Iodine in PDB 3nsj: The X-Ray Crystal Structure of Lymphocyte Perforin

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj was solved by R.H.Law, J.C.Whisstock, T.T.Caradoc-Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.36 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.640, 109.800, 141.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.5

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	2 atoms

The binding sites of Iodine atom in the The X-Ray Crystal Structure of Lymphocyte Perforin (pdb code 3nsj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:I710 b:0.1 occ:0.70 O A:HOH848 3.7 83.1 1.0 O A:LEU196 3.8 0.3 1.0 ND2 A:ASN353 3.8 0.3 1.0 NZ A:LYS355 3.9 0.1 1.0 C A:LEU196 3.9 99.5 1.0 CE A:LYS355 3.9 0.8 1.0 CB A:LEU196 4.0 90.5 1.0 N A:ARG197 4.0 97.3 1.0 CA A:ARG197 4.2 98.8 1.0 CG A:ARG197 4.3 0.8 1.0 CD A:LYS355 4.5 0.2 1.0 CA A:LEU196 4.6 91.9 1.0 CG A:ASN353 4.7 0.3 1.0 OD1 A:ASN353 4.7 0.7 1.0 CB A:ARG197 4.9 98.9 1.0

Iodine binding site 2 out of 4 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:I711 b:0.1 occ:0.40 CD A:ARG478 4.1 76.8 1.0 CZ A:PHE441 4.3 73.2 1.0 NE A:ARG478 4.3 77.3 1.0 CE2 A:PHE441 4.3 75.4 1.0 NE2 A:GLN480 4.4 82.0 1.0 CE1 A:PHE441 4.5 73.9 1.0 CD2 A:PHE441 4.7 72.5 1.0 CD1 A:PHE441 4.8 72.8 1.0 CD A:GLN480 4.8 86.5 1.0 O A:HOH860 4.9 73.7 1.0 CG A:PHE441 5.0 70.4 1.0 OE1 A:GLN480 5.0 78.7 1.0

Iodine binding site 3 out of 4 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:I712 b:0.6 occ:0.50 NE2 A:GLN410 3.4 92.9 1.0 CB A:ARG409 3.6 94.2 1.0 O A:VAL401 3.6 0.3 1.0 CG1 A:VAL401 3.7 0.8 1.0 CB A:VAL401 3.8 0.7 1.0 CD1 A:LEU413 3.9 91.4 1.0 CA A:VAL401 4.0 0.3 1.0 C A:VAL401 4.3 0.7 1.0 CD A:GLN410 4.4 0.5 1.0 CG A:GLN410 4.4 98.0 1.0 CD2 A:LEU413 4.4 92.6 1.0 CA A:ARG409 4.7 93.6 1.0 CG A:LEU413 4.7 90.9 1.0 N A:GLN410 4.8 91.6 1.0 N A:ARG409 4.9 93.7 1.0

Iodine binding site 4 out of 4 in the The X-Ray Crystal Structure of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:I713 b:0.9 occ:0.50 CD A:PRO306 3.6 83.7 1.0 O A:SER309 3.6 0.9 1.0 CA A:TRP327 3.7 55.8 1.0 CB A:SER309 3.9 0.8 1.0 CB A:TRP327 4.0 53.8 1.0 N A:TRP327 4.0 58.2 1.0 OG A:SER330 4.2 58.2 1.0 CG A:PRO306 4.2 89.3 1.0 CD1 A:TRP327 4.3 55.9 1.0 C A:THR326 4.4 64.2 1.0 O A:THR326 4.5 63.9 1.0 CG2 A:THR326 4.6 66.9 1.0 CG A:TRP327 4.6 53.4 1.0 C A:SER309 4.6 0.9 1.0 CB A:SER330 4.7 51.2 1.0 N A:PRO306 4.8 81.1 1.0 CA A:SER309 4.9 0.0 1.0 C A:TRP327 4.9 57.8 1.0

R.H.Law, N.Lukoyanova, I.Voskoboinik, T.T.Caradoc-Davies, K.Baran, M.A.Dunstone, M.E.D'angelo, E.V.Orlova, F.Coulibaly, S.Verschoor, K.A.Browne, A.Ciccone, M.J.Kuiper, P.I.Bird, J.A.Trapani, H.R.Saibil, J.C.Whisstock. The Structural Basis For Membrane Binding and Pore Formation By Lymphocyte Perforin. Nature V. 468 447 2010.
ISSN: ISSN 0028-0836
PubMed: 21037563
DOI: 10.1038/NATURE09518