Zinc in PDB 8bst: Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution

The structure of Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution, PDB code: 8bst was solved by R.Venskutonyte, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.88 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.412, 101.597, 83.407, 90, 111.99, 90
R / Rfree (%)	20.4 / 23.8

The structure of Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution (pdb code 8bst). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution, PDB code: 8bst:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:41.6 occ:0.75 OD2 A:ASP790 2.0 37.8 1.0 NE2 C:HIS475 2.3 42.2 0.8 ND1 A:HIS793 2.3 48.2 0.8 CG A:ASP790 2.7 49.6 1.0 CE1 C:HIS475 2.8 45.3 0.2 OD1 A:ASP790 2.8 58.9 1.0 CD2 C:HIS475 3.0 45.2 0.8 CE1 A:HIS793 3.1 48.4 0.8 ND1 C:HIS475 3.2 45.0 0.2 CE1 C:HIS475 3.4 47.3 0.8 CG A:HIS793 3.4 53.8 0.8 CG A:HIS793 3.5 48.1 0.2 ND1 A:HIS793 3.7 49.0 0.2 CD2 A:HIS793 3.7 48.9 0.2 CB A:HIS793 3.9 43.9 0.8 CB A:HIS793 3.9 43.5 0.2 NE2 C:HIS475 3.9 47.5 0.2 CE1 A:HIS793 4.0 50.5 0.2 NE2 A:HIS793 4.0 51.6 0.2 CB A:ASP790 4.1 45.0 1.0 NE2 A:HIS793 4.3 51.8 0.8 CG C:HIS475 4.3 45.0 0.8 ND1 C:HIS475 4.4 47.0 0.8 CD2 A:HIS793 4.4 50.6 0.8 CG C:HIS475 4.5 45.6 0.2 C3 B:GOL915 4.7 59.2 1.0 CD2 C:HIS475 4.8 47.2 0.2 O A:ASP790 5.0 40.2 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:68.5 occ:0.50 OE1 C:GLU797 2.0 54.9 1.0 NE2 A:HIS475 2.3 54.8 0.5 CD C:GLU797 2.9 64.1 1.0 CE1 A:HIS475 2.9 49.7 0.5 OE2 C:GLU797 3.1 72.3 1.0 CD2 A:HIS475 3.3 54.9 0.5 NE2 C:HIS793 3.5 68.9 1.0 CE1 C:HIS793 3.6 71.4 1.0 ND1 A:HIS475 3.7 53.2 0.5 CE1 A:HIS475 3.8 52.1 0.5 ND1 A:HIS475 4.0 48.1 0.5 CG A:HIS475 4.2 48.5 0.5 CG C:GLU797 4.2 64.4 1.0 CD2 C:HIS793 4.5 69.0 1.0 ND1 C:HIS793 4.6 72.7 1.0 CB C:GLU797 4.9 52.1 1.0 CG A:HIS475 4.9 48.2 0.5 O A:HOH1021 5.0 39.7 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn905 b:87.6 occ:0.75 O4 A:SO4910 2.1 60.2 0.8 ND1 A:HIS510 2.3 64.8 1.0 O A:HOH1013 3.0 47.2 1.0 CE1 A:HIS510 3.2 70.1 1.0 CG A:HIS510 3.3 67.6 1.0 S A:SO4910 3.3 81.4 0.8 O2 A:SO4910 3.6 69.3 0.8 CB A:HIS510 3.7 63.5 1.0 O3 A:SO4910 4.2 66.1 0.8 O1 A:SO4910 4.3 73.9 0.8 NE2 A:HIS510 4.3 76.5 1.0 CD2 A:HIS510 4.4 70.2 1.0 CA A:HIS510 4.7 54.1 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn906 b:43.2 occ:0.25 OE1 A:GLU797 2.2 56.0 1.0 NE2 C:HIS475 2.3 47.5 