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Zinc in PDB 4ys4: Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum

Protein crystallography data

The structure of Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum, PDB code: 4ys4 was solved by M.L.Parker, F.Peng, M.J.Boulanger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 2.45
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 133.760, 133.760, 133.760, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.8

Other elements in 4ys4:

The structure of Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum (pdb code 4ys4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum, PDB code: 4ys4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ys4

Go back to Zinc Binding Sites List in 4ys4
Zinc binding site 1 out of 3 in the Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum


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 PF41 Tandem 6-Cys Domains From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.8
occ:1.00
OD2 A:ASP134 1.9 35.8 1.0
OD2 A:ASP132 2.0 34.9 1.0
CG A:ASP134 2.8 40.1 1.0
OD1 A:ASP134 3.0 42.3 1.0
CG A:ASP132 3.0 43.2 1.0
OD1 A:ASP132 3.4 44.7 1.0
CB A:ASP134 4.2 41.7 1.0
CB A:ASP132 4.4 37.5 1.0

Zinc binding site 2 out of 3 in 4ys4

Go back to Zinc Binding Sites List in 4ys4
Zinc binding site 2 out of 3 in the Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum


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 PF41 Tandem 6-Cys Domains From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:39.8
occ:1.00
NE2 A:HIS324 2.0 41.3 1.0
CL A:CL404 2.3 35.9 1.0
CL A:CL405 2.5 48.9 1.0
CD2 A:HIS324 2.8 36.2 1.0
CE1 A:HIS324 3.0 38.1 1.0
N A:GLY94 3.7 34.8 1.0
CG A:HIS324 3.9 38.6 1.0
ND1 A:HIS324 4.0 37.2 1.0
ND2 A:ASN322 4.4 32.9 1.0
CA A:GLY94 4.5 37.2 1.0
CA A:TYR93 4.5 32.2 1.0
C A:TYR93 4.6 31.9 1.0
CG A:ASN322 4.8 28.4 1.0
N A:LYS323 4.9 34.1 1.0
OD1 A:ASN322 4.9 36.4 1.0
CB A:TYR93 4.9 31.2 1.0

Zinc binding site 3 out of 3 in 4ys4

Go back to Zinc Binding Sites List in 4ys4
Zinc binding site 3 out of 3 in the Crystal Structure of PF41 Tandem 6-Cys Domains From Plasmodium Falciparum


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 PF41 Tandem 6-Cys Domains From Plasmodium Falciparum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:0.5
occ:1.00
ND1 A:HIS336 2.1 76.2 1.0
O A:HOH553 2.8 67.0 1.0
CE1 A:HIS336 2.9 69.7 1.0
CG A:HIS336 3.2 68.5 1.0
CB A:HIS336 3.7 52.1 1.0
NE2 A:HIS336 4.1 63.7 1.0
CD2 A:HIS336 4.2 64.4 1.0
N A:HIS336 4.6 51.4 1.0
CA A:HIS336 4.8 50.4 1.0

Reference:

M.L.Parker, F.Peng, M.J.Boulanger. The Structure of Plasmodium Falciparum Blood-Stage 6-Cys Protein PF41 Reveals An Unexpected Intra-Domain Insertion Required For PF12 Coordination. Plos One V. 10 39407 2015.
ISSN: ESSN 1932-6203
PubMed: 26414347
DOI: 10.1371/JOURNAL.PONE.0139407
Page generated: Wed Dec 16 05:58:10 2020

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