Iodine in PDB 6x42: High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum

The structure of High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum, PDB code: 6x42 was solved by O.B.Clarke, N.A.Smith, M.Lee, B.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.47 / 1.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.288, 102.288, 71.718, 90.00, 90.00, 120.00
R / Rfree (%)	12.6 / 14.7

The structure of High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iodine atom in the High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum (pdb code 6x42). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum, PDB code: 6x42:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ X:I904 b:25.3 occ:0.37 I3 X:I3C904 0.0 25.3 0.4 C6 X:I3C904 2.1 24.6 0.4 HN1A X:I3C904 2.9 21.3 0.4 C1 X:I3C904 3.1 30.0 0.4 C5 X:I3C904 3.1 22.9 0.4 N13 X:I3C904 3.2 17.7 0.4 C7 X:I3C904 3.3 31.9 0.4 HG23 X:VAL773 3.5 23.4 1.0 HB3 X:ASN771 3.6 24.4 1.0 O8 X:I3C904 3.7 31.9 0.4 O9 X:I3C904 3.7 33.2 0.4 HG2 X:LYS779 3.8 31.4 1.0 HA X:TYR772 3.9 20.1 1.0 HN13 X:I3C904 3.9 21.3 0.4 HG22 X:VAL773 4.0 23.4 1.0 HB2 X:ASN771 4.0 24.4 1.0 CG2 X:VAL773 4.2 19.5 1.0 N X:TYR772 4.2 17.2 1.0 O X:TYR772 4.2 19.0 1.0 C X:TYR772 4.3 17.0 1.0 CB X:ASN771 4.3 20.4 1.0 CA X:TYR772 4.3 16.8 1.0 C2 X:I3C904 4.4 33.8 0.4 C4 X:I3C904 4.4 25.3 0.4 H X:TYR772 4.4 20.6 1.0 C X:ASN771 4.5 18.1 1.0 HG21 X:VAL773 4.5 23.4 1.0 O X:ASN771 4.7 18.6 1.0 CG X:LYS779 4.7 26.1 1.0 O X:HOH1142 4.7 54.9 1.0 N X:VAL773 4.8 17.2 1.0 HB3 X:LYS779 4.9 26.3 1.0 C3 X:I3C904 4.9 29.9 0.4 HA X:LYS779 5.0 23.3 1.0 CD X:LYS779 5.0 29.8 1.0

Iodine binding site 2 out of 3 in the High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ X:I904 b:25.3 occ:0.37 I2 X:I3C904 0.0 25.3 0.4 C4 X:I3C904 2.1 25.3 0.4 HN13 X:I3C904 2.9 21.3 0.4 C5 X:I3C904 3.1 22.9 0.4 C3 X:I3C904 3.1 29.9 0.4 O X:HOH1157 3.1 48.2 1.0 N13 X:I3C904 3.2 17.7 0.4 C10 X:I3C904 3.3 31.3 0.4 HB3 X:LYS779 3.5 26.3 1.0 O12 X:I3C904 3.7 31.6 0.4 HG X:SER781 3.7 25.3 1.0 O11 X:I3C904 3.8 31.8 0.4 HN1A X:I3C904 3.9 21.3 0.4 O X:LYS780 3.9 17.5 1.0 OG X:SER781 4.0 21.1 1.0 OD1 X:ASN771 4.0 22.9 1.0 HB3 X:ASN771 4.0 24.4 1.0 CG X:ASN771 4.2 22.4 1.0 C X:LYS780 4.3 16.2 1.0 N X:LYS780 4.3 17.4 1.0 HA X:LYS780 4.4 21.1 1.0 C X:LYS779 4.4 18.8 1.0 CB X:LYS779 4.4 21.9 1.0 C6 X:I3C904 4.4 24.6 0.4 C2 X:I3C904 4.4 33.8 0.4 O X:LYS779 4.5 20.5 1.0 H X:LYS780 4.5 21.0 1.0 HB2 X:LYS779 4.6 26.3 1.0 CA X:LYS780 4.6 17.6 1.0 ND2 X:ASN771 4.6 25.5 1.0 CB X:ASN771 4.7 20.4 1.0 HD21 X:ASN771 4.7 30.6 1.0 C1 X:I3C904 4.9 30.0 0.4 CA X:LYS779 5.0 19.4 1.0

Iodine binding site 3 out of 3 in the High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of High Resolution Crystal Structure Analysis of SERA5E From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ X:I904 b:41.3 occ:0.37 I1 X:I3C904 0.0 41.3 0.4 C2 X:I3C904 2.1 33.8 0.4 C3 X:I3C904 3.0 29.9 0.4 C1 X:I3C904 3.1 30.0 0.4 C10 X:I3C904 3.2 31.3 0.4 C7 X:I3C904 3.3 31.9 0.4 O11 X:I3C904 3.6 31.8 0.4 O9 X:I3C904 3.7 33.2 0.4 O12 X:I3C904 3.7 31.6 0.4 O8 X:I3C904 3.8 31.9 0.4 C4 X:I3C904 4.4 25.3 0.4 C6 X:I3C904 4.4 24.6 0.4 O X:HOH1142 4.7 54.9 1.0 C5 X:I3C904 4.9 22.9 0.4

N.A.Smith, O.B.Clarke, M.Lee, A.N.Hodder, B.J.Smith. Structure of the Plasmodium Falciparum PFSERA5 Pseudo-Zymogen. Protein Sci. V. 29 2245 2020.
ISSN: ESSN 1469-896X
PubMed: 32955133
DOI: 10.1002/PRO.3956