Iodine in PDB 6mcj: Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon

The structure of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon, PDB code: 6mcj was solved by M.Sutter, M.A.Dominguez-Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.26 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.162, 71.635, 56.341, 90.00, 92.32, 90.00
R / Rfree (%)	16.7 / 19.9

The binding sites of Iodine atom in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon (pdb code 6mcj). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon, PDB code: 6mcj:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:24.4 occ:0.70 HA A:PRO36 3.2 17.2 1.0 HB3 B:ASN44 3.2 20.2 1.0 HG3 A:PRO36 3.4 30.5 1.0 HE2 A:LYS35 3.6 29.2 1.0 HG2 A:LYS35 3.6 26.6 1.0 HA B:SER45 3.7 23.9 1.0 O A:HOH357 3.7 38.8 1.0 HB2 B:ASN44 3.9 20.2 1.0 HD3 A:LYS35 3.9 26.5 1.0 HB3 A:PRO36 3.9 23.9 1.0 CA A:PRO36 4.0 14.3 1.0 CB B:ASN44 4.0 16.8 1.0 HB2 B:SER45 4.0 28.7 1.0 C B:ASN44 4.2 19.0 1.0 CG A:PRO36 4.2 25.4 1.0 N B:SER45 4.2 17.6 1.0 CB A:PRO36 4.2 19.9 1.0 O B:ASN44 4.3 21.7 1.0 CA B:SER45 4.3 19.9 1.0 N A:PRO36 4.3 15.9 1.0 CE A:LYS35 4.4 24.4 1.0 CD A:LYS35 4.4 22.1 1.0 CG A:LYS35 4.4 22.2 1.0 HZ2 A:LYS35 4.4 29.8 1.0 H B:SER45 4.5 21.1 1.0 HD3 A:PRO36 4.6 22.9 1.0 CB B:SER45 4.6 23.9 1.0 CD A:PRO36 4.7 19.1 1.0 HB3 A:LYS35 4.7 21.0 1.0 CA B:ASN44 4.7 19.1 1.0 C A:LYS35 4.8 18.0 1.0 NZ A:LYS35 4.9 24.8 1.0 O A:LYS35 5.0 13.7 1.0 HG2 A:PRO36 5.0 30.5 1.0

Iodine binding site 2 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:39.7 occ:0.54 HG3 A:PRO43 3.3 62.5 1.0 HB3 A:ALA91 3.3 17.5 1.0 HA A:ALA91 3.4 16.9 1.0 HD22 A:ASN90 3.5 44.6 1.0 HD21 A:ASN90 3.8 44.6 1.0 HA B:GLN37 3.8 36.2 1.0 O A:HOH308 3.8 32.2 1.0 HB A:THR48 3.9 59.4 1.0 ND2 A:ASN90 3.9 37.2 1.0 HG22 A:THR48 4.0 68.2 1.0 CB A:ALA91 4.0 14.6 1.0 CA A:ALA91 4.1 14.1 1.0 HG2 B:GLN37 4.1 49.6 1.0 CG A:PRO43 4.2 52.0 1.0 HB2 A:ALA91 4.3 17.5 1.0 HG2 A:GLU94 4.3 48.6 1.0 HG2 A:PRO43 4.4 62.5 1.0 HB2 A:GLU94 4.4 21.6 1.0 HD2 A:PRO49 4.5 49.8 1.0 N A:ALA91 4.5 14.4 1.0 OE1 A:GLU94 4.6 51.1 1.0 HB2 A:ALA50 4.6 24.3 1.0 O B:PRO36 4.7 32.1 1.0 CA B:GLN37 4.7 30.1 1.0 HB3 A:PRO43 4.7 54.9 1.0 H A:ALA91 4.7 17.3 1.0 CB A:THR48 4.8 49.5 1.0 CG2 A:THR48 4.8 56.9 1.0 HB3 B:GLN37 4.8 32.8 1.0 HB3 A:ALA50 4.8 24.3 1.0 HB2 A:PRO43 4.9 54.9 1.0 CB A:PRO43 4.9 45.7 1.0 HB1 A:ALA91 4.9 17.5 1.0 H A:ALA50 4.9 20.8 1.0 HB3 A:GLU94 4.9 21.6 1.0 CG B:GLN37 5.0 41.3 1.0 CB A:GLU94 5.0 18.0 1.0

