Iodine in PDB 8ok5: Variant Surface Glycoprotein VSG11 Monomer with Iodine

The structure of Variant Surface Glycoprotein VSG11 Monomer with Iodine, PDB code: 8ok5 was solved by J.P.Zeelen, C.E.Stebbins, F.Aresta-Branco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.26 / 1.27
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.426, 75.426, 106.441, 90, 90, 120
R / Rfree (%)	20.6 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Iodine atom in the Variant Surface Glycoprotein VSG11 Monomer with Iodine (pdb code 8ok5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the Variant Surface Glycoprotein VSG11 Monomer with Iodine, PDB code: 8ok5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:14.6 occ:0.45 HB2 A:LYS94 3.2 11.9 1.0 HA A:LYS94 3.4 13.0 1.0 O A:HOH1007 3.5 29.2 0.3 O A:HOH1027 3.6 11.0 0.3 HG3 A:LYS94 3.7 10.4 1.0 CB A:LYS94 3.9 9.9 1.0 HG22 A:THR93 3.9 17.4 1.0 HD2 A:LYS94 3.9 11.5 1.0 CA A:LYS94 4.0 10.8 1.0 CG A:LYS94 4.2 8.7 1.0 N A:LYS94 4.4 9.5 1.0 H A:LYS94 4.5 11.4 1.0 CD A:LYS94 4.6 9.6 1.0 HB3 A:LYS94 4.8 11.9 1.0 HB A:THR93 4.8 16.1 1.0 CG2 A:THR93 4.8 14.6 1.0 HG21 A:THR93 5.0 17.4 1.0

Iodine binding site 2 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range:

Iodine binding site 3 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:18.0 occ:0.67 HB3 A:ALA133 3.0 23.0 1.0 HA A:LYS131 3.0 20.7 1.0 H A:ALA133 3.2 20.4 1.0 H A:GLY134 3.3 21.5 1.0 HA A:LYS128 3.6 21.5 1.0 HD3 A:LYS128 3.6 36.7 1.0 HD3 A:LYS131 3.8 31.8 1.0 CB A:ALA133 3.8 19.2 1.0 N A:ALA133 3.9 17.0 1.0 CA A:LYS131 3.9 17.3 1.0 N A:GLY134 3.9 17.9 1.0 O A:HOH659 4.0 20.4 1.0 C A:LYS131 4.1 16.6 1.0 HB2 A:ALA133 4.1 23.0 1.0 HD2 A:LYS131 4.2 31.8 1.0 CA A:ALA133 4.3 16.3 1.0 O A:LYS128 4.3 18.0 1.0 N A:LEU132 4.4 16.2 1.0 HB3 A:LYS131 4.4 23.6 1.0 HD2 A:LYS128 4.4 36.7 1.0 CD A:LYS128 4.4 30.6 1.0 O A:LYS131 4.4 20.4 1.0 H A:LEU132 4.4 19.4 1.0 CD A:LYS131 4.4 26.6 1.0 C A:ALA133 4.4 17.3 1.0 H A:LYS131 4.5 21.3 1.0 CA A:LYS128 4.5 18.0 1.0 HB1 A:ALA133 4.5 23.0 1.0 HA3 A:GLY134 4.7 23.6 1.0 CB A:LYS131 4.7 19.7 1.0 N A:LYS131 4.7 17.8 1.0 O A:LEU127 4.8 14.7 0.7 O A:LEU127 4.8 16.0 0.3 HB3 A:LYS128 4.8 23.0 1.0 C A:LEU132 4.9 17.1 1.0 C A:LYS128 4.9 16.5 1.0 CA A:GLY134 4.9 19.7 1.0

Iodine binding site 4 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:25.8 occ:0.61 H A:THR316 2.7 17.2 1.0 HA A:THR316 3.5 19.4 1.0 N A:THR316 3.5 14.4 1.0 HE1 A:PHE313 3.6 19.0 1.0 O A:HOH863 3.7 34.4 1.0 HA A:ALA315 3.7 20.5 1.0 HZ A:PHE313 3.9 22.9 1.0 HB2 A:ALA216 3.9 20.7 1.0 CA A:THR316 4.1 16.2 1.0 HB3 A:ALA216 4.3 20.7 1.0 CE1 A:PHE313 4.4 15.9 1.0 HG1 A:THR316 4.4 26.0 1.0 HB1 A:ALA216 4.4 20.7 1.0 CB A:ALA216 4.4 17.3 1.0 CZ A:PHE313 4.5 19.1 1.0 C A:ALA315 4.5 16.4 1.0 CA A:ALA315 4.5 17.1 1.0 HB1 A:ALA315 4.8 22.1 1.0 OG1 A:THR316 4.9 21.7 1.0 C A:THR316 4.9 14.7 1.0

