Zinc in PDB 4w4o: High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri

The structure of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri, PDB code: 4w4o was solved by J.M.M.Caaveiro, M.Kiyoshi, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.980, 126.500, 71.610, 90.00, 118.95, 90.00
R / Rfree (%)	17.3 / 21.5

The binding sites of Zinc atom in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri (pdb code 4w4o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri, PDB code: 4w4o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:34.5 occ:1.00 O A:ACT515 1.8 40.3 1.0 O A:ACT513 2.0 33.4 1.0 NE2 A:HIS310 2.1 33.5 1.0 C A:ACT515 2.6 41.1 1.0 OXT A:ACT513 2.6 40.6 1.0 C A:ACT513 2.7 27.9 1.0 OXT A:ACT515 2.7 29.8 1.0 CD2 A:HIS310 2.8 32.6 1.0 CE1 A:HIS310 3.3 35.3 1.0 CE1 A:HIS435 3.9 35.7 1.0 CG A:HIS310 4.1 29.7 1.0 CH3 A:ACT515 4.1 42.9 1.0 CH3 A:ACT513 4.2 33.6 1.0 ND1 A:HIS310 4.3 31.1 1.0 ND1 A:HIS435 4.5 37.4 1.0 O A:HOH684 4.5 52.7 1.0 CD1 A:LEU314 4.5 36.6 1.0 NE2 A:HIS435 4.8 35.4 1.0 CD1 A:ILE253 5.0 51.8 1.0

Zinc binding site 2 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:42.5 occ:1.00 NE2 A:HIS268 1.9 35.7 1.0 OE1 A:GLU294 2.1 40.5 1.0 CD A:GLU294 2.7 36.8 1.0 CE1 A:HIS268 2.9 47.2 1.0 OE2 A:GLU294 2.9 39.6 1.0 CD2 A:HIS268 3.0 37.0 1.0 ND1 A:HIS268 4.0 42.0 1.0 OH A:TYR300 4.0 64.8 1.0 CG A:HIS268 4.1 33.2 1.0 CG A:GLU294 4.2 31.2 1.0 CZ A:TYR300 4.6 55.2 1.0 CB A:SER298 4.7 35.2 1.0 O A:SER298 4.8 36.1 1.0 OG A:SER298 4.8 36.8 1.0 CA A:SER298 4.8 33.4 1.0 CE2 A:TYR300 4.8 55.5 1.0

Zinc binding site 3 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:62.1 occ:1.00 O A:HOH609 2.3 52.3 1.0 NE2 A:HIS435 2.4 35.4 1.0 O A:HOH766 2.7 54.7 1.0 CD2 A:HIS435 3.3 35.6 1.0 CE1 A:HIS435 3.5 35.7 1.0 O A:GLU430 3.7 33.5 1.0 OXT A:ACT513 3.7 40.6 1.0 O A:HOH651 3.8 54.2 1.0 CH3 A:ACT515 4.4 42.9 1.0 OXT A:ACT515 4.4 29.8 1.0 C A:ACT515 4.5 41.1 1.0 CG A:HIS435 4.5 33.7 1.0 ND1 A:HIS435 4.5 37.4 1.0 C A:ACT513 4.7 27.9 1.0 C A:GLU430 4.7 33.6 1.0 O A:HOH641 4.9 53.0 1.0 CH3 A:ACT513 5.0 33.6 1.0

Zinc binding site 4 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn510 b:50.4 occ:1.00 OE1 B:GLU345 2.1 37.8 1.0 O B:HOH709 2.2 42.3 1.0 O B:HOH603 2.2 43.2 1.0 O B:ACT512 2.2 39.8 1.0 O B:HOH743 2.3 48.7 1.0 O B:HOH746 2.3 45.0 1.0 CD B:GLU345 3.0 43.9 1.0 C B:ACT512 3.2 45.1 1.0 OE2 B:GLU345 3.2 49.9 1.0 OXT B:ACT512 3.4 48.3 1.0 N B:HIS433 4.0 32.7 1.0 O B:HOH759 4.3 54.6 1.0 CG B:GLU345 4.4 38.3 1.0 O B:ALA431 4.4 33.4 1.0 O B:HOH766 4.5 63.0 1.0 CH3 B:ACT512 4.5 39.3 1.0 CA B:LEU432 4.5 29.8 1.0 CB B:HIS433 4.6 35.4 1.0 C B:LEU432 4.7 32.7 1.0 CB B:GLU345 4.8 41.4 1.0 CA B:HIS433 4.9 34.0 1.0 CD2 B:LEU432 5.0 35.9 1.0

Zinc binding site 5 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn511 b:30.2 occ:1.00 NE2 B:HIS310 2.0 33.4 1.0 NE2 B:HIS435 2.0 29.7 1.0 CE1 B:HIS310 2.9 31.2 1.0 CD2 B:HIS435 3.0 29.4 1.0 CD2 B:HIS310 3.0 32.2 1.0 CE1 B:HIS435 3.0 30.4 1.0 CD1 B:LEU314 4.0 40.8 1.0 ND1 B:HIS310 4.0 32.5 1.0 ND1 B:HIS435 4.1 31.2 1.0 CG B:HIS310 4.1 31.5 1.0 CG B:HIS435 4.1 32.1 1.0 O B:HOH769 4.3 43.1 0.5 CD1 B:ILE253 4.5 55.7 1.0

Zinc binding site 6 out of 6 in the High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High-Resolution Crystal Structure of Fc Bound to Its Human Receptor Fc-Gamma-Ri within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn309 b:54.6 occ:0.50 O C:HOH537 2.0 40.1 0.5 ND1 C:HIS174 2.4 41.1 1.0 O C:HOH546 2.6 39.8 0.5 O C:HOH484 2.6 42.6 1.0 O A:HOH789 2.9 48.4 0.5 CE1 C:HIS174 3.4 42.1 1.0 CG C:HIS174 3.4 38.0 1.0 CB C:HIS174 3.6 34.4 1.0 CA C:HIS174 3.8 30.5 1.0 O C:LYS173 4.2 31.7 1.0 NE2 C:HIS174 4.5 41.8 1.0 CD2 C:HIS174 4.5 37.0 1.0 O A:HOH802 4.6 45.5 1.0 N C:ARG175 4.7 30.4 1.0 N C:HIS174 4.8 30.8 1.0 C C:HIS174 4.8 31.0 1.0 C C:LYS173 4.9 32.8 1.0

M.Kiyoshi, J.M.M.Caaveiro, T.Kawai, S.Tashiro, T.Ide, Y.Asaoka, K.Hatayama, K.Tsumoto. Structural Basis For Binding of Human IGG1 to Its High-Affinity Human Receptor Fc Gamma Ri Nat Commun V. 6 6866 2015.
ISSN: ESSN 2041-1723
PubMed: 25925696
DOI: 10.1038/NCOMMS7866