0.2 CE1 C:HIS475 2.8 47.3 0.8 CD A:GLU797 3.2 56.1 1.0 CD2 C:HIS475 3.2 47.2 0.2 CE1 A:HIS793 3.3 50.5 0.2 CE1 C:HIS475 3.3 45.3 0.2 ND1 C:HIS475 3.5 47.0 0.8 OE2 A:GLU797 3.6 70.2 1.0 CE1 A:HIS793 3.7 48.4 0.8 NE2 A:HIS793 3.9 51.8 0.8 NE2 C:HIS475 3.9 42.2 0.8 ND1 A:HIS793 4.0 49.0 0.2 NE2 A:HIS793 4.2 51.6 0.2 CG C:HIS475 4.4 45.6 0.2 CG A:GLU797 4.4 48.7 1.0 ND1 C:HIS475 4.4 45.0 0.2 ND1 A:HIS793 4.6 48.2 0.8 NH2 A:ARG801 4.6 77.0 1.0 CG C:HIS475 4.7 45.0 0.8 O C:HOH1016 4.7 47.6 1.0 CD2 A:HIS793 4.8 50.6 0.8 CD2 C:HIS475 4.9 45.2 0.8 CB A:GLU797 5.0 36.2 1.0 O3 A:SO4909 5.0 82.6 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:84.3 occ:0.50 NE2 B:HIS793 2.3 74.4 0.5 O B:HOH1022 2.3 59.4 0.5 CD2 B:HIS793 2.9 70.2 0.5 OE2 B:GLU797 2.9 76.3 1.0 CE1 B:HIS793 3.0 73.9 0.5 CE1 B:HIS793 3.5 74.2 0.5 ND1 B:HIS793 3.5 73.6 0.5 NE2 B:HIS793 3.7 74.2 0.5 CD B:GLU797 3.7 73.4 1.0 OE1 B:GLU797 3.9 88.9 1.0 CG B:HIS793 4.2 70.0 0.5 CG B:HIS793 4.4 70.3 0.5 ND1 B:HIS793 4.4 72.7 0.5 CD2 B:HIS793 4.4 73.8 0.5 OD2 B:ASP790 4.7 70.3 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:94.8 occ:0.75 ND1 B:HIS475 2.3 57.1 0.8 CD2 B:HIS475 2.6 55.7 0.2 OE1 B:GLU472 2.9 69.8 1.0 CE1 B:HIS475 3.1 59.8 0.8 CG B:HIS475 3.3 47.0 0.8 CD B:GLU472 3.3 68.2 1.0 CG B:HIS475 3.4 46.8 0.2 OE2 B:GLU472 3.5 83.9 1.0 NE2 B:HIS475 3.7 58.3 0.2 CB B:HIS475 3.7 43.2 0.8 CB B:HIS475 3.7 44.1 0.2 ZN B:ZN906 4.2 51.3 0.2 NE2 B:HIS475 4.3 56.8 0.8 CD2 B:HIS475 4.4 47.5 0.8 CG B:GLU472 4.4 41.9 1.0 CA B:GLU472 4.4 33.4 1.0 ND1 B:HIS475 4.6 47.5 0.2 CE1 B:HIS475 4.7 54.6 0.2 CB B:GLU472 4.8 31.9 1.0 O B:GLU472 4.9 38.2 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:72.0 occ:0.50 OD1 B:ASP790 2.0 48.0 1.0 ND1 B:HIS793 2.3 73.6 0.5 O2 B:SO4911 2.5 62.4 0.5 O4 B:SO4911 3.0 61.7 0.5 S B:SO4911 3.0 68.6 0.5 CG B:ASP790 3.1 59.9 1.0 CG B:HIS793 3.1 70.3 0.5 O1 B:SO4911 3.2 55.9 0.5 CE1 B:HIS793 3.2 73.9 0.5 CG B:HIS793 3.2 70.0 0.5 OD2 B:ASP790 3.4 70.3 1.0 CB B:HIS793 3.4 67.2 0.5 CB B:HIS793 3.4 67.3 0.5 CD2 B:HIS793 3.5 70.2 0.5 ND1 B:HIS793 3.6 72.7 0.5 NE2 B:HIS793 4.1 74.4 0.5 CE1 B:HIS793 4.1 74.2 0.5 O A:ILE760 4.2 55.8 1.0 CD2 B:HIS793 4.2 73.8 0.5 NE2 B:HIS793 4.2 74.2 0.5 CB B:ASP790 4.4 46.0 1.0 O3 B:SO4911 4.5 57.6 0.5 O B:HOH1013 4.5 45.0 1.0 O B:HOH1020 4.7 61.6 1.0 CA B:ASP790 4.9 49.3 1.0 CA B:HIS793 4.9 62.8 0.5 CA B:HIS793 4.9 62.7 0.5

