Sodium in PDB 6d7a: Structure of T. Gondii PLP1 Beta-Rich Domain

The structure of Structure of T. Gondii PLP1 Beta-Rich Domain, PDB code: 6d7a was solved by A.J.Guerra, N.M.Koropatkin, Z.Wawrzak, C.M.E.Bahr, V.B.Carruthers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.88 / 1.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.980, 50.850, 105.340, 90.00, 90.13, 90.00
R / Rfree (%)	14.1 / 16.4

The binding sites of Sodium atom in the Structure of T. Gondii PLP1 Beta-Rich Domain (pdb code 6d7a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of T. Gondii PLP1 Beta-Rich Domain, PDB code: 6d7a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of T. Gondii PLP1 Beta-Rich Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of T. Gondii PLP1 Beta-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1201 b:15.4 occ:1.00 O A:HOH1499 2.3 19.4 1.0 O A:ASP894 2.4 10.6 1.0 O A:HOH1490 2.4 15.6 1.0 OE2 A:GLU895 2.4 12.7 1.0 O A:GLU892 2.4 13.3 1.0 HH21 A:ARG1043 3.2 19.5 1.0 HG2 A:GLU895 3.2 12.8 1.0 HA A:GLU892 3.2 19.0 1.0 HB3 A:GLN1040 3.2 13.6 1.0 C A:GLU892 3.3 12.2 1.0 CD A:GLU895 3.4 11.3 1.0 HA A:PRO840 3.5 14.4 1.0 C A:ASP894 3.5 9.8 1.0 HG3 A:PRO840 3.7 19.2 1.0 HB3 A:PRO840 3.7 16.6 1.0 CA A:GLU892 3.8 15.8 1.0 HA A:GLU895 3.8 10.7 1.0 CG A:GLU895 3.8 10.7 1.0 NH2 A:ARG1043 3.8 16.2 1.0 HB2 A:GLN1040 3.8 13.6 1.0 HH22 A:ARG1043 3.9 19.5 1.0 CB A:GLN1040 4.0 11.3 1.0 H A:ASP894 4.0 12.3 1.0 O A:SER891 4.0 14.8 1.0 N A:ASP894 4.1 10.3 1.0 HD2 A:PRO841 4.2 15.1 1.0 CA A:PRO840 4.3 12.0 1.0 HD3 A:PRO841 4.3 15.1 1.0 CB A:PRO840 4.3 13.9 1.0 HB2 A:ASP894 4.3 13.3 1.0 HB3 A:GLU892 4.4 24.5 1.0 CA A:ASP894 4.4 9.7 1.0 N A:THR893 4.4 12.7 1.0 O A:HOH1617 4.4 38.0 1.0 N A:GLU895 4.4 9.2 1.0 CG A:PRO840 4.4 16.0 1.0 CA A:GLU895 4.4 8.9 1.0 HG3 A:GLU895 4.5 12.8 1.0 HA A:GLN1040 4.5 12.3 1.0 C A:THR893 4.6 10.3 1.0 OE1 A:GLU895 4.6 11.3 1.0 HA A:THR893 4.7 14.0 1.0 CB A:GLU892 4.7 20.4 1.0 CD A:PRO841 4.7 12.6 1.0 O A:HOH1318 4.7 38.3 1.0 CB A:GLU895 4.8 9.8 1.0 HG2 A:GLU892 4.8 32.8 1.0 CA A:THR893 4.8 11.7 1.0 O A:HOH1607 4.8 38.7 1.0 N A:PRO840 4.8 11.3 1.0 HE A:ARG1043 4.8 14.5 1.0 CA A:GLN1040 4.8 10.2 1.0 N A:GLU892 4.9 16.6 1.0 CB A:ASP894 4.9 11.1 1.0 C A:SER891 4.9 15.8 1.0 HG3 A:GLN1040 5.0 14.0 1.0