Iodine binding site 3 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:21.5 occ:0.60 H A:ASP19 2.7 20.5 1.0 HD1 A:PHE18 3.0 24.3 1.0 O A:HOH362 3.3 36.6 1.0 HG2 A:PRO118 3.4 27.5 1.0 OG1 A:THR22 3.4 16.4 1.0 HB3 A:ASP19 3.6 22.5 1.0 N A:ASP19 3.6 17.1 1.0 HG1 A:THR22 3.6 19.7 1.0 HA A:PHE18 3.6 15.7 1.0 HB2 A:ASP19 3.6 22.5 1.0 HG23 A:THR22 3.6 17.6 1.0 HB3 A:PHE18 3.8 19.0 1.0 HB A:THR22 3.8 17.6 1.0 HB2 A:PRO118 3.9 26.3 1.0 CD1 A:PHE18 3.9 20.2 1.0 CB A:ASP19 4.0 18.8 1.0 CB A:THR22 4.0 14.6 1.0 CG A:PRO118 4.3 22.9 1.0 CA A:PHE18 4.3 13.1 1.0 O A:HOH366 4.3 40.2 1.0 CG2 A:THR22 4.3 14.6 1.0 CB A:PHE18 4.3 15.8 1.0 CA A:ASP19 4.4 14.8 1.0 O A:HOH345 4.4 26.8 1.0 C A:PHE18 4.4 13.4 1.0 CB A:PRO118 4.4 21.9 1.0 O A:HOH319 4.5 40.4 1.0 CG A:PHE18 4.6 17.8 1.0 HB3 A:PRO118 4.7 26.3 1.0 HD2 A:PRO118 4.8 28.2 1.0 HE1 A:PHE18 4.8 25.8 1.0 HG3 A:PRO118 4.8 27.5 1.0 CE1 A:PHE18 4.9 21.5 1.0 HG21 A:THR22 4.9 17.6 1.0 HG22 A:THR22 5.0 17.6 1.0

Iodine binding site 4 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:44.6 occ:0.49 HG3 A:GLN127 3.0 63.9 1.0 HA A:PHE124 3.2 23.8 1.0 HA A:ALA11 3.4 30.7 1.0 HG2 A:ARG14 3.5 29.6 1.0 HD1 A:PHE124 3.5 32.3 1.0 HB2 A:GLN127 3.6 32.0 1.0 HB2 A:ARG14 3.7 29.4 1.0 HB3 A:ARG14 3.8 29.4 1.0 CG A:GLN127 3.9 53.2 1.0 CB A:ARG14 4.1 24.5 1.0 CB A:GLN127 4.1 26.7 1.0 HB2 A:PHE124 4.1 21.8 1.0 HB3 A:GLN127 4.1 32.0 1.0 HG2 A:GLN127 4.2 63.9 1.0 CA A:PHE124 4.2 19.8 1.0 CG A:ARG14 4.2 24.7 1.0 CA A:ALA11 4.3 25.6 1.0 HB2 A:PRO10 4.4 38.4 1.0 CD1 A:PHE124 4.4 26.9 1.0 O A:PRO10 4.4 26.6 1.0 HB2 A:ALA11 4.5 33.0 1.0 CB A:PHE124 4.6 18.1 1.0 HD3 A:ARG14 4.6 36.1 1.0 N A:ALA11 4.6 26.7 1.0 C A:PRO10 4.7 30.6 1.0 O A:GLU123 4.7 24.9 1.0 N A:PHE124 4.7 21.7 1.0 O A:HOH352 4.7 35.6 1.0 CB A:ALA11 4.9 27.6 1.0 HG3 A:ARG14 4.9 29.6 1.0 C A:GLU123 4.9 24.0 1.0 CG A:PHE124 5.0 21.7 1.0

