Iodine in PDB 3wn5: Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia

The structure of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia, PDB code: 3wn5 was solved by S.Kadono, F.Mimoto, H.Katada, T.Igawa, T.Kamikawa, K.Hattori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.030, 72.490, 163.480, 90.00, 91.15, 90.00
R / Rfree (%)	23.6 / 27.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia (pdb code 3wn5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia, PDB code: 3wn5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ A:I1010 b:71.5 occ:0.50 N A:GLN438 4.0 53.1 1.0 CA A:THR437 4.2 53.5 1.0 OG1 A:THR437 4.5 54.7 1.0 C A:THR437 4.5 53.8 1.0 O A:TYR436 4.6 53.5 1.0 CD2 A:TYR436 4.7 49.1 1.0 O A:GLN438 4.7 54.8 1.0 CB A:GLN438 4.8 54.1 1.0 CE2 A:TYR436 4.8 48.6 1.0 CA A:GLN438 4.9 53.0 1.0 CB A:THR437 4.9 53.8 1.0

Iodine binding site 2 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ A:I1011 b:75.5 occ:0.50 N2 A:NAG1005 3.6 58.1 1.0 C8 A:NAG1005 3.7 55.2 1.0 C7 A:NAG1005 4.2 56.8 1.0 CE1 A:PHE243 4.2 38.5 1.0 CD1 A:PHE243 4.3 38.4 1.0 C1 A:MAN1004 4.4 53.6 1.0 C6 A:BMA1003 4.4 49.0 1.0 O5 A:MAN1004 4.7 54.7 1.0 C2 A:NAG1005 4.7 58.3 1.0 C1 A:NAG1005 4.8 57.8 1.0 O6 A:BMA1003 5.0 51.3 1.0

Iodine binding site 3 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ B:I1010 b:49.9 occ:1.00 OG1 B:THR350 3.0 40.0 1.0 N B:THR350 3.6 41.8 1.0 OG A:SER354 3.7 45.1 1.0 CG B:LYS439 3.7 40.4 1.0 CE B:LYS439 3.9 41.0 1.0 N A:CYS356 4.0 50.7 1.0 O B:VAL348 4.1 43.6 1.0 CB B:THR350 4.1 39.9 1.0 CB A:CYS356 4.2 53.0 1.0 CA B:CYS349 4.3 45.5 1.0 CZ A:ARG355 4.4 56.9 1.0 CB A:ARG355 4.4 50.7 1.0 CA B:THR350 4.4 40.1 1.0 C B:CYS349 4.4 43.8 1.0 CA A:CYS356 4.4 52.8 1.0 CD B:LYS439 4.5 40.2 1.0 O B:THR350 4.5 39.1 1.0 CG2 B:THR350 4.5 40.0 1.0 NH1 A:ARG355 4.5 57.3 1.0 NH2 A:ARG355 4.5 57.7 1.0 C A:ARG355 4.6 49.5 1.0 NE A:ARG355 4.6 56.0 1.0 O B:HOH1105 4.7 35.9 1.0 N A:ARG355 4.7 47.8 1.0 CA A:ARG355 4.8 49.3 1.0 C B:VAL348 4.9 44.4 1.0 CB B:LYS439 5.0 39.6 1.0 C B:THR350 5.0 39.3 1.0

Iodine binding site 4 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ B:I1011 b:83.7 occ:1.00 N B:VAL240 3.6 46.7 1.0 NZ B:LYS334 3.7 60.1 1.0 CA B:MET239 4.1 51.9 1.0 O B:VAL240 4.3 45.8 1.0 CG2 B:ILE332 4.3 67.4 1.0 C B:MET239 4.4 49.7 1.0 CD1 B:ILE332 4.4 68.3 1.0 CB B:MET239 4.4 54.3 1.0 CA B:VAL240 4.5 45.6 1.0 CB B:VAL240 4.6 45.5 1.0 CE B:LYS334 4.7 59.2 1.0 O B:PRO238 4.7 55.1 1.0 CG B:MET239 4.8 56.1 1.0 C B:VAL240 4.9 44.7 1.0 CG2 B:VAL240 5.0 44.9 1.0

Iodine binding site 5 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ B:I1012 b:80.4 occ:0.50 N2 B:NAG1005 3.6 69.5 1.0 C8 B:NAG1005 3.8 67.8 1.0 C1 B:MAN1004 4.0 63.2 1.0 CE1 B:PHE243 4.1 38.7 1.0 C7 B:NAG1005 4.1 68.9 1.0 CD1 B:PHE243 4.1 39.2 1.0 C6 B:BMA1003 4.2 60.3 1.0 C1 B:NAG1005 4.3 67.9 1.0 C2 B:NAG1005 4.5 69.0 1.0 O5 B:MAN1004 4.6 63.2 1.0 O2 B:MAN1004 4.7 65.2 1.0 O6 B:BMA1003 4.7 62.0 1.0 C2 B:MAN1004 4.8 63.7 1.0 C3 B:NAG1005 5.0 69.8 1.0

