Zinc in PDB 3vuv: Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc

The structure of Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc, PDB code: 3vuv was solved by P.E.Czabotar, A.N.Hodder, O.B.Clarke, C.S.Lin, B.J.Smith, A.F.Cowman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.44 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.690, 102.070, 38.245, 90.00, 101.76, 90.00
R / Rfree (%)	17.4 / 23.3

The binding sites of Zinc atom in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc (pdb code 3vuv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc, PDB code: 3vuv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.9 occ:1.00 O A:HOH662 2.1 36.5 1.0 NE2 A:HIS249 2.1 48.7 1.0 O A:HOH661 2.2 51.3 1.0 OH A:TYR356 2.3 64.5 1.0 CE1 A:HIS249 2.6 53.5 1.0 O A:HOH609 3.3 37.6 1.0 CD2 A:HIS249 3.4 40.4 1.0 CZ A:TYR356 3.5 62.4 1.0 ND1 A:HIS249 3.8 51.2 1.0 CE1 A:TYR356 4.2 60.0 1.0 CG A:HIS249 4.3 43.7 1.0 CE2 A:TYR356 4.5 57.5 1.0 CB A:ALA259 4.7 19.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:44.9 occ:1.00 O A:HOH642 2.1 11.6 1.0 ND1 A:HIS257 2.1 41.1 1.0 OE2 A:GLU254 2.2 53.9 1.0 OE1 A:GLU254 2.3 49.4 1.0 O A:HOH643 2.4 19.5 1.0 CD A:GLU254 2.5 45.2 1.0 CE1 A:HIS257 3.1 39.9 1.0 CG A:HIS257 3.1 34.5 1.0 CB A:HIS257 3.4 27.2 1.0 CG A:GLU254 4.1 39.4 1.0 NE2 A:HIS257 4.2 39.6 1.0 CB A:THR335 4.2 31.0 1.0 OG1 A:THR335 4.3 31.9 1.0 CD2 A:HIS257 4.3 37.1 1.0 CG2 A:THR335 4.6 27.6 1.0 CA A:GLU254 4.7 34.7 1.0 CB A:GLU254 4.9 33.9 1.0 CA A:HIS257 5.0 22.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:79.7 occ:1.00 OE1 A:GLU319 2.1 52.9 1.0 ND1 A:HIS316 2.2 67.4 1.0 O A:HOH644 2.3 45.9 1.0 O A:HOH653 2.4 57.5 1.0 O A:HOH645 2.4 52.7 1.0 CE1 A:HIS316 2.9 68.1 1.0 CD A:GLU319 3.3 55.2 1.0 CG A:HIS316 3.3 57.8 1.0 CA A:HIS316 3.8 35.5 1.0 CB A:HIS316 3.8 45.7 1.0 OE2 A:GLU319 3.9 57.4 1.0 NE2 A:HIS316 4.1 67.9 1.0 CD2 A:HIS316 4.3 62.9 1.0 N A:HIS316 4.4 34.0 1.0 CG A:GLU319 4.5 47.1 1.0 ND1 A:HIS315 4.6 59.8 1.0 CB A:GLU319 4.7 33.2 1.0 CD1 A:ILE167 4.9 48.9 1.0 CG2 A:ILE167 4.9 49.6 1.0 C A:HIS315 4.9 27.8 1.0 O A:HIS315 5.0 25.8 1.0 C A:HIS316 5.0 28.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Merozoite Surface Protein MSPDBL2 From P. Falciparum Bound to Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:92.2 occ:1.00 OD2 A:ASP278 2.2 57.7 1.0 CG A:ASP278 3.0 53.1 1.0 OD1 A:ASP278 3.1 58.1 1.0 CB A:ASP278 4.4 49.8 1.0 NZ A:LYS283 4.9 51.7 1.0

A.N.Hodder, P.E.Czabotar, A.D.Uboldi, O.B.Clarke, C.S.Lin, J.Healer, B.J.Smith, A.F.Cowman. Insights Into Duffy Binding-Like Domains Through the Crystal Structure and Function of the Merozoite Surface Protein MSPDBL2 From Plasmodium Falciparum J.Biol.Chem. V. 287 32922 2012.
ISSN: ISSN 0021-9258
PubMed: 22843685
DOI: 10.1074/JBC.M112.350504