Iodine in PDB 6u2d: Pmtcd Peptide Exporter Basket Domain

The structure of Pmtcd Peptide Exporter Basket Domain, PDB code: 6u2d was solved by N.Zeytuni, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.21 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.190, 39.783, 56.499, 90.00, 108.94, 90.00
R / Rfree (%)	20.9 / 26.1

The binding sites of Iodine atom in the Pmtcd Peptide Exporter Basket Domain (pdb code 6u2d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Pmtcd Peptide Exporter Basket Domain, PDB code: 6u2d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:54.5 occ:0.39 N A:ARG224 3.8 39.6 1.0 CA A:ARG224 3.9 39.6 1.0 CD A:ARG224 3.9 46.0 1.0 C A:ASP223 4.0 39.5 1.0 O A:ASP223 4.1 38.3 1.0 CB A:ASP223 4.2 41.5 1.0 CD A:LYS227 4.3 46.4 1.0 CB A:ARG224 4.4 42.0 1.0 CB A:LYS227 4.6 40.7 1.0 CA A:ASP223 4.7 40.0 1.0 CG A:ARG224 4.8 44.6 1.0

Iodine binding site 2 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:38.8 occ:0.87 CB A:HIS244 3.7 38.0 1.0 O A:HOH425 3.9 46.0 1.0 CB A:MET246 4.2 36.9 1.0 O A:ASN237 4.3 35.9 1.0 CB A:ASN237 4.4 45.9 1.0 C A:ASN237 4.4 37.3 1.0 CB A:ASP239 4.4 33.1 1.0 N A:ASP239 4.4 34.0 1.0 C A:VAL238 4.5 33.7 1.0 N A:VAL238 4.5 36.0 1.0 C A:HIS244 4.6 34.1 1.0 CA A:VAL238 4.6 34.0 1.0 CG A:HIS244 4.6 39.7 1.0 O A:HIS244 4.6 32.6 1.0 N A:MET246 4.7 32.2 1.0 CA A:HIS244 4.8 35.7 1.0 CG2 A:ILE214 4.8 32.9 1.0 CD1 A:ILE214 4.8 35.0 1.0 N A:LEU245 4.8 32.7 1.0 O A:VAL238 4.9 32.7 1.0 C A:LEU245 5.0 32.7 1.0 CG A:ASN237 5.0 51.3 1.0 CD2 A:HIS244 5.0 39.6 1.0 CA A:MET246 5.0 33.8 1.0

Iodine binding site 3 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:46.2 occ:0.80 O B:HOH432 3.1 62.4 1.0 CB B:HIS244 3.8 36.8 1.0 CE B:MET246 3.9 52.0 1.0 CB B:MET246 3.9 47.3 1.0 CB B:ASN237 4.0 60.0 1.0 N B:ASP239 4.0 44.8 1.0 C B:VAL238 4.1 45.2 1.0 ND2 B:ASN237 4.1 64.0 1.0 C B:ASN237 4.1 53.2 1.0 N B:MET246 4.1 42.9 1.0 O B:ASN237 4.2 53.4 1.0 N B:VAL238 4.2 49.6 1.0 CA B:VAL238 4.2 46.3 1.0 O B:HIS244 4.2 37.3 1.0 CB B:ASP239 4.2 44.5 1.0 C B:HIS244 4.3 37.1 1.0 CG B:ASN237 4.4 64.1 1.0 N B:LEU245 4.5 37.3 1.0 C B:LEU245 4.5 40.7 1.0 O B:VAL238 4.6 45.1 1.0 CA B:LEU245 4.6 38.3 1.0 CA B:MET246 4.6 44.8 1.0 CA B:ASN237 4.7 57.2 1.0 CA B:HIS244 4.7 36.8 1.0 CA B:ASP239 4.8 44.2 1.0 CG B:HIS244 4.9 38.0 1.0 CG2 B:ILE214 4.9 46.8 1.0