Sodium binding site 2 out of 4 in the Structure of T. Gondii PLP1 Beta-Rich Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of T. Gondii PLP1 Beta-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1202 b:9.4 occ:1.00 O A:ALA832 2.2 10.8 1.0 O A:THR830 2.3 10.4 1.0 OE2 A:GLU1051 2.3 9.3 1.0 O A:HOH1434 2.3 9.2 1.0 O A:HOH1530 2.4 15.7 1.0 HG2 A:GLU1051 2.8 10.9 1.0 CD A:GLU1051 3.2 8.8 1.0 CG A:GLU1051 3.3 9.1 1.0 C A:THR830 3.4 9.8 1.0 C A:ALA832 3.4 10.0 1.0 HG3 A:GLU1051 3.5 10.9 1.0 HG3 A:GLN834 3.6 10.2 1.0 O A:HOH1399 3.7 11.9 1.0 HA A:THR833 3.7 11.9 1.0 HE21 A:GLN834 3.8 10.4 1.0 HA A:THR830 3.8 12.4 1.0 N A:ALA832 4.0 11.6 1.0 C A:GLN831 4.0 12.1 1.0 O A:LEU829 4.1 10.7 1.0 H A:GLN834 4.1 9.9 1.0 CA A:THR830 4.2 10.3 1.0 H A:ALA832 4.2 13.9 1.0 HA A:GLN831 4.2 15.5 1.0 HD11 A:LEU901 4.2 13.5 1.0 N A:GLN831 4.3 10.7 1.0 OE1 A:GLU1051 4.3 10.0 1.0 CA A:ALA832 4.3 10.8 1.0 O A:GLN831 4.3 14.3 1.0 N A:THR833 4.4 10.1 1.0 CA A:GLN831 4.4 12.9 1.0 CA A:THR833 4.4 10.0 1.0 NE2 A:GLN834 4.5 8.7 1.0 CG A:GLN834 4.5 8.5 1.0 O A:VAL1028 4.5 8.0 1.0 HG23 A:THR830 4.5 18.6 1.0 O A:HOH1566 4.6 34.7 1.0 N A:GLN834 4.7 8.3 1.0 HG22 A:THR830 4.7 18.6 1.0 CB A:GLU1051 4.7 9.2 1.0 HB3 A:ALA832 4.8 15.1 1.0 HD12 A:LEU901 4.8 13.5 1.0 HG2 A:GLN834 4.9 10.2 1.0 O A:HOH1385 4.9 33.1 1.0 C A:THR833 4.9 9.6 1.0 CD1 A:LEU901 4.9 11.3 1.0 HB3 A:GLU1051 5.0 11.0 1.0 CD A:GLN834 5.0 8.1 1.0 HB2 A:GLU1051 5.0 11.0 1.0 C A:LEU829 5.0 10.1 1.0

Sodium binding site 3 out of 4 in the Structure of T. Gondii PLP1 Beta-Rich Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of T. Gondii PLP1 Beta-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1201 b:14.4 occ:1.00 O B:HOH1505 2.3 18.3 1.0 O B:ASP894 2.3 9.9 1.0 OE2 B:GLU895 2.4 12.3 1.0 O B:GLU892 2.4 13.4 1.0 O B:HOH1442 2.5 15.2 1.0 HG2 B:GLU895 3.1 12.1 1.0 HH21 B:ARG1043 3.2 18.7 1.0 HB3 B:GLN1040 3.2 11.7 1.0 HA B:GLU892 3.3 18.4 1.0 C B:GLU892 3.3 12.8 1.0 CD B:GLU895 3.4 10.8 1.0 C B:ASP894 3.5 8.8 1.0 HA B:PRO840 3.5 12.7 1.0 HG3 B:PRO840 3.7 19.4 1.0 CG B:GLU895 3.8 10.1 1.0 HB3 B:PRO840 3.8 16.8 1.0 HA B:GLU895 3.8 10.0 1.0 CA B:GLU892 3.8 15.3 1.0 HB2 B:GLN1040 3.8 11.7 1.0 NH2 B:ARG1043 3.9 15.6 1.0 HH22 B:ARG1043 3.9 18.7 1.0 CB B:GLN1040 4.0 9.8 1.0 O B:SER891 4.0 14.5 1.0 H B:ASP894 4.1 11.3 1.0 N B:ASP894 4.1 9.4 1.0 HD2 B:PRO841 4.3 12.2 1.0 HD3 B:PRO841 4.3 12.2 1.0 CA B:PRO840 4.3 10.6 1.0 HB2 B:ASP894 4.3 12.2 1.0 CB B:PRO840 4.4 14.0 1.0 CA B:ASP894 4.4 9.3 1.0 N B:THR893 4.4 11.3 1.0 N B:GLU895 4.4 8.8 1.0 O B:HOH1575 4.4 37.9 1.0 HG3 B:GLU895 4.4 12.1 1.0 CA B:GLU895 4.4 8.3 1.0 CG B:PRO840 4.5 16.2 1.0 HB3 B:GLU892 4.5 23.2 1.0 OE1 B:GLU895 4.5 10.6 1.0 HA B:GLN1040 4.5 10.2 1.0 C B:THR893 4.5 9.1 1.0 HA B:THR893 4.6 11.9 1.0 CB B:GLU895 4.7 9.4 1.0 CD B:PRO841 4.7 10.2 1.0 CA B:THR893 4.8 9.9 1.0 CB B:GLU892 4.8 19.4 1.0 CA B:GLN1040 4.8 8.5 1.0 N B:GLU892 4.9 16.0 1.0 CB B:ASP894 4.9 10.2 1.0 HE B:ARG1043 4.9 14.3 1.0 N B:PRO840 4.9 9.6 1.0 C B:SER891 4.9 15.1 1.0 HG3 B:GLN1040 4.9 13.1 1.0 O B:HOH1504 5.0 41.0 1.0

