Zinc in PDB 5yfi: Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment

The structure of Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment, PDB code: 5yfi was solved by Y.Toyoda, K.Morimoto, R.Suno, S.Horita, S.Iwata, T.Kobayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.94 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.703, 60.784, 200.182, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.2

The binding sites of Zinc atom in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment (pdb code 5yfi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment, PDB code: 5yfi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:64.4 occ:0.98 OE1 L:GLU207 2.1 0.4 1.0 NE2 L:HIS211 2.2 61.7 1.0 CD L:GLU207 2.8 88.3 1.0 OE2 L:GLU207 2.8 92.8 1.0 CD2 L:HIS211 3.0 59.3 1.0 CE1 L:HIS211 3.4 63.1 1.0 CG L:HIS211 4.2 59.7 1.0 CG L:GLU207 4.2 72.8 1.0 ND1 L:HIS211 4.4 62.8 1.0 CB L:ARG210 4.6 61.4 1.0 O L:GLU207 4.6 55.9 1.0 CB L:GLU207 5.0 67.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:77.0 occ:0.92 NZ L:LYS171 2.2 61.2 1.0 OE1 L:GLU217 2.5 74.6 1.0 CE L:LYS171 3.2 59.5 1.0 CD L:LYS171 3.3 56.0 1.0 CD L:GLU217 3.6 73.2 1.0 O L:HOH432 4.1 57.5 1.0 OE2 L:GLU217 4.1 77.0 1.0 CG L:LYS171 4.7 50.6 1.0 CG L:GLU217 4.9 62.1 1.0 CG2 L:VAL228 4.9 52.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn303 b:57.1 occ:0.81 OE2 L:GLU101 2.2 78.6 1.0 CD L:GLU101 3.4 70.7 1.0 OE1 L:GLU101 4.0 75.5 1.0 CG L:GLU101 4.5 60.0 1.0 NH1 L:ARG83 4.6 37.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:48.3 occ:1.00 OD2 L:ASP189 1.9 53.1 1.0 NE2 H:HIS191 2.2 54.2 1.0 O L:HOH513 2.4 46.5 1.0 O L:HOH518 2.5 57.3 1.0 CG L:ASP189 2.9 44.8 1.0 CD2 H:HIS191 3.1 48.9 1.0 OD1 L:ASP189 3.2 47.4 1.0 CE1 H:HIS191 3.2 52.9 1.0 ND2 L:ASN160 3.8 47.5 1.0 O L:HOH453 4.1 29.4 1.0 CB L:ASP189 4.2 36.0 1.0 CG H:HIS191 4.3 43.3 1.0 ND1 H:HIS191 4.3 48.3 1.0 OD1 L:ASP192 4.6 43.8 1.0 OD2 L:ASP192 4.7 48.5 1.0 O H:VAL190 4.7 35.7 1.0 CG L:ASN160 4.9 41.1 1.0 CG L:ASP192 4.9 46.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:20.2 occ:1.00 O H:HOH507 2.1 18.3 1.0 NE2 H:HIS101 2.1 17.1 1.0 OG H:SER36 2.2 22.6 1.0 CE1 H:HIS101 3.0 17.4 1.0 CD2 H:HIS101 3.1 17.2 1.0 CB H:SER36 3.2 21.3 1.0 ND1 H:HIS101 4.1 16.9 1.0 CG H:HIS101 4.2 14.8 1.0 CA H:SER36 4.6 16.5 1.0 C H:SER36 4.9 21.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment


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 Anti-Human Prostaglandin E Receptor EP4 Antibody Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn303 b:30.8 occ:0.92 O H:HOH444 1.9 29.8 1.0 OE1 H:GLU20 2.2 48.3 1.0 CD H:GLU20 3.0 41.4 1.0 OE2 H:GLU20 3.1 46.4 1.0 OE1 H:GLN22 4.4 52.2 1.0 CG H:GLU20 4.4 35.1 1.0 NE2 H:GLN22 4.4 38.4 1.0 CD H:GLN22 4.8 41.2 1.0 CB H:GLU20 4.9 35.1 1.0

Y.Toyoda, K.Morimoto, R.Suno, S.Horita, K.Yamashita, K.Hirata, Y.Sekiguchi, S.Yasuda, M.Shiroishi, T.Shimizu, Y.Urushibata, Y.Kajiwara, T.Inazumi, Y.Hotta, H.Asada, T.Nakane, Y.Shiimura, T.Nakagita, K.Tsuge, S.Yoshida, T.Kuribara, T.Hosoya, Y.Sugimoto, N.Nomura, M.Sato, T.Hirokawa, M.Kinoshita, T.Murata, K.Takayama, M.Yamamoto, S.Narumiya, S.Iwata, T.Kobayashi. Ligand Binding to Human Prostaglandin E Receptor EP4AT the Lipid-Bilayer Interface. Nat. Chem. Biol. V. 15 18 2019.
ISSN: ESSN 1552-4469
PubMed: 30510193
DOI: 10.1038/S41589-018-0131-3