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Zinc in PDB 3h6t: Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution

Protein crystallography data

The structure of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution, PDB code: 3h6t was solved by H.Hald, M.Gajhede, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.84 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.486, 163.136, 47.354, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.8

Other elements in 3h6t:

The structure of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution (pdb code 3h6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution, PDB code: 3h6t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3h6t

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Zinc binding site 1 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn266

b:28.0
occ:1.00
 OE1 B:GLU166 2.1 19.4 1.0
NE2 A:HIS46 2.2 32.1 1.0
OE1 A:GLU42 2.3 27.5 1.0
O2 B:CAC274 2.3 58.3 1.0
OE2 B:GLU166 2.6 21.2 1.0
CD B:GLU166 2.7 19.4 1.0
CD2 A:HIS46 3.1 30.8 1.0
CD A:GLU42 3.2 27.8 1.0
CE1 A:HIS46 3.2 32.1 1.0
AS B:CAC274 3.2 59.3 1.0
O1 B:CAC274 3.5 59.0 1.0
OE2 A:GLU42 3.5 27.3 1.0
C1 B:CAC274 3.8 57.5 1.0
CD2 A:LEU241 4.1 19.6 1.0
CG B:GLU166 4.2 21.4 1.0
CG A:HIS46 4.2 30.6 1.0
ND1 A:HIS46 4.3 30.1 1.0
N B:SER168 4.4 22.0 1.0
CG A:GLU42 4.4 23.9 1.0
O B:ALA165 4.6 24.8 1.0
CB B:GLU166 4.8 25.4 1.0
CB A:GLU42 4.9 20.8 1.0
CB B:SER168 4.9 21.2 1.0
CA B:SER168 4.9 21.1 1.0
CA B:GLU166 5.0 25.8 1.0
C B:PRO167 5.0 22.2 1.0

Zinc binding site 2 out of 10 in 3h6t

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Zinc binding site 2 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn267

b:29.7
occ:1.00
 O A:ACT271 2.2 35.0 1.0
NE2 A:HIS23 2.2 23.1 1.0
O A:HOH843 2.3 27.9 1.0
C A:ACT271 2.9 37.2 1.0
OXT A:ACT271 3.0 37.0 1.0
CD2 A:HIS23 3.1 23.4 1.0
CE1 A:HIS23 3.3 22.4 1.0
CG A:HIS23 4.3 24.3 1.0
ND1 A:HIS23 4.4 23.9 1.0
CH3 A:ACT271 4.4 37.1 1.0
OE1 A:GLU24 4.5 52.3 1.0
OE2 A:GLU24 4.6 52.4 1.0
CB A:MET19 4.8 25.4 1.0
CD A:GLU24 4.9 50.0 1.0

Zinc binding site 3 out of 10 in 3h6t

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Zinc binding site 3 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn268

b:0.0
occ:1.00
 O A:HOH566 2.5 58.9 1.0
O A:HOH955 2.7 59.8 1.0
O A:HOH953 3.3 50.5 1.0
O A:HOH954 3.4 53.1 1.0
OE2 A:GLU122 3.6 52.9 1.0
OD1 A:ASP126 3.7 43.3 1.0
OD2 A:ASP126 3.8 47.0 1.0
CD A:GLU122 3.9 52.3 1.0
CG A:GLU122 4.0 48.5 1.0
CG A:ASP126 4.2 43.9 1.0
OE1 A:GLU125 4.5 53.0 1.0
O A:HOH857 4.6 51.8 1.0
OE1 A:GLU122 4.8 52.6 1.0
O A:HOH630 4.9 62.8 1.0

Zinc binding site 4 out of 10 in 3h6t

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Zinc binding site 4 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn266

b:28.0
occ:1.00
 O B:HOH971 2.1 15.6 1.0
NE2 B:HIS46 2.2 16.1 1.0
OE1 B:GLU42 2.2 20.8 1.0
CD B:GLU42 3.0 20.1 1.0
CE1 B:HIS46 3.1 18.3 1.0
OE2 B:GLU42 3.2 21.0 1.0
CD2 B:HIS46 3.2 19.1 1.0
CD1 B:LEU241 3.6 14.5 1.0
CE B:LYS45 3.7 20.1 1.0
NZ B:LYS45 3.8 19.6 1.0
OE1 B:GLN244 3.8 32.4 1.0
O B:HOH633 3.8 44.7 1.0
ND1 B:HIS46 4.2 20.1 1.0
CG B:HIS46 4.3 20.9 1.0
CG B:GLU42 4.4 16.7 1.0
CD B:GLN244 4.7 31.0 1.0
NE2 B:GLN244 4.8 32.0 1.0
CB B:GLU42 4.8 16.0 1.0
CG B:LEU241 5.0 19.7 1.0