Iodine binding site 5 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:19.7 occ:0.66 H A:GLY260 2.6 14.7 1.0 HE A:ARG237 3.3 29.5 1.0 HA A:ASN258 3.3 14.7 1.0 HH21 A:ARG237 3.3 31.7 1.0 HA3 A:GLY260 3.4 13.3 1.0 N A:GLY260 3.5 12.3 1.0 HD2 A:PRO259 3.5 12.2 1.0 HG23 A:THR238 3.6 29.8 1.0 HB2 A:ASN258 3.8 18.6 1.0 C A:ASN258 3.8 10.4 1.0 HB3 A:ARG237 3.8 19.2 1.0 CA A:ASN258 3.9 12.3 1.0 N A:PRO259 3.9 10.9 1.0 CA A:GLY260 3.9 11.1 1.0 O A:HOH926 4.0 16.6 1.0 NE A:ARG237 4.1 24.6 1.0 NH2 A:ARG237 4.1 26.4 1.0 CD A:PRO259 4.1 10.2 1.0 HG21 A:THR238 4.2 29.8 1.0 O A:ASN258 4.2 12.6 1.0 CG2 A:THR238 4.2 24.9 1.0 H A:VAL261 4.2 16.7 1.0 HG2 A:PRO259 4.3 14.7 1.0 O A:HOH866 4.3 14.6 1.0 HG23 A:VAL261 4.3 19.2 1.0 HG22 A:THR238 4.4 29.8 1.0 CB A:ASN258 4.4 15.5 1.0 O A:HOH797 4.4 24.3 1.0 CZ A:ARG237 4.6 19.8 1.0 C A:PRO259 4.6 11.7 1.0 CB A:ARG237 4.7 16.0 1.0 N A:VAL261 4.7 14.0 1.0 HH22 A:ARG237 4.7 31.7 1.0 C A:GLY260 4.7 14.3 1.0 HA2 A:GLY260 4.7 13.3 1.0 HB2 A:ARG237 4.8 19.2 1.0 HB3 A:ASN258 4.8 18.6 1.0 CG A:PRO259 4.8 12.2 1.0 CA A:PRO259 4.8 11.3 1.0 H A:ARG237 4.9 14.9 1.0 HD3 A:PRO259 4.9 12.2 1.0

Iodine binding site 6 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:25.1 occ:0.48 HG22 A:THR376 3.1 21.5 1.0 HD12 A:LEU380 3.4 16.5 1.0 HD11 A:LEU380 3.4 16.5 1.0 O A:HOH663 3.5 24.1 1.0 HG21 A:THR376 3.7 21.5 1.0 CD1 A:LEU380 3.7 13.8 1.0 CG2 A:THR376 3.9 17.9 1.0 HD13 A:LEU380 3.9 16.5 1.0 HG12 A:ILE377 4.0 16.8 1.0 HG13 A:ILE377 4.0 16.8 1.0 HB A:THR376 4.5 18.6 1.0 CG1 A:ILE377 4.5 14.0 1.0 HG23 A:THR376 4.5 21.5 1.0 HA A:ILE377 4.7 16.4 1.0 CB A:THR376 4.8 15.5 1.0 O A:HOH995 4.8 25.4 0.3 HE3 A:LYS157 4.9 30.0 1.0 O A:HOH608 4.9 27.8 1.0 HD21 A:LEU150 4.9 14.5 1.0 HD11 A:ILE377 5.0 21.7 1.0 HD22 A:LEU150 5.0 14.5 1.0

Iodine binding site 7 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:15.4 occ:0.26 HD22 A:LEU32 3.3 23.6 1.0 HB2 A:LEU32 3.5 16.5 1.0 O A:HOH846 3.6 18.8 1.0 CD2 A:LEU32 4.2 19.7 1.0 CB A:LEU32 4.3 13.8 1.0 HB3 A:LEU32 4.4 16.5 1.0 HD23 A:LEU32 4.5 23.6 1.0 O A:HOH658 4.6 25.6 1.0 HD13 A:LEU32 4.6 26.6 1.0 CG A:LEU32 4.8 18.9 1.0 HD21 A:LEU32 4.8 23.6 1.0 H A:LEU32 4.9 14.3 1.0

