Zinc in PDB 3pd8: X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution

The structure of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution, PDB code: 3pd8 was solved by K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.32 / 2.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.618, 164.002, 47.620, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 26.1

The structure of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution (pdb code 3pd8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution, PDB code: 3pd8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn260 b:71.4 occ:1.00 NE2 A:HIS43 2.6 0.8 1.0 OE1 A:GLU39 2.7 63.9 1.0 NZ A:LYS42 3.3 63.2 1.0 CD2 A:HIS43 3.4 30.3 1.0 CD A:GLU39 3.5 28.5 1.0 CE A:LYS42 3.5 57.0 1.0 CE1 A:HIS43 3.6 81.4 1.0 OE2 A:GLU39 3.6 56.7 1.0 CD2 A:LEU238 4.4 21.7 1.0 OE1 A:GLN241 4.4 48.6 1.0 CG A:HIS43 4.6 53.6 1.0 ND1 A:HIS43 4.7 49.3 1.0 CG A:GLU39 4.8 35.9 1.0 CD A:LYS42 5.0 49.7 1.0

Zinc binding site 2 out of 5 in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn260 b:27.7 occ:1.00 OE1 C:GLU163 2.1 34.9 1.0 O2 C:CAC263 2.1 55.3 1.0 NE2 B:HIS43 2.2 27.1 1.0 OE1 B:GLU39 2.2 39.4 1.0 OE2 C:GLU163 2.6 15.5 1.0 CD C:GLU163 2.7 36.9 1.0 CD B:GLU39 2.9 43.1 1.0 OE2 B:GLU39 3.0 20.5 1.0 CD2 B:HIS43 3.2 20.2 1.0 CE1 B:HIS43 3.2 56.4 1.0 AS C:CAC263 3.3 55.5 1.0 C2 C:CAC263 3.8 6.6 1.0 C1 C:CAC263 3.9 46.7 1.0 CD2 B:LEU238 4.1 17.8 1.0 N C:SER165 4.1 13.2 1.0 CG C:GLU163 4.2 20.6 1.0 CG B:GLU39 4.3 34.7 1.0 ND1 B:HIS43 4.3 28.4 1.0 CG B:HIS43 4.3 43.5 1.0 O C:ALA162 4.5 11.5 1.0 CA C:PRO164 4.7 34.9 1.0 CB C:GLU163 4.7 20.8 1.0 O1 C:CAC263 4.8 45.1 1.0 C C:PRO164 4.8 36.8 1.0 CA C:SER165 4.8 23.1 1.0 CA C:GLU163 4.8 15.0 1.0 CB C:SER165 4.9 9.6 1.0 CB B:GLU39 4.9 18.3 1.0

Zinc binding site 3 out of 5 in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn261 b:45.2 occ:1.00 NE2 B:HIS20 2.2 43.3 1.0 O B:HOH396 2.3 26.9 1.0 O B:HOH308 2.4 31.3 1.0 CE1 B:HIS20 2.8 49.0 1.0 CD2 B:HIS20 3.4 25.0 1.0 OE2 B:GLU21 3.8 70.6 1.0 ND1 B:HIS20 4.1 31.1 1.0 O B:HOH264 4.3 37.0 1.0 CG B:HIS20 4.4 83.9 1.0 CD B:GLU21 4.7 0.7 1.0 CG B:GLU21 4.9 55.9 1.0

Zinc binding site 4 out of 5 in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn260 b:29.4 occ:1.00 NE2 C:HIS20 2.1 28.3 1.0 OE2 C:GLU27 2.1 29.4 1.0 O C:HOH395 2.3 38.5 1.0 CE1 C:HIS20 2.9 16.4 1.0 CD C:GLU27 3.0 39.0 1.0 CD2 C:HIS20 3.2 34.1 1.0 OE1 C:GLU27 3.3 34.1 1.0 ND1 C:HIS20 4.1 23.9 1.0 NZ C:LYS17 4.1 23.2 1.0 CD C:LYS17 4.2 29.6 1.0 CG C:HIS20 4.2 18.9 1.0 CG C:GLU27 4.4 23.3 1.0 O C:GLU27 4.5 16.3 1.0 CE C:LYS17 4.8 34.8 1.0

Zinc binding site 5 out of 5 in the X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of the Ligand-Binding Core of GLUA2 in Complex with (S)-7-Hpca at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn261 b:27.5 occ:1.00 NE2 C:HIS43 2.1 12.9 1.0 O C:HOH358 2.3 32.0 1.0 OE1 C:GLU39 2.4 29.5 1.0 CE1 C:HIS43 2.9 42.6 1.0 CD C:GLU39 3.0 34.0 1.0 OE2 C:GLU39 3.1 46.9 1.0 CD2 C:HIS43 3.2 16.1 1.0 OE1 C:GLN241 3.7 50.5 1.0 CD2 C:LEU238 3.7 10.2 1.0 O C:HOH377 3.8 36.5 1.0 NZ C:LYS42 3.8 34.3 1.0 CE C:LYS42 3.9 14.8 1.0 ND1 C:HIS43 4.1 21.7 1.0 CG C:HIS43 4.3 44.9 1.0 CG C:GLU39 4.3 29.2 1.0 CD C:GLN241 4.6 39.5 1.0 NE2 C:GLN241 4.6 60.3 1.0 CB C:GLU39 4.7 27.6 1.0 CG C:LEU243 5.0 39.3 1.0

K.Frydenvang, D.S.Pickering, J.R.Greenwood, N.Krogsgaard-Larsen, L.Brehm, B.Nielsen, S.B.Vogensen, H.Hald, J.S.Kastrup, P.Krogsgaard-Larsen, R.P.Clausen. Biostructural and Pharmacological Studies of Bicyclic Analogues of the 3-Isoxazolol Glutamate Receptor Agonist Ibotenic Acid. J. Med. Chem. V. 53 8354 2010.
ISSN: ISSN 1520-4804
PubMed: 21067182
DOI: 10.1021/JM101218A