Iridium in PDB 4akm: Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp)

The structure of Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp), PDB code: 4akm was solved by J.Krausze, S.Wilke, K.Buessow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.30 / 2.69
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	52.600, 52.600, 141.980, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 24.9

The binding sites of Iridium atom in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp) (pdb code 4akm). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 4 binding sites of Iridium where determined in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp), PDB code: 4akm:
Jump to Iridium binding site number: 1; 2; 3; 4;

Iridium binding site 1 out of 4 in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir1378 b:89.7 occ:1.00 OG A:SER348 3.8 47.3 1.0 O A:GLN320 3.9 41.8 1.0 ND1 A:HIS350 4.0 76.3 1.0 CB A:SER348 4.1 46.4 1.0 N A:GLN320 4.6 39.6 1.0 CB A:HIS350 4.8 60.0 1.0 CG A:HIS350 4.8 72.0 1.0 CE1 A:HIS350 4.9 79.8 1.0 CD1 A:TYR319 5.0 51.1 1.0 C A:GLN320 5.0 43.6 1.0

Iridium binding site 2 out of 4 in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir1380 b:0.4 occ:0.65 N A:PHE329 4.1 56.0 1.0 CA A:PHE329 4.4 63.2 1.0 CZ A:PHE337 4.8 70.0 1.0 CD1 A:PHE329 4.8 62.4 1.0 N A:GLN330 4.8 65.3 1.0 CE1 A:PHE337 4.9 76.7 1.0 CB A:CYS376 5.0 92.2 1.0

Iridium binding site 3 out of 4 in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir1379 b:96.3 occ:0.28 NH2 B:ARG258 2.6 73.9 1.0 NZ B:LYS354 3.2 60.8 1.0 CZ B:ARG258 3.7 78.2 1.0 NH1 B:ARG258 4.4 76.8 1.0 NE B:ARG258 4.6 78.5 1.0 CE B:LYS354 4.7 61.0 1.0 OE1 B:GLN352 4.9 53.3 1.0

Iridium binding site 4 out of 4 in the Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp)


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of the Human Lysosome-Associated Membrane Protein Lamp-3 (Aka Dc-Lamp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir1381 b:96.9 occ:1.00 O B:GLN320 4.0 43.1 1.0 OG B:SER348 4.0 54.0 1.0 CD2 B:HIS350 4.1 67.9 1.0 CB B:SER348 4.4 50.9 1.0 N B:GLN320 4.6 45.0 1.0 CG B:HIS350 4.8 63.8 1.0 CB B:HIS350 4.9 53.5 1.0 CD1 B:TYR319 4.9 52.9 1.0

S.Wilke, J.Krausze, K.Bussow. Crystal Structure of the Conserved Domain of the Dc Lysosomal Associated Membrane Protein: Implications For the Lysosomal Glycocalyx. Bmc Biol. V. 10 62 2012.
ISSN: ESSN 1741-7007
PubMed: 22809326
DOI: 10.1186/1741-7007-10-62