Iodine binding site 4 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:I302 b:62.3 occ:0.75 CB C:MET246 3.7 59.5 1.0 CB C:HIS244 3.9 52.3 1.0 O C:ASN237 4.0 59.3 1.0 C C:ASN237 4.1 60.0 1.0 N C:ASP239 4.2 60.5 1.0 N C:MET246 4.2 52.1 1.0 C C:VAL238 4.2 57.6 1.0 CA C:VAL238 4.2 55.9 1.0 N C:VAL238 4.3 57.4 1.0 CB C:ASN237 4.3 66.0 1.0 CB C:ASP239 4.3 65.6 1.0 O C:HIS244 4.4 47.5 1.0 C C:HIS244 4.4 48.9 1.0 C C:LEU245 4.6 49.5 1.0 CA C:MET246 4.6 55.1 1.0 N C:LEU245 4.6 48.1 1.0 SD C:MET246 4.7 71.1 1.0 O C:VAL238 4.7 56.7 1.0 CA C:LEU245 4.7 46.6 1.0 CA C:ASN237 4.8 63.6 1.0 CG C:MET246 4.8 65.4 1.0 CA C:HIS244 4.8 51.2 1.0 CA C:ASP239 4.9 63.8 1.0 CG C:HIS244 5.0 53.6 1.0

Iodine binding site 5 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:I303 b:0.3 occ:1.00 O C:HOH422 3.3 39.3 1.0 CA C:TYR228 4.0 42.1 1.0 CB C:TYR228 4.1 41.3 1.0 CD1 C:TYR228 4.2 41.1 1.0 CE1 C:HIS232 4.3 41.1 1.0 CE C:LYS227 4.3 55.5 1.0 OE1 C:GLU231 4.3 48.6 1.0 N C:TYR228 4.4 43.9 1.0 CD C:LYS227 4.5 54.3 1.0 CG C:LYS227 4.5 51.0 1.0 CG C:TYR228 4.7 41.6 1.0 CD1 C:LEU263 4.8 39.7 1.0 C C:LYS227 4.9 44.9 1.0 NZ C:LYS227 5.0 56.7 1.0

Iodine binding site 6 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:I304 b:99.9 occ:0.40 OD1 C:ASP264 2.9 63.9 1.0 CG C:ASP264 4.1 63.5 1.0 O C:GLU262 4.6 45.8 1.0 OD2 C:ASP264 4.8 70.0 1.0 CB C:ASP264 4.9 57.6 1.0

Iodine binding site 7 out of 7 in the Pmtcd Peptide Exporter Basket Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Pmtcd Peptide Exporter Basket Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:I305 b:70.5 occ:0.39 O C:ASP223 3.9 44.6 1.0 CD C:LYS227 4.0 54.3 1.0 C C:ASP223 4.0 45.5 1.0 N C:ARG224 4.1 44.4 1.0 CG C:ARG224 4.1 44.3 1.0 CA C:ARG224 4.1 43.3 1.0 CD B:LYS227 4.1 68.2 1.0 CB C:ASP223 4.2 48.9 1.0 CB C:LYS227 4.3 48.9 1.0 CE B:LYS227 4.5 70.4 1.0 CG B:LYS227 4.5 65.5 1.0 CG C:LYS227 4.7 51.0 1.0 CA C:ASP223 4.7 47.6 1.0 CB C:ARG224 4.7 44.3 1.0 CB B:LYS227 4.9 61.9 1.0

N.Zeytuni, S.W.Dickey, J.Hu, H.T.Chou, L.J.Worrall, J.A.N.Alexander, M.L.Carlson, M.Nosella, F.Duong, Z.Yu, M.Otto, N.C.J.Strynadka. Structural Insight Into the Staphylococcus Aureus Atp-Driven Exporter of Virulent Peptide Toxins Sci Adv V. 6 B8219 2020.
ISSN: ESSN 2375-2548
PubMed: 32998902
DOI: 10.1126/SCIADV.ABB8219