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Calcium in PDB 4eoy: Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide

Protein crystallography data

The structure of Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide, PDB code: 4eoy was solved by A.U.P.Hain, J.Bosch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.22
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.300, 111.080, 57.090, 90.00, 92.58, 90.00
R / Rfree (%) 20.5 / 28

Other elements in 4eoy:

The structure of Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide (pdb code 4eoy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide, PDB code: 4eoy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4eoy

Go back to Calcium Binding Sites List in 4eoy
Calcium binding site 1 out of 3 in the Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:46.6
occ:1.00
O A:PRO3 2.2 44.2 1.0
O A:HOH390 2.3 52.1 1.0
O A:HOH350 2.6 22.8 1.0
O A:HOH394 2.8 36.9 1.0
OE2 A:GLU34 3.3 35.9 1.0
C A:PRO3 3.4 41.4 1.0
O A:HOH363 3.8 43.8 1.0
CG A:GLU34 3.8 34.9 1.0
CD A:GLU34 4.0 39.3 1.0
CG A:PRO3 4.2 42.1 1.0
N A:SER4 4.3 36.3 1.0
CA A:SER4 4.3 33.9 1.0
CA A:PRO3 4.4 34.6 1.0
NZ A:LYS47 4.4 49.1 1.0
O A:HOH393 4.5 56.9 1.0
CB A:PRO3 4.5 38.6 1.0
N A:PRO3 4.6 38.5 1.0
N A:ARG35 4.6 20.6 1.0
CD A:PRO3 4.7 41.4 1.0
O A:ARG35 4.9 26.2 1.0
CB A:GLU34 5.0 27.1 1.0
CB A:ARG35 5.0 25.4 1.0

Calcium binding site 2 out of 3 in 4eoy

Go back to Calcium Binding Sites List in 4eoy
Calcium binding site 2 out of 3 in the Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:75.0
occ:1.00
O A:SER10 1.9 37.3 1.0
O A:PHE11 2.0 42.3 1.0
N A:ARG14 2.0 30.8 1.0
C A:PHE11 2.1 37.9 1.0
N A:ASN13 2.5 33.8 1.0
N A:GLU12 2.6 44.2 1.0
C A:SER10 2.8 33.7 1.0
CA A:ARG14 2.8 27.0 1.0
CA A:PHE11 2.8 33.2 1.0
CB A:ARG14 2.9 31.9 1.0
C A:GLU12 2.9 43.2 1.0
C A:ASN13 2.9 40.5 1.0
CA A:ASN13 3.1 38.0 1.0
N A:PHE11 3.2 34.6 1.0
CA A:GLU12 3.2 49.5 1.0
N A:VAL15 3.3 30.1 1.0
C A:ARG14 3.5 25.9 1.0
CG A:ARG14 3.6 32.9 1.0
O A:GLU12 3.6 42.2 1.0
CB A:ASN13 3.8 41.1 1.0
CD A:ARG14 3.9 35.3 1.0
O A:ASN13 4.0 58.3 1.0
CA A:SER10 4.2 38.8 1.0
CB A:PHE11 4.3 30.3 1.0
OG A:SER10 4.3 42.1 1.0
NE A:ARG14 4.3 43.4 1.0
CG1 A:VAL9 4.5 32.0 1.0
CA A:VAL15 4.6 32.6 1.0
N A:SER10 4.6 28.5 1.0
CB A:GLU12 4.6 54.8 1.0
CB A:SER10 4.7 44.8 1.0
CG2 A:VAL15 4.7 34.1 1.0
CG A:PHE11 4.7 33.9 1.0
O A:ARG14 4.8 21.1 1.0
CZ A:ARG14 4.8 30.5 1.0
CB A:VAL15 4.8 36.1 1.0
NH1 A:ARG14 4.9 35.3 1.0
CG A:GLU12 4.9 72.4 1.0
O A:VAL9 5.0 33.9 1.0
C A:VAL9 5.0 26.6 1.0
CG A:ASN13 5.0 45.8 1.0

Calcium binding site 3 out of 3 in 4eoy

Go back to Calcium Binding Sites List in 4eoy
Calcium binding site 3 out of 3 in the Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Plasmodium Falciparum ATG8 in Complex with Plasmodium Falciparum ATG3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:77.3
occ:1.00
OD1 C:ASN37 2.3 31.3 1.0
O C:ASN37 2.6 27.1 1.0
OG C:SER39 3.1 32.7 1.0
C C:ASN37 3.3 29.4 1.0
CG C:ASN37 3.4 31.9 1.0
NE C:ARG35 3.5 44.1 1.0
CG C:ARG35 3.6 43.2 1.0
N C:ASN37 3.8 29.9 1.0
CA C:ASN37 3.9 31.2 1.0
CB C:LEU41 3.9 26.0 1.0
CZ C:ARG35 4.0 36.7 1.0
N C:SER39 4.0 30.6 1.0
NH2 C:ARG35 4.1 34.7 1.0
CD1 C:LEU41 4.1 18.5 1.0
CD C:ARG35 4.1 34.7 1.0
CB C:SER39 4.1 32.3 1.0
N C:ARG38 4.2 35.6 1.0
N C:SER120 4.2 28.6 1.0
CB C:ASN37 4.2 29.0 1.0
ND2 C:ASN37 4.3 33.8 1.0
CA C:SER119 4.4 30.2 1.0
CG C:LEU41 4.4 21.1 1.0
O C:TYR118 4.4 36.6 1.0
C C:ARG38 4.4 32.8 1.0
CA C:ARG38 4.5 39.0 1.0
CA C:SER39 4.6 31.7 1.0
O C:LEU41 4.6 35.7 1.0
C C:SER119 4.6 27.8 1.0
CE1 C:TYR118 4.8 31.2 1.0
CD1 C:TYR118 4.8 29.7 1.0
OG C:SER120 4.8 29.1 1.0
MG C:MG203 4.8 63.8 1.0
N C:ALA36 4.8 29.4 1.0
NH1 C:ARG35 4.8 32.1 1.0
CB C:SER120 4.9 32.6 1.0
CA C:LEU41 4.9 28.3 1.0
N C:LEU41 5.0 33.6 1.0
C C:SER39 5.0 31.0 1.0
CB C:ARG35 5.0 35.6 1.0
C C:ALA36 5.0 26.1 1.0

Reference:

A.U.Hain, R.R.Weltzer, H.Hammond, B.Jayabalasingham, R.R.Dinglasan, D.R.Graham, D.R.Colquhoun, I.Coppens, J.Bosch. Structural Characterization and Inhibition of the Plasmodium ATG8-ATG3 Interaction. J.Struct.Biol. V. 180 551 2012.
ISSN: ISSN 1047-8477
PubMed: 22982544
DOI: 10.1016/J.JSB.2012.09.001
Page generated: Sat Dec 12 04:45:24 2020

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