Iodine binding site 5 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:21.5 occ:0.76 HG1 B:THR48 3.0 39.3 1.0 HG3 B:PRO43 3.1 25.2 1.0 OG1 B:THR48 3.3 32.7 1.0 HG3 B:GLU94 3.3 25.7 1.0 HB2 B:ALA91 3.3 19.6 1.0 HA B:ALA91 3.4 17.7 1.0 HG2 A:GLN37 3.4 27.5 1.0 O A:HOH332 3.7 23.2 1.0 HD22 B:ASN90 3.7 31.0 1.0 HA A:GLN37 3.8 21.0 1.0 HB B:THR48 3.8 34.2 1.0 HD21 B:ASN90 4.0 31.0 1.0 CG B:PRO43 4.0 21.0 1.0 CB B:ALA91 4.0 16.4 1.0 ND2 B:ASN90 4.1 25.8 1.0 CA B:ALA91 4.1 14.8 1.0 CB B:THR48 4.1 28.5 1.0 HB1 B:ALA91 4.2 19.6 1.0 HB3 A:GLN37 4.2 22.5 1.0 CG B:GLU94 4.3 21.4 1.0 HG2 B:PRO43 4.3 25.2 1.0 CG A:GLN37 4.3 22.9 1.0 N B:ALA91 4.5 16.6 1.0 HD2 B:PRO49 4.5 40.8 1.0 HB3 B:PRO43 4.5 21.2 1.0 HG2 B:GLU94 4.6 25.7 1.0 CB A:GLN37 4.6 18.8 1.0 CA A:GLN37 4.6 17.5 1.0 HB2 B:GLU94 4.7 18.4 1.0 HA B:THR48 4.7 41.0 1.0 HB2 B:ALA50 4.7 24.3 1.0 CB B:PRO43 4.7 17.7 1.0 H B:ALA91 4.7 19.9 1.0 OE1 A:GLN37 4.8 33.5 1.0 HB2 B:PRO43 4.8 21.2 1.0 HD3 B:PRO43 4.9 24.2 1.0 OE2 B:GLU94 4.9 24.9 1.0 HB3 B:ALA91 4.9 19.6 1.0 HG3 A:GLN37 4.9 27.5 1.0 HB3 B:ALA50 4.9 24.3 1.0 C B:ASN90 4.9 16.4 1.0 H B:ALA50 4.9 23.2 1.0 O B:ASN90 5.0 14.7 1.0

Iodine binding site 6 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:33.6 occ:0.60 HB3 A:ASN44 3.1 45.5 1.0 HE2 B:LYS35 3.4 31.1 1.0 HA B:PRO36 3.5 25.3 1.0 HG2 B:LYS35 3.6 27.7 1.0 HA A:SER45 3.7 69.4 1.0 HD3 B:LYS35 3.8 26.4 1.0 HG3 B:PRO36 3.8 31.4 1.0 HB2 A:ASN44 3.8 45.5 1.0 CB A:ASN44 3.9 38.0 1.0 N A:SER45 4.1 56.5 1.0 C A:ASN44 4.1 48.2 1.0 HZ2 B:LYS35 4.1 33.8 1.0 CE B:LYS35 4.2 25.9 1.0 O A:ASN44 4.2 53.5 1.0 HB2 A:SER45 4.2 69.3 1.0 CD B:LYS35 4.3 22.0 1.0 HB3 B:PRO36 4.3 33.4 1.0 CA A:SER45 4.3 57.8 1.0 CA B:PRO36 4.3 21.1 1.0 H A:SER45 4.3 67.8 1.0 CG B:LYS35 4.3 23.1 1.0 CG B:PRO36 4.5 26.2 1.0 N B:PRO36 4.5 19.5 1.0 NZ B:LYS35 4.6 28.2 1.0 CB B:PRO36 4.6 27.8 1.0 CA A:ASN44 4.7 47.2 1.0 HB3 B:LYS35 4.7 20.1 1.0 CB A:SER45 4.8 57.7 1.0 HD3 B:PRO36 4.8 28.6 1.0 HZ3 B:LYS35 4.9 33.8 1.0 CD B:PRO36 4.9 23.8 1.0 C B:LYS35 5.0 19.6 1.0 HE3 B:LYS35 5.0 31.1 1.0