Sodium binding site 4 out of 4 in the Structure of T. Gondii PLP1 Beta-Rich Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of T. Gondii PLP1 Beta-Rich Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1202 b:9.0 occ:1.00 O B:ALA832 2.2 9.8 1.0 O B:THR830 2.3 9.7 1.0 OE2 B:GLU1051 2.3 9.2 1.0 O B:HOH1422 2.4 8.7 1.0 O B:HOH1509 2.5 15.7 1.0 HG2 B:GLU1051 2.9 10.9 1.0 CD B:GLU1051 3.2 8.5 1.0 C B:THR830 3.3 9.5 1.0 CG B:GLU1051 3.4 9.1 1.0 C B:ALA832 3.4 9.3 1.0 HG3 B:GLN834 3.4 9.8 1.0 HG3 B:GLU1051 3.5 10.9 1.0 HZ3 A:TRP1069 3.6 11.2 1.0 HA B:THR833 3.7 11.5 1.0 O B:HOH1394 3.7 11.3 1.0 HA B:THR830 3.7 10.8 1.0 HE21 B:GLN834 3.7 10.6 1.0 C B:GLN831 3.9 10.5 1.0 N B:ALA832 4.0 9.2 1.0 H B:GLN834 4.1 10.4 1.0 O B:LEU829 4.1 9.4 1.0 O B:GLN831 4.1 11.8 1.0 CA B:THR830 4.1 9.0 1.0 HD11 B:LEU901 4.2 12.3 1.0 N B:GLN831 4.3 9.9 1.0 H B:ALA832 4.3 11.1 1.0 N B:THR833 4.3 9.4 1.0 CA B:ALA832 4.3 9.6 1.0 OE1 B:GLU1051 4.4 9.6 1.0 CA B:THR833 4.4 9.6 1.0 HA B:GLN831 4.4 13.6 1.0 CG B:GLN834 4.4 8.1 1.0 HH2 A:TRP1069 4.4 10.1 1.0 NE2 B:GLN834 4.4 8.8 1.0 CZ3 A:TRP1069 4.5 9.3 1.0 CA B:GLN831 4.5 11.3 1.0 O B:VAL1028 4.5 7.6 1.0 N B:GLN834 4.6 8.7 1.0 HG23 B:THR830 4.6 14.0 1.0 HG22 B:THR830 4.6 14.0 1.0 HD12 B:LEU901 4.7 12.3 1.0 HG2 B:GLN834 4.8 9.8 1.0 CB B:GLU1051 4.8 8.0 1.0 C B:THR833 4.8 9.3 1.0 HB3 B:ALA832 4.8 12.3 1.0 CD1 B:LEU901 4.9 10.3 1.0 CH2 A:TRP1069 4.9 8.4 1.0 CD B:GLN834 4.9 8.4 1.0 C B:LEU829 5.0 8.4 1.0 CG2 B:THR830 5.0 11.7 1.0 HE22 B:GLN834 5.0 10.6 1.0

A.J.Guerra, O.Zhang, C.M.E.Bahr, M.H.Huynh, J.Delproposto, W.C.Brown, Z.Wawrzak, N.M.Koropatkin, V.B.Carruthers. Structural Basis of Toxoplasma Gondii Perforin-Like Protein 1 Membrane Interaction and Activity During Egress. Plos Pathog. V. 14 07476 2018.
ISSN: ESSN 1553-7374
PubMed: 30513119
DOI: 10.1371/JOURNAL.PPAT.1007476