Zinc binding site 8 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn905 b:72.8 occ:0.50 ND1 B:HIS510 2.3 64.7 0.5 O B:HOH1027 2.9 48.2 1.0 ND1 B:HIS510 3.0 65.3 0.5 CG B:HIS510 3.2 60.6 0.5 CE1 B:HIS510 3.2 63.3 0.5 CG B:HIS510 3.3 60.4 0.5 CE1 B:HIS510 3.5 65.0 0.5 CB B:HIS510 3.6 58.0 0.5 CB B:HIS510 3.6 57.6 0.5 CD2 B:HIS510 3.8 59.0 0.5 ZN B:ZN907 3.9 79.8 0.5 NE2 B:HIS510 3.9 60.6 0.5 OD1 B:ASP513 4.4 49.1 1.0 NE2 B:HIS510 4.4 61.2 0.5 CA B:HIS510 4.4 53.0 0.5 CA B:HIS510 4.4 53.5 0.5 CD2 B:HIS510 4.4 60.1 0.5 O B:HIS510 4.8 49.1 1.0 CG B:PRO770 4.8 36.6 1.0 CB B:PRO770 5.0 40.0 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn906 b:51.3 occ:0.25 CE1 B:HIS475 2.0 59.8 0.8 NE2 B:HIS475 2.3 58.3 0.2 NE2 B:HIS475 2.7 56.8 0.8 CD2 B:HIS475 3.0 55.7 0.2 ND1 B:HIS475 3.1 57.1 0.8 CE1 B:HIS475 3.3 54.6 0.2 CD2 B:HIS475 3.9 47.5 0.8 CG B:HIS475 4.1 47.0 0.8 CG B:HIS475 4.2 46.8 0.2 ZN B:ZN903 4.2 94.8 0.8 ND1 B:HIS475 4.3 47.5 0.2

Zinc binding site 10 out of 13 in the Crystal Structure of the Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A 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 Kainate Receptor GLUK3-H523A Ligand Binding Domain in Complex with Kainate at 2.7A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn907 b:79.8 occ:0.50 ND1 B:HIS510 2.3 65.3 0.5 CG B:HIS510 3.1 60.6 0.5 CG B:HIS510 3.2 60.4 0.5 ND1 B:HIS510 3.3 64.7 0.5 CB B:HIS510 3.3 57.6 0.5 CB B:HIS510 3.3 58.0 0.5 CE1 B:HIS510 3.4 65.0 0.5 CD2 B:HIS510 3.8 60.1 0.5 ZN B:ZN905 3.9 72.8 0.5 CE1 B:HIS510 4.0 63.3 0.5 NE2 B:HIS510 4.2 61.2 0.5 CD2 B:HIS510 4.3 59.0 0.5 NE2 B:HIS510 4.4 60.6 0.5 CA B:HIS510 4.8 53.0 0.5 CA B:HIS510 4.8 53.5 0.5

Y.Bay, R.Venskutonyte, S.M.Frantsen, T.S.Thorsen, M.Musgaard, K.Frydenvang, P.Francotte, B.Pirotte, P.C.Biggin, A.S.Kristensen, T.Boesen, D.S.Pickering, M.Gajhede, J.S.Kastrup. Small Molecule Positive Allosteric Modulation of Homomeric Kainate Receptors GLUK1-3: Development of Screening Assays and Insight Into GLUK3 Structure To Be Published.