Iodine binding site 7 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ B:I204 b:34.5 occ:0.54 HB3 B:ASP134 2.9 42.2 1.0 H B:ASP134 3.0 29.1 1.0 HB2 A:PRO89 3.2 28.1 1.0 HB3 B:PHE133 3.2 31.0 1.0 HG2 A:PRO89 3.2 26.8 1.0 O A:HOH304 3.4 34.0 1.0 N B:ASP134 3.7 24.3 1.0 CB B:ASP134 3.8 35.2 1.0 HD2 B:PHE133 3.8 35.3 1.0 HD13 A:LEU141 3.9 25.0 1.0 HD22 A:LEU141 3.9 27.0 1.0 CB A:PRO89 3.9 23.4 1.0 OD1 B:ASP134 4.0 42.8 1.0 CG A:PRO89 4.0 22.3 1.0 O A:HOH377 4.0 32.9 1.0 O A:HOH389 4.1 42.7 1.0 CG B:ASP134 4.1 45.7 1.0 HB3 A:LEU141 4.1 22.7 1.0 CB B:PHE133 4.2 25.8 1.0 H B:PHE133 4.2 38.3 1.0 HB3 B:GLU132 4.2 48.4 1.0 HB3 A:PRO89 4.2 28.1 1.0 HD2 A:PRO89 4.3 26.1 1.0 CA B:ASP134 4.3 31.4 1.0 HB2 B:ASP134 4.5 42.2 1.0 N B:PHE133 4.6 31.9 1.0 C B:PHE133 4.6 26.7 1.0 CD2 B:PHE133 4.6 29.4 1.0 HA B:ASP134 4.6 37.7 1.0 HB2 B:PHE133 4.7 31.0 1.0 CA B:PHE133 4.7 28.0 1.0 CD A:PRO89 4.7 21.8 1.0 HG3 A:PRO89 4.7 26.8 1.0 CD1 A:LEU141 4.8 20.9 1.0 CD2 A:LEU141 4.8 22.5 1.0 H A:ASN90 4.8 22.1 1.0 OD2 B:ASP134 4.9 65.5 1.0 CG B:PHE133 4.9 28.9 1.0 CB A:LEU141 5.0 18.9 1.0 O B:HOH335 5.0 35.4 1.0

Iodine binding site 8 out of 8 in the Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Helical Carotenoid Protein 2 From Fremyella Diplosiphon within 5.0Å range: probe atom residue distance (Å) B Occ B:I205 b:92.3 occ:0.64 HG11 B:VAL128 3.1 59.7 1.0 O B:HOH364 3.3 40.8 1.0 HA3 B:GLY30 3.3 19.1 1.0 HA2 B:GLY30 3.8 19.1 1.0 HE1 B:PHE139 4.0 29.2 1.0 CA B:GLY30 4.0 15.9 1.0 CG1 B:VAL128 4.1 49.8 1.0 HG23 B:VAL128 4.1 41.1 1.0 HZ B:PHE124 4.2 28.3 1.0 CE1 B:PHE139 4.3 24.3 1.0 HG13 B:VAL128 4.4 59.7 1.0 HD1 B:PHE139 4.4 30.6 1.0 HG12 B:VAL128 4.5 59.7 1.0 CD1 B:PHE139 4.5 25.5 1.0 SD B:MET140 4.6 22.9 1.0 O B:HOH370 4.8 41.5 1.0 HD11 B:LEU34 4.8 32.6 1.0 CG2 B:VAL128 4.8 34.3 1.0 CZ B:PHE139 4.9 19.0 1.0 HE2 B:PHE124 4.9 29.1 1.0 HG2 B:ARG136 4.9 47.2 1.0 H B:GLY30 4.9 19.7 1.0 HG2 B:MET140 4.9 24.1 1.0 HG22 B:VAL128 5.0 41.1 1.0 CZ B:PHE124 5.0 23.6 1.0 O B:LEU26 5.0 16.6 1.0 N B:GLY30 5.0 16.4 1.0

M.A.Dominguez-Martin, T.Polivka, M.Sutter, B.Ferlez, S.Lechno-Yossef, B.L.Montgomery, C.A.Kerfeld. Structural and Spectroscopic Characterization of HCP2. Biochim Biophys Acta V.1860 414 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 30880081
DOI: 10.1016/J.BBABIO.2019.03.004