Iodine in PDB 4gus: Crystal Structure of LSD2-Npac with H3 in Space Group P3221

The structure of Crystal Structure of LSD2-Npac with H3 in Space Group P3221, PDB code: 4gus was solved by F.Chen, Z.Dong, J.Fang, Y.Yang, Z.Li, Y.Xu, H.Yang, P.Wang, R.Fang, Y.Shi, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.04 / 2.23
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.083, 101.083, 177.372, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.7

The structure of Crystal Structure of LSD2-Npac with H3 in Space Group P3221 also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Iodine atom in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221 (pdb code 4gus). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221, PDB code: 4gus:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I902 b:60.4 occ:1.00 OD1 A:ASP415 4.0 47.1 1.0 CB A:LYS414 4.0 39.7 1.0 N A:ASP415 4.0 41.1 1.0 CA A:LYS414 4.0 39.6 1.0 CG A:LYS414 4.2 41.9 1.0 CG A:ASP415 4.3 46.9 1.0 C A:LYS414 4.5 41.7 1.0 CB A:ASP415 4.7 45.3 1.0 OD2 A:ASP415 4.8 52.9 1.0 NZ A:LYS414 4.9 40.8 1.0 CE A:LYS414 5.0 41.9 1.0 CA A:ASP415 5.0 42.8 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I903 b:48.0 occ:1.00 NE2 A:GLN274 3.7 48.2 1.0 N A:PHE272 3.8 40.4 1.0 O A:PHE272 3.9 44.6 1.0 CA A:GLN270 3.9 37.4 1.0 C A:GLN270 4.0 37.5 1.0 CD A:PRO271 4.0 39.1 1.0 N A:PRO271 4.0 38.4 1.0 CB A:PHE272 4.1 41.4 1.0 CB A:LEU219 4.2 42.7 1.0 CA A:PHE272 4.3 40.9 1.0 CD2 A:PHE272 4.4 41.0 1.0 CB A:GLN270 4.4 38.4 1.0 O A:GLN270 4.5 35.4 1.0 C A:PHE272 4.5 41.3 1.0 CG A:PRO271 4.5 40.1 1.0 O A:LEU219 4.6 44.6 1.0 CD2 A:LEU219 4.7 46.7 1.0 CG A:PHE272 4.7 40.9 1.0 CD1 A:LEU219 4.7 43.3 1.0 CG A:LEU219 4.8 44.1 1.0 O A:PHE269 4.8 39.7 1.0 C A:PRO271 4.8 39.5 1.0 CD A:GLN274 4.9 50.0 1.0 CA A:PRO271 5.0 37.9 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I904 b:72.6 occ:1.00 CG A:LYS128 3.6 48.5 1.0 CD A:PRO127 3.7 54.0 1.0 CD A:LYS128 3.9 49.5 1.0 N A:LYS128 3.9 49.0 1.0 CB A:LYS128 4.0 49.0 1.0 CB A:SER126 4.2 53.8 1.0 CG A:PRO127 4.2 53.1 1.0 CE1 A:PHE96 4.3 55.1 1.0 CE A:LYS128 4.3 50.6 1.0 N A:PRO127 4.4 52.1 1.0 O A:HOH1257 4.4 57.3 1.0 CB A:PRO127 4.4 53.5 1.0 OG A:SER126 4.5 51.7 1.0 CA A:LYS128 4.6 49.5 1.0 CA A:PRO127 4.8 51.1 1.0 C A:PRO127 4.9 49.1 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I905 b:0.3 occ:1.00 O A:SER203 4.3 47.0 1.0 CD1 A:ILE206 4.5 47.3 1.0 NZ A:LYS55 4.5 55.6 1.0 O A:LEU205 4.6 44.0 1.0 O A:ILE206 4.7 43.5 1.0 CA A:ILE206 4.7 45.9 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I906 b:78.5 occ:1.00 NZ A:LYS128 3.7 48.5 1.0 CD A:LYS55 3.9 53.4 1.0 OE1 A:GLU54 3.9 50.7 1.0 CD A:GLU54 4.0 54.8 1.0 CD1 A:ILE206 4.0 47.3 1.0 CG A:GLU54 4.1 54.5 1.0 CB A:LYS55 4.1 52.6 1.0 CB A:HIS84 4.5 45.8 1.0 CG1 A:ILE206 4.5 46.7 1.0 OE2 A:GLU54 4.6 57.8 1.0 CG A:LYS55 4.6 54.0 1.0 CA A:LYS55 4.7 54.2 1.0 O A:HIS84 4.8 44.5 1.0 CD2 A:HIS84 4.8 46.6 1.0 CG A:HIS84 4.9 45.0 1.0 CE A:LYS55 5.0 53.1 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of LSD2-Npac with H3 in Space Group P3221


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 LSD2-Npac with H3 in Space Group P3221 within 5.0Å range: probe atom residue distance (Å) B Occ A:I907 b:0.5 occ:1.00 CE A:MET171 3.9 66.0 1.0 O A:MET171 4.0 77.5 1.0 CG2 A:ILE163 4.6 55.5 1.0 CD1 A:ILE157 4.7 59.1 1.0 C A:MET171 4.8 75.7 1.0 CB A:MET171 4.8 71.3 1.0 CG2 A:ILE157 5.0 59.1 1.0

R.Fang, F.Chen, Z.Dong, D.Hu, A.J.Barbera, E.A.Clark, J.Fang, Y.Yang, P.Mei, M.Rutenberg, Z.Li, Y.Zhang, Y.Xu, H.Yang, P.Wang, M.D.Simon, Q.Zhou, J.Li, M.P.Marynick, X.Li, H.Lu, U.B.Kaiser, R.E.Kingston, Y.Xu, Y.G.Shi. LSD2/KDM1B and Its Cofactor Npac/GLYR1 Endow A Structural and Molecular Model For Regulation of H3K4 Demethylation Mol.Cell V. 49 558 2013.
ISSN: ISSN 1097-2765
PubMed: 23260659
DOI: 10.1016/J.MOLCEL.2012.11.019