Iodine in PDB 6z79: Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks.

The structure of Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks., PDB code: 6z79 was solved by J.P.Zeelen, M.Straaten Van, C.E.Stebbins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.15 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.955, 70.893, 129.652, 90, 90, 90
R / Rfree (%)	23.4 / 25.3

The binding sites of Iodine atom in the Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks. (pdb code 6z79). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks., PDB code: 6z79:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks.


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 Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks. within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:102.6 occ:1.00 I3 A:I3C506 0.0 102.6 1.0 C6 A:I3C506 2.1 104.2 1.0 C1 A:I3C506 3.0 103.8 1.0 C5 A:I3C506 3.1 106.2 1.0 C7 A:I3C506 3.2 103.2 1.0 N13 A:I3C506 3.2 106.7 1.0 O9 A:I3C506 3.3 102.3 1.0 CE1 A:HIS122 3.7 28.8 1.0 O8 A:I3C506 3.9 103.3 1.0 ND1 A:HIS122 4.1 27.5 1.0 C2 A:I3C506 4.4 102.4 1.0 C4 A:I3C506 4.4 105.4 1.0 NE2 A:HIS122 4.4 29.2 1.0 O A:HOH634 4.8 43.5 1.0 C3 A:I3C506 4.9 103.2 1.0

Iodine binding site 2 out of 3 in the Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks.


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 Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks. within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:106.1 occ:1.00 I2 A:I3C506 0.0 106.1 1.0 C4 A:I3C506 2.1 105.4 1.0 C3 A:I3C506 3.1 103.2 1.0 C5 A:I3C506 3.1 106.2 1.0 O12 A:I3C506 3.1 98.7 1.0 N13 A:I3C506 3.2 106.7 1.0 C10 A:I3C506 3.2 100.0 1.0 O A:HIS122 3.7 23.1 1.0 CB A:HIS122 3.7 25.4 1.0 CA A:HIS122 3.8 24.3 1.0 CG A:HIS122 4.0 27.0 1.0 C A:HIS122 4.1 23.2 1.0 O11 A:I3C506 4.1 98.7 1.0 CD2 A:HIS122 4.2 27.9 1.0 O A:HOH616 4.2 39.8 1.0 C2 A:I3C506 4.4 102.4 1.0 C6 A:I3C506 4.4 104.2 1.0 C1 A:I3C506 4.9 103.8 1.0 ND1 A:HIS122 4.9 27.5 1.0

Iodine binding site 3 out of 3 in the Variant Surface Glycoprotein Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks.


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 Vsgsur, I3C ("Magic Triangle") Derivative Used For Phasing of the Structure and Subsequently As A Model For Molecular Replacement of Native, Mutants, and Drug Soaks. within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:99.8 occ:1.00 I1 A:I3C506 0.0 99.8 1.0 C2 A:I3C506 2.1 102.4 1.0 C3 A:I3C506 3.1 103.2 1.0 C1 A:I3C506 3.1 103.8 1.0 O11 A:I3C506 3.1 98.7 1.0 C10 A:I3C506 3.2 100.0 1.0 C7 A:I3C506 3.3 103.2 1.0 O8 A:I3C506 3.4 103.3 1.0 O A:HOH634 3.9 43.5 1.0 O9 A:I3C506 4.0 102.3 1.0 O A:HOH712 4.0 27.8 1.0 O12 A:I3C506 4.1 98.7 1.0 O A:HOH784 4.2 43.5 1.0 C6 A:I3C506 4.4 104.2 1.0 C4 A:I3C506 4.4 105.4 1.0 O A:HOH602 4.4 38.0 1.0 O A:HOH737 4.7 51.0 1.0 O A:HOH616 4.8 39.8 1.0 C5 A:I3C506 4.9 106.2 1.0

J.Zeelen, M.Van Straaten, J.Verdi, A.Hempelmann, H.Hashemi, K.Perez, P.D.Jeffrey, S.Halg, N.Wiedemar, P.Maser, F.N.Papavasiliou, C.E.Stebbins. Structure of Trypanosome Coat Protein Vsgsur and Function in Suramin Resistance. Nat Microbiol V. 6 392 2021.
ISSN: ESSN 2058-5276
PubMed: 33462435
DOI: 10.1038/S41564-020-00844-1