.0
HG3 B:GLN367 3.4 69.9 1.0
HE1 B:TYR142 3.5 74.6 1.0
HB3 B:ASN122 3.5 60.2 1.0
HD21 B:ASN403 3.5 65.5 1.0
NE2 B:GLN367 3.5 66.0 1.0
HB3 B:SER407 3.8 67.3 1.0
HD1 B:PHE126 3.8 67.9 1.0
CE1 B:TYR142 3.8 70.5 1.0
CB B:SER407 3.8 66.9 1.0
ND2 B:ASN403 3.9 66.5 1.0
HE22 B:GLN367 4.1 64.1 1.0
HB2 B:PHE126 4.1 63.4 1.0
HD22 B:ASN403 4.1 66.2 1.0
HD21 B:ASN122 4.2 61.3 1.0
O B:GLN367 4.2 68.3 1.0
HB2 B:SER407 4.3 68.3 1.0
HA B:ALA368 4.3 75.8 1.0
CG B:GLN367 4.3 68.3 1.0
HB2 B:ASN122 4.3 60.3 1.0
CD B:GLN367 4.3 66.8 1.0
CB B:ASN122 4.4 63.5 1.0
CA B:SER371 4.4 65.8 1.0
CD1 B:PHE126 4.5 67.3 1.0
CE2 B:TYR142 4.5 70.8 1.0
H B:SER371 4.6 67.1 1.0
HD12 B:LEU146 4.6 78.8 1.0
HG2 B:GLN367 4.7 69.9 1.0
HE2 B:TYR142 4.7 75.5 1.0
CG B:ASN403 4.8 67.4 1.0
HA B:CYS404 4.8 74.6 1.0
HA B:ASN122 4.9 59.1 1.0
O B:ASN403 4.9 67.6 1.0
HA B:SER371 4.9 64.0 1.0
C B:GLN367 4.9 69.4 1.0
CB B:PHE126 5.0 65.2 1.0

Chlorine binding site 2 out of 2 in 6zpl

Go back to Chlorine Binding Sites List in 6zpl
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl703

b:70.0
occ:1.00
 HE21 A:GLN367 2.1 61.1 1.0
HH A:TYR142 2.2 68.4 1.0
OH A:TYR142 2.6 67.8 1.0
OG A:SER407 2.8 64.5 1.0
HB3 A:SER371 2.9 59.0 1.0
HG3 A:GLN367 3.0 67.8 1.0
HD1 A:PHE126 3.1 67.7 1.0
NE2 A:GLN367 3.1 64.0 1.0
HG A:SER371 3.1 63.1 1.0
OG A:SER371 3.1 64.7 1.0
HB2 A:SER371 3.2 58.2 1.0
CB A:SER371 3.3 63.1 1.0
CZ A:TYR142 3.3 69.5 1.0
HB2 A:PHE126 3.4 61.3 1.0
HB3 A:SER407 3.4 64.6 1.0
HB3 A:ASN122 3.4 54.4 1.0
HG A:SER407 3.5 61.6 1.0
HE1 A:TYR142 3.5 73.5 1.0
CB A:SER407 3.7 65.5 1.0
HE22 A:GLN367 3.7 59.8 1.0
CE1 A:TYR142 3.7 70.2 1.0
CD1 A:PHE126 3.7 67.3 1.0
CG A:GLN367 3.8 67.1 1.0
CD A:GLN367 3.9 65.3 1.0
HD22 A:ASN403 3.9 57.8 1.0
HB2 A:ASN122 4.0 54.9 1.0
HG2 A:GLN367 4.1 68.4 1.0
HD21 A:ASN403 4.1 58.9 1.0
HB2 A:SER407 4.2 65.3 1.0
CB A:ASN122 4.2 60.9 1.0
O A:GLN367 4.3 66.6 1.0
CB A:PHE126 4.3 64.3 1.0
ND2 A:ASN403 4.3 62.9 1.0
CG A:PHE126 4.3 66.0 1.0
CE2 A:TYR142 4.3 70.8 1.0
HD21 A:ASN122 4.4 54.0 1.0
HA A:ASN122 4.4 53.9 1.0
CE1 A:PHE126 4.5 69.1 1.0
HE1 A:PHE126 4.5 73.1 1.0
HA A:ALA368 4.6 72.7 1.0
HE2 A:TYR142 4.6 75.3 1.0
HB3 A:PHE126 4.7 60.6 1.0
CA A:SER371 4.8 62.6 1.0
HA A:SER407 4.8 61.3 1.0
C A:GLN367 4.9 68.1 1.0
H A:SER371 4.9 60.8 1.0
CD1 A:TYR142 4.9 72.1 1.0
CA A:SER407 4.9 64.7 1.0
CA A:ASN122 5.0 60.5 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: Mon Jul 29 18:10:10 2024

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