Zinc binding site 5 out of 10 in 3h6t

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Zinc binding site 5 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn267

b:24.2
occ:1.00
 NE2 B:HIS23 2.3 17.2 1.0
O B:HOH859 2.3 24.0 1.0
OE1 B:GLU30 2.5 29.4 1.0
OE2 B:GLU30 2.7 34.1 1.0
CD B:GLU30 3.0 31.5 1.0
CD2 B:HIS23 3.2 20.2 1.0
CE1 B:HIS23 3.2 16.5 1.0
NZ B:LYS20 3.9 23.3 1.0
CD B:LYS20 4.0 23.3 1.0
O B:GLU30 4.2 25.5 1.0
ND1 B:HIS23 4.3 18.3 1.0
CG B:HIS23 4.4 19.9 1.0
CG B:GLU30 4.5 31.8 1.0
CE B:LYS20 4.6 21.5 1.0

Zinc binding site 6 out of 10 in 3h6t

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Zinc binding site 6 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn268

b:0.0
occ:1.00
 OD1 B:ASP156 2.5 37.6 1.0
O B:HOH390 2.6 60.5 1.0
O B:HOH484 3.4 50.7 1.0
O B:HOH308 3.6 22.9 1.0
CG B:ASP156 3.7 34.1 1.0
OD2 B:ASP156 4.2 37.3 1.0
NH1 B:ARG163 4.4 39.7 1.0
CD1 B:TRP159 4.5 24.3 1.0
O B:HOH616 4.7 47.5 1.0
CB B:ASP156 4.8 30.0 1.0
O B:HOH411 4.8 51.1 1.0
OG1 B:THR160 4.9 25.6 1.0

Zinc binding site 7 out of 10 in 3h6t

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Zinc binding site 7 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn269

b:0.0
occ:1.00
 OD1 B:ASP126 2.5 28.1 1.0
O B:HOH952 2.5 56.6 1.0
OD2 B:ASP126 3.2 26.0 1.0
CG B:ASP126 3.2 24.4 1.0
O B:HOH659 3.6 57.0 1.0
OE1 B:GLU122 4.0 45.4 1.0
O B:HOH960 4.2 50.9 1.0
CB B:ASP126 4.6 22.2 1.0
OG B:SER123 4.7 27.0 1.0

Zinc binding site 8 out of 10 in 3h6t

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Zinc binding site 8 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn270

b:90.0
occ:1.00
 O B:HOH321 3.1 50.3 1.0
OE2 B:GLU201 3.7 38.6 1.0
OE1 B:GLU201 3.8 39.5 1.0
O B:LYS210 4.1 19.1 1.0
CD B:GLU201 4.1 36.4 1.0
O B:HOH324 4.4 39.2 1.0
CB B:LYS210 4.6 18.0 1.0
CD B:LYS210 4.9 24.7 1.0
O B:HOH564 4.9 64.2 1.0
C B:LYS210 5.0 19.0 1.0

Zinc binding site 9 out of 10 in 3h6t

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Zinc binding site 9 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn266

b:52.2
occ:1.00
 NE2 C:HIS46 2.3 41.9 1.0
OE1 C:GLU42 2.4 38.8 1.0
O C:HOH339 2.7 41.9 1.0
O C:HOH342 2.8 42.7 1.0
CE1 C:HIS46 3.0 40.6 1.0
O C:HOH676 3.2 45.2 1.0
NZ C:LYS45 3.3 44.6 1.0
CD C:GLU42 3.4 35.3 1.0
CD2 C:HIS46 3.4 40.5 1.0
OE2 C:GLU42 3.7 39.3 1.0
CE C:LYS45 3.7 41.8 1.0
O C:HOH1020 4.0 47.0 1.0
CD2 C:LEU241 4.1 23.7 1.0
O C:HOH547 4.1 46.4 1.0
ND1 C:HIS46 4.2 40.3 1.0
CG C:HIS46 4.5 39.7 1.0
CG C:GLU42 4.7 31.7 1.0

Zinc binding site 10 out of 10 in 3h6t

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Zinc binding site 10 out of 10 in the Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the IGLUR2 Ligand-Binding Core (S1S2J-N754S) in Complex with Glutamate and Cyclothiazide at 2.25 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn267

b:0.0
occ:1.00
 O C:HOH632 2.7 56.5 1.0
OD2 C:ASP156 2.8 43.3 1.0
O C:HOH509 3.2 57.1 1.0
CG C:ASP156 3.3 44.0 1.0
OD1 C:ASP156 3.3 43.3 1.0
O C:HOH329 3.5 35.8 1.0
O C:HOH375 3.8 44.7 1.0
OG1 C:THR160 4.0 44.4 1.0
CD1 C:TRP159 4.1 44.3 1.0
O C:ASP156 4.2 43.3 1.0
O C:HOH934 4.2 51.7 1.0
CB C:ASP156 4.5 43.8 1.0
CA C:ASP156 4.8 42.7 1.0
C C:ASP156 4.8 43.4 1.0
O C:HOH392 4.9 44.6 1.0
NE1 C:TRP159 5.0 44.4 1.0

Reference:

H.Hald, P.K.Ahring, D.B.Timmermann, T.Liljefors, M.Gajhede, J.S.Kastrup. Distinct Structural Features of Cyclothiazide Are Responsible For Effects on Peak Current Amplitude and Desensitization Kinetics at IGLUR2. J.Mol.Biol. V. 391 906 2009.
ISSN: ISSN 0022-2836
PubMed: 19591837
DOI: 10.1016/J.JMB.2009.07.002
Page generated: Thu Oct 24 14:15:51 2024

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