Zinc in PDB 8w4m: Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz

The structure of Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz, PDB code: 8w4m was solved by H.H.Guan, C.C.Lin, Y.C.Hsieh, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.34 / 2.18
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.088, 147.668, 75.198, 90, 90, 90
R / Rfree (%)	20.8 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz (pdb code 8w4m). 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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz, PDB code: 8w4m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:26.0 occ:1.00 CE1 A:HIS310 2.0 24.8 1.0 NE2 A:HIS435 2.0 19.9 1.0 O A:HOH682 2.2 31.2 1.0 NE2 A:HIS310 2.3 26.5 1.0 O A:HOH697 2.5 23.6 1.0 O A:HOH705 2.8 52.4 1.0 CE1 A:HIS435 3.0 22.1 1.0 CD2 A:HIS435 3.0 19.8 1.0 ND1 A:HIS310 3.2 28.2 1.0 CD2 A:HIS310 3.7 18.2 1.0 CD1 A:LEU314 3.8 23.2 1.0 ND1 A:HIS435 4.1 18.9 1.0 CG A:HIS310 4.1 25.5 1.0 CG A:HIS435 4.2 25.1 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:86.4 occ:1.00 OE2 A:GLU318 2.1 66.8 1.0 OE1 A:GLU318 2.2 64.5 1.0 CD A:GLU318 2.4 59.2 1.0 CG2 A:THR335 3.6 38.6 1.0 CG A:GLU318 3.8 48.5 1.0 CB A:THR335 4.3 35.5 1.0 O A:HOH702 4.3 48.0 1.0 CB A:GLU318 4.6 33.3 1.0 OG1 A:THR335 4.6 45.0 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:75.7 occ:1.00 CD2 A:HIS285 2.9 53.7 1.0 CG A:HIS285 3.7 52.1 1.0 CB A:HIS285 3.9 49.4 1.0 NE2 A:HIS285 4.0 65.1 1.0 O A:HOH630 4.0 38.4 1.0 CA A:HIS285 4.1 48.4 1.0 O A:HIS285 4.6 49.3 1.0 O A:VAL284 4.7 45.5 1.0 C A:HIS285 4.8 48.0 1.0 ND1 A:HIS285 4.9 56.2 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:92.0 occ:1.00 OE1 A:GLU345 2.2 53.7 1.0 O A:HOH695 2.6 44.6 1.0 CD A:GLU345 2.7 41.6 1.0 O A:HOH631 2.7 50.7 1.0 OE2 A:GLU345 2.7 58.4 1.0 O A:HOH611 2.8 46.0 1.0 O A:HOH703 3.4 33.3 1.0 CG A:GLU345 4.0 36.6 1.0 O A:ALA431 4.6 30.3 1.0 N A:HIS433 4.6 23.7 1.0 CB A:GLU345 4.7 30.9 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:77.4 occ:1.00 O A:TRP313 2.7 20.8 1.0 O A:LYS317 2.8 21.6 1.0 N A:LYS338 3.1 19.7 1.0 C A:GLY316 3.3 23.6 1.0 CA A:GLY316 3.3 20.5 1.0 N A:LYS317 3.4 21.5 1.0 C A:TRP313 3.5 21.8 1.0 CB A:LYS338 3.6 23.3 1.0 CA A:TRP313 3.6 23.8 1.0 CB A:SER337 3.6 24.1 1.0 N A:GLY316 3.7 18.9 1.0 C A:LYS317 3.8 25.8 1.0 CE3 A:TRP313 3.8 23.3 1.0 CA A:SER337 3.8 23.6 1.0 CD2 A:TRP313 3.9 20.8 1.0 O A:GLY316 3.9 24.4 1.0 CA A:LYS338 3.9 22.8 1.0 C A:SER337 3.9 22.9 1.0 O A:ASP312 4.0 22.5 1.0 CA A:LYS317 4.1 27.1 1.0 O A:HOH640 4.2 27.6 1.0 CG A:TRP313 4.2 22.9 1.0 CZ3 A:TRP313 4.3 20.5 1.0 CE2 A:TYR319 4.4 26.2 1.0 CE2 A:TRP313 4.4 18.8 1.0 CB A:TRP313 4.5 23.1 1.0 OG A:SER337 4.6 27.1 1.0 N A:TRP313 4.7 18.7 1.0 C A:ASP312 4.8 24.1 1.0 N A:LEU314 4.8 22.4 1.0 CH2 A:TRP313 4.8 21.0 1.0 CD1 A:TRP313 4.8 17.5 1.0 CD2 A:TYR319 4.8 25.5 1.0 CB A:LYS317 4.8 21.3 1.0 CZ2 A:TRP313 4.9 21.0 1.0 O A:HOH637 4.9 27.6 1.0 C A:ASN315 4.9 19.4 1.0 O A:LYS338 4.9 20.0 1.0 N A:GLU318 4.9 24.6 1.0 NE1 A:TRP313 5.0 21.4 1.0 C A:LYS338 5.0 22.5 1.0 CG A:LYS338 5.0 23.4 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:72.0 occ:1.00 O A:HIS310 2.7 21.5 