Iodine binding site 8 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:17.5 occ:0.48 HH11 A:ARG86 3.2 18.9 1.0 O A:HOH845 3.4 24.1 1.0 HB3 A:SER87 3.4 19.2 1.0 HD3 A:ARG86 3.5 14.8 1.0 HG3 A:ARG86 3.5 14.7 1.0 HG2 A:ARG86 3.6 14.7 1.0 HH12 A:ARG86 3.6 18.9 1.0 NH1 A:ARG86 3.6 15.8 1.0 CG A:ARG86 3.9 12.2 1.0 CD A:ARG86 4.2 12.4 1.0 O A:HOH829 4.2 26.0 1.0 CB A:SER87 4.4 16.1 1.0 H A:SER87 4.6 11.9 1.0 HB2 A:SER87 4.7 19.2 1.0 CZ A:ARG86 4.7 13.1 1.0 HG A:SER87 4.9 16.0 1.0 N A:SER87 4.9 10.0 1.0 NE A:ARG86 4.9 14.1 1.0 HD2 A:ARG86 4.9 14.8 1.0

Iodine binding site 9 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:23.4 occ:0.41 HD21 A:ASN145 3.1 33.6 1.0 HD3 A:ARG148 3.1 19.8 1.0 HA A:ASN145 3.2 17.3 1.0 HH11 A:ARG148 3.2 27.6 1.0 HB2 A:ASN145 3.5 20.3 1.0 HG2 A:ARG144 3.8 19.0 0.4 HG2 A:ARG144 3.8 18.1 0.6 OE2 A:GLU141 3.9 41.3 1.0 ND2 A:ASN145 3.9 28.1 1.0 CA A:ASN145 3.9 14.4 1.0 CD A:ARG148 3.9 16.5 1.0 NH1 A:ARG148 3.9 23.0 1.0 HD2 A:ARG148 4.0 19.8 1.0 HD2 A:ARG144 4.0 20.2 0.6 CB A:ASN145 4.1 16.9 1.0 N A:ASN145 4.2 14.4 1.0 H A:ASN145 4.3 17.2 1.0 HB3 A:ARG144 4.4 18.4 0.4 HB3 A:ARG144 4.4 18.3 0.6 HH12 A:ARG148 4.4 27.6 1.0 NE A:ARG148 4.5 13.8 1.0 HE A:ARG144 4.5 20.2 0.4 HD22 A:ASN145 4.5 33.6 1.0 CZ A:ARG148 4.5 17.1 1.0 CG A:ARG144 4.6 15.1 0.6 CG A:ASN145 4.6 21.9 1.0 CD A:ARG144 4.6 16.9 0.6 HD3 A:ARG144 4.6 20.2 0.6 CG A:ARG144 4.7 15.8 0.4 C A:ARG144 4.7 13.0 0.4 C A:ARG144 4.7 12.7 0.6 O A:HOH830 4.7 27.3 1.0 HB2 A:ARG148 4.8 13.7 1.0 CD A:GLU141 4.9 35.4 1.0 O A:ARG144 4.9 12.8 0.4 O A:ARG144 4.9 12.7 0.6 O A:GLU141 4.9 19.9 1.0 HD2 A:ARG144 5.0 17.0 0.4 CB A:ARG144 5.0 15.3 0.6 HB3 A:ASN145 5.0 20.3 1.0

Iodine binding site 10 out of 21 in the Variant Surface Glycoprotein VSG11 Monomer with Iodine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Variant Surface Glycoprotein VSG11 Monomer with Iodine within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:25.2 occ:0.37 HG2 A:LYS99 3.2 19.9 1.0 HA A:ASP100 3.4 15.2 1.0 O A:HOH1040 3.4 34.1 1.0 HB3 A:ASP100 3.5 17.0 1.0 HD3 A:LYS99 3.7 26.3 1.0 O A:HOH1011 3.7 29.8 1.0 HB3 A:LYS99 3.9 16.5 1.0 CG A:LYS99 4.0 16.6 1.0 CA A:ASP100 4.0 12.7 1.0 N A:ASP100 4.1 12.9 1.0 CB A:ASP100 4.1 14.2 1.0 C A:LYS99 4.1 11.7 1.0 O A:LYS99 4.1 13.9 1.0 HE3 A:LYS99 4.3 30.8 1.0 CD A:LYS99 4.3 22.0 1.0 HB2 A:ASP100 4.3 17.0 1.0 CB A:LYS99 4.4 13.8 1.0 H A:ASP100 4.4 15.4 1.0 HG3 A:LYS99 4.7 19.9 1.0 CE A:LYS99 4.8 25.7 1.0 CA A:LYS99 4.9 12.4 1.0

S.Dakovic, J.P.Zeelen, A.Gkeka, M.Chandra, M.Van Straaten, K.Foti, J.Zhong, E.P.Vlachou, F.Aresta-Branco, J.P.Verdi, F.N.Papavasiliou, C.E.Stebbins. A Structural Classification of the Variant Surface Glycoproteins of the African Trypanosomey. Plos Negl Trop Dis V. 17 11621 2023.
ISSN: ESSN 1935-2735
PubMed: 37656766
DOI: 10.1371/JOURNAL.PNTD.0011621