Sodium in PDB 4jdo: Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion

The structure of Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion, PDB code: 4jdo was solved by A.Galaleldeen, A.B.Taylor, D.Chen, S.P.Holloway, G.Zhong, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.46 / 2.30
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	146.240, 146.240, 160.996, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 24.2

The binding sites of Sodium atom in the Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion (pdb code 4jdo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion, PDB code: 4jdo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.0 occ:1.00 OH A:TYR197 2.4 25.8 1.0 OH C:TYR197 2.5 26.6 1.0 OH B:TYR197 2.5 25.5 1.0 O A:HOH412 2.5 28.7 1.0 O B:HOH308 2.7 26.0 1.0 O C:HOH328 2.7 26.7 1.0 O B:HOH344 3.4 33.4 1.0 CZ C:TYR197 3.5 26.1 1.0 CZ A:TYR197 3.5 25.3 1.0 CZ B:TYR197 3.5 25.0 1.0 OE2 B:GLU175 3.8 31.6 1.0 OE1 C:GLU175 3.8 31.5 1.0 OE1 A:GLU175 4.0 37.4 1.0 OE2 A:GLU175 4.0 33.1 1.0 CE2 C:TYR197 4.1 25.1 1.0 CE2 B:TYR197 4.1 23.3 1.0 CE2 A:TYR197 4.2 26.7 1.0 OE1 B:GLU175 4.3 33.1 1.0 CD B:GLU175 4.5 32.5 1.0 CE1 A:TYR197 4.5 22.4 1.0 CD A:GLU175 4.5 30.7 1.0 CE1 C:TYR197 4.5 21.2 1.0 CE1 B:TYR197 4.5 22.1 1.0 CB A:SER199 4.5 24.7 1.0 CB B:SER199 4.5 23.5 1.0 CB C:SER199 4.6 24.4 1.0 CD C:GLU175 4.7 33.1 1.0 OE2 C:GLU175 4.7 34.5 1.0

Sodium binding site 2 out of 3 in the Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:32.7 occ:1.00 OH D:TYR197 2.3 34.3 1.0 O D:HOH485 2.4 34.2 1.0 OH E:TYR197 2.5 28.3 1.0 OH F:TYR197 2.7 35.0 1.0 CZ D:TYR197 3.4 29.0 1.0 OE2 D:GLU175 3.6 40.8 1.0 CZ E:TYR197 3.6 28.1 1.0 CZ F:TYR197 3.7 30.1 1.0 OE2 E:GLU175 3.8 37.7 1.0 OE1 D:GLU175 3.9 38.7 1.0 CE2 E:TYR197 4.0 27.1 1.0 CE2 D:TYR197 4.0 28.8 1.0 OE1 E:GLU175 4.1 38.4 1.0 CD D:GLU175 4.1 36.3 1.0 CE2 F:TYR197 4.2 29.2 1.0 OE1 F:GLU175 4.2 35.4 1.0 CB E:SER199 4.3 26.1 1.0 CE1 D:TYR197 4.3 26.6 1.0 CD E:GLU175 4.4 36.5 1.0 OE2 F:GLU175 4.4 35.7 1.0 CB D:SER199 4.4 29.3 1.0 CE1 F:TYR197 4.6 29.8 1.0 CE1 E:TYR197 4.7 25.5 1.0 CD F:GLU175 4.8 36.0 1.0 CB F:SER199 4.8 28.0 1.0 CA E:SER199 4.9 26.2 1.0

Sodium binding site 3 out of 3 in the Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Secreted Chlamydial Protein PGP3, Coiled-Coil Deletion within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:29.3 occ:1.00 OH H:TYR197 2.4 25.4 1.0 OH G:TYR197 2.5 24.3 1.0 O H:HOH343 2.5 29.0 1.0 OH I:TYR197 2.5 24.3 1.0 O I:HOH361 2.7 28.8 1.0 CZ H:TYR197 3.3 26.2 1.0 CZ I:TYR197 3.4 23.8 1.0 CZ G:TYR197 3.4 22.4 1.0 CE2 I:TYR197 3.7 22.3 1.0 CE2 H:TYR197 3.8 23.0 1.0 CE2 G:TYR197 3.8 22.8 1.0 OE1 I:GLU175 3.9 33.8 1.0 OE2 H:GLU175 4.0 33.0 1.0 OE1 G:GLU175 4.1 35.5 1.0 OE1 H:GLU175 4.2 34.5 1.0 CE1 H:TYR197 4.3 24.1 1.0 CB I:SER199 4.4 21.0 1.0 CE1 G:TYR197 4.4 22.3 1.0 CB G:SER199 4.4 23.3 1.0 CB H:SER199 4.5 23.7 1.0 OE2 I:GLU175 4.5 34.0 1.0 CE1 I:TYR197 4.5 23.2 1.0 CD H:GLU175 4.6 31.5 1.0 CD I:GLU175 4.6 32.1 1.0 OE2 G:GLU175 4.7 33.2 1.0 CD G:GLU175 4.8 34.1 1.0

A.Galaleldeen, A.B.Taylor, D.Chen, J.P.Schuermann, S.P.Holloway, S.Hou, S.Gong, G.Zhong, P.J.Hart. Structure of the Chlamydia Trachomatis Immunodominant Antigen PGP3. J.Biol.Chem. V. 288 22068 2013.
ISSN: ISSN 0021-9258
PubMed: 23703617
DOI: 10.1074/JBC.M113.475012