1.0 O A:THR250 2.8 21.7 1.0 CA A:HIS310 3.2 29.6 1.0 C A:HIS310 3.3 25.5 1.0 CA A:THR250 3.4 21.9 1.0 CB A:THR250 3.5 18.8 1.0 CB A:TRP313 3.5 23.1 1.0 CG A:LEU314 3.5 23.1 1.0 C A:THR250 3.5 21.5 1.0 CD2 A:HIS310 3.8 18.2 1.0 CD1 A:TRP313 3.8 17.5 1.0 O A:HOH627 3.8 26.3 1.0 CG A:HIS310 3.9 25.5 1.0 CB A:HIS310 3.9 25.2 1.0 CG A:TRP313 4.0 22.9 1.0 N A:LEU314 4.0 22.4 1.0 CD1 A:LEU314 4.1 23.2 1.0 CD2 A:LEU314 4.2 23.4 1.0 CG2 A:THR250 4.2 25.8 1.0 N A:HIS310 4.3 26.3 1.0 O A:LEU309 4.4 26.4 1.0 CG A:PRO257 4.5 25.0 1.0 CB A:LEU314 4.5 21.0 1.0 CA A:TRP313 4.5 23.8 1.0 C A:TRP313 4.6 21.8 1.0 OG1 A:THR250 4.6 21.8 1.0 N A:GLN311 4.7 23.9 1.0 NE2 A:HIS310 4.7 26.5 1.0 CA A:LEU314 4.8 19.5 1.0 N A:TRP313 4.8 18.7 1.0 N A:THR250 4.8 22.6 1.0 C A:LEU309 4.8 24.1 1.0 ND1 A:HIS310 4.8 28.2 1.0 O A:ASP249 4.8 27.6 1.0 N A:LEU251 4.9 22.1 1.0 CB A:PRO257 4.9 23.6 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:83.8 occ:1.00 OH A:TYR319 2.1 27.3 1.0 OD2 A:ASP312 2.3 32.5 1.0 CB A:ASP312 2.7 27.8 1.0 CG A:ASP312 2.9 34.5 1.0 CZ A:TYR319 3.2 28.1 1.0 O A:HOH668 3.3 33.7 1.0 N A:LEU309 3.4 27.8 1.0 CE1 A:TYR319 3.5 26.8 1.0 CB A:VAL308 4.0 29.3 1.0 CA A:VAL308 4.0 31.7 1.0 CG A:LEU309 4.1 37.9 1.0 CB A:LEU309 4.1 29.2 1.0 CA A:ASP312 4.1 22.4 1.0 OD1 A:ASP312 4.2 30.8 1.0 C A:VAL308 4.2 26.4 1.0 CA A:LEU309 4.3 27.1 1.0 O A:LEU309 4.3 26.4 1.0 CE2 A:TYR319 4.5 26.2 1.0 CG1 A:VAL279 4.5 31.2 1.0 O A:HOH681 4.6 50.2 1.0 C A:ASP312 4.6 24.1 1.0 CG1 A:VAL308 4.7 33.9 1.0 N A:TRP313 4.7 18.7 1.0 C A:LEU309 4.8 24.1 1.0 N A:ASP312 4.8 23.8 1.0 CD1 A:LEU309 4.9 36.4 1.0 CG2 A:VAL279 4.9 25.1 1.0 CD1 A:TYR319 4.9 21.8 1.0 CD A:LYS317 5.0 34.7 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:115.6 occ:1.00 NE2 A:HIS285 1.7 65.1 1.0 OE1 A:GLU283 2.1 66.2 1.0 CE1 A:HIS285 2.2 61.1 1.0 CD2 A:HIS285 3.0 53.7 1.0 CD A:GLU283 3.2 63.4 1.0 ND1 A:HIS285 3.4 56.2 1.0 CG A:HIS285 3.8 52.1 1.0 CG A:GLU283 3.8 55.4 1.0 OE2 A:GLU283 4.2 57.9 1.0 CB A:GLU283 4.5 46.0 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:96.4 occ:1.00 NE2 A:HIS433 2.1 50.8 1.0 O A:HOH707 2.2 51.7 1.0 CE1 A:HIS433 2.2 55.1 1.0 CD2 A:HIS433 3.5 42.4 1.0 ND1 A:HIS433 3.5 47.1 1.0 CG A:HIS433 4.1 44.7 1.0 ND2 A:ASN434 4.4 41.3 1.0 OD1 A:ASN434 4.6 36.5 1.0 CG A:ASN434 4.8 31.7 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Open Conformation of Human Immunoglobulin Fc in Presence of Endosz


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 Open Conformation of Human Immunoglobulin Fc in Presence of Endosz within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:116.0 occ:1.00 OE1 A:GLU380 2.9 62.9 1.0 OE2 A:GLU380 3.0 75.9 1.0 CD A:GLU380 3.3 64.9 1.0 NZ A:LYS248 4.5 58.0 1.0 CG A:GLU380 4.8 48.1 1.0 OE2 A:GLU382 5.0 59.1 1.0

Y.C.Hsieh, H.H.Guan, C.C.Lin, T.Y.Huang, P.Chuankhayan, N.C.Chen, N.H.Wang, P.L.Hu, Y.C.Tsai, Y.C.Huang, M.Yoshimura, P.J.Lin, Y.H.Hsieh, C.J.Chen. Structure-Based High-Efficiency Homogeneous Antibody Platform By Endoglycosidase Sz Provides Insights Into Its Transglycosylation Mechanism Jacs Au V. 4 2130 2024.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.4C00004