Iodine binding site 6 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ C:I208 b:36.5 occ:1.00 NE C:ARG15 3.7 39.7 1.0 O C:ALA92 3.7 38.3 1.0 CB C:ARG15 3.9 38.4 1.0 N C:ARG15 3.9 37.4 1.0 N C:ALA92 3.9 34.4 1.0 CD C:ARG15 4.0 39.6 1.0 NE1 C:TRP95 4.1 43.9 1.0 CG C:GLN91 4.1 32.5 1.0 CA C:GLN91 4.1 32.7 1.0 CD1 C:TYR14 4.1 36.4 1.0 N C:TYR14 4.1 37.5 1.0 CB C:GLN91 4.1 32.5 1.0 CB C:TRP13 4.2 35.9 1.0 CA C:TRP13 4.3 36.7 1.0 O C:ARG15 4.3 38.8 1.0 CE1 C:TYR14 4.3 36.7 1.0 CZ2 C:TRP95 4.3 43.3 1.0 CA C:ARG15 4.4 37.7 1.0 CG C:ARG15 4.5 39.3 1.0 CE3 C:TRP13 4.5 34.5 1.0 C C:GLN91 4.6 33.5 1.0 CE2 C:TRP95 4.6 43.7 1.0 C C:TRP13 4.6 37.3 1.0 C C:ALA92 4.7 37.9 1.0 CZ C:ARG15 4.7 40.0 1.0 C C:ARG15 4.9 37.7 1.0 CA C:ALA92 4.9 35.9 1.0 C C:TYR14 4.9 37.3 1.0 NH2 C:ARG15 4.9 39.8 1.0 O C:LEU90 5.0 32.5 1.0 CG C:TYR14 5.0 36.6 1.0

Iodine binding site 7 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ C:I209 b:91.2 occ:1.00 N C:GLU43 3.3 69.3 1.0 CA C:GLU43 3.7 70.2 1.0 CD C:ARG67 3.8 48.1 1.0 CG C:ARG67 3.9 47.3 1.0 NH1 C:ARG67 3.9 49.4 1.0 O C:GLU65 4.0 50.1 1.0 CB C:PHE40 4.0 59.4 1.0 CB C:GLU65 4.0 54.5 1.0 CB C:ARG67 4.0 47.0 1.0 N C:ARG67 4.1 45.7 1.0 C C:GLU65 4.1 49.6 1.0 N C:ASN42 4.2 62.0 1.0 CB C:GLU43 4.2 72.4 1.0 O C:PHE40 4.2 58.5 1.0 C C:PHE40 4.3 58.6 1.0 N C:TYR66 4.3 47.2 1.0 C C:TYR66 4.4 45.4 1.0 OE1 C:GLU65 4.4 59.2 1.0 C C:ASN42 4.4 66.8 1.0 CA C:TYR66 4.4 45.7 1.0 N C:HIS41 4.5 58.2 1.0 C C:HIS41 4.6 59.5 1.0 CA C:ASN42 4.6 64.2 1.0 CA C:HIS41 4.7 57.8 1.0 CA C:ARG67 4.7 46.3 1.0 CA C:GLU65 4.7 51.5 1.0 NE C:ARG67 4.8 49.0 1.0 CA C:PHE40 4.8 59.0 1.0 CZ C:ARG67 4.8 49.8 1.0

Iodine binding site 8 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ D:I1009 b:86.4 occ:0.50 NZ D:LYS414 3.2 74.8 1.0 OE1 D:GLN418 3.7 86.6 1.0 CD1 D:TRP417 3.9 66.8 1.0 CE D:LYS414 3.9 73.8 1.0 NE1 D:TRP417 4.1 64.9 1.0 CG1 D:VAL363 4.3 68.4 1.0 CG D:PRO353 4.5 70.0 1.0 CB D:PRO353 4.9 69.5 1.0 O D:GLU357 4.9 88.8 1.0 CG D:LYS414 4.9 73.3 1.0 CD D:GLN418 4.9 87.7 1.0

Iodine binding site 9 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ E:I1010 b:0.5 occ:1.00 OG1 E:THR350 3.3 71.4 1.0 N D:CYS356 3.7 83.2 1.0 N E:THR350 3.7 74.5 1.0 OG D:SER354 3.8 75.5 1.0 CG E:LYS439 3.8 83.3 1.0 CB D:CYS356 3.9 85.5 1.0 CB D:ARG355 4.1 76.3 1.0 CA D:CYS356 4.1 84.2 1.0 CA E:CYS349 4.2 76.9 1.0 O E:THR350 4.3 72.9 1.0 C D:ARG355 4.3 80.8 1.0 O E:VAL348 4.3 73.7 1.0 CB E:THR350 4.5 72.2 1.0 C E:CYS349 4.5 76.2 1.0 N D:ARG355 4.5 75.3 1.0 CA E:THR350 4.5 73.2 1.0 CA D:ARG355 4.5 77.9 1.0 CB E:LYS439 4.7 84.1 1.0 CE E:LYS439 4.8 80.2 1.0 CD E:LYS439 4.9 82.0 1.0 C E:THR350 4.9 73.3 1.0 CB E:CYS349 5.0 79.8 1.0

Iodine binding site 10 out of 16 in the Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Asymmetrically Engineered Fc Variant in Complex with Fcgriiia within 5.0Å range: probe atom residue distance (Å) B Occ E:I1011 b:85.9 occ:1.00 OG E:SER254 2.9 65.8 1.0 CG E:MET252 3.9 76.7 1.0 CB E:MET252 4.0 72.0 1.0 CB E:SER254 4.0 65.8 1.0 N E:SER254 4.2 64.8 1.0 N E:ILE253 4.3 65.8 1.0 SD E:MET252 4.3 84.0 1.0 CG2 E:ILE253 4.4 64.2 1.0 CA E:MET252 4.5 67.7 1.0 C E:MET252 4.6 67.0 1.0 CA E:SER254 4.8 65.0 1.0

F.Mimoto, S.Kadono, H.Katada, T.Igawa, T.Kamikawa, K.Hattori. Crystal Structure of A Novel Asymmetrically Engineered Fc Variant with Improved Affinity For Fc Gamma Rs. Mol.Immunol. V. 58 132 2014.
ISSN: ISSN 0161-5890
PubMed: 24334029
DOI: 10.1016/J.MOLIMM.2013.11.017