Sodium in PDB 7uda: Structure of the Estg

The structure of Structure of the Estg, PDB code: 7uda was solved by Z.Chen, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 2.47
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	110.321, 110.321, 55.918, 90, 90, 90
R / Rfree (%)	18 / 21.9

The binding sites of Sodium atom in the Structure of the Estg (pdb code 7uda). 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 the Estg, PDB code: 7uda:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Estg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Estg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:62.1 occ:1.00 O A:SER204 2.5 47.4 1.0 O A:LEU206 2.7 41.3 1.0 N A:ARG137 3.1 52.8 1.0 N A:LEU206 3.2 42.5 1.0 C A:SER204 3.3 46.9 1.0 C A:GLY205 3.3 45.5 1.0 C A:LEU206 3.4 44.0 1.0 CA A:LEU136 3.5 49.0 1.0 CA A:GLY205 3.6 46.8 1.0 O A:ASN135 3.7 57.5 1.0 C A:LEU136 3.8 49.9 1.0 N A:GLY205 3.8 43.1 1.0 CD2 A:LEU136 3.9 47.0 1.0 CA A:LEU206 3.9 42.4 1.0 NH2 A:ARG137 3.9 110.8 1.0 O A:GLY205 3.9 47.0 1.0 NE A:ARG137 4.0 96.0 1.0 O A:ARG137 4.0 45.7 1.0 O A:VAL203 4.0 40.8 1.0 CB A:ARG137 4.1 55.6 1.0 CA A:ARG137 4.1 49.0 1.0 N A:PRO207 4.4 48.1 1.0 N A:LEU136 4.4 49.6 1.0 CZ A:ARG137 4.4 98.4 1.0 C A:ASN135 4.4 53.0 1.0 CA A:SER204 4.4 45.4 1.0 CB A:LEU136 4.5 48.0 1.0 C A:ARG137 4.6 44.9 1.0 O A:HOH701 4.7 37.4 1.0 CA A:PRO207 4.7 48.9 1.0 CG A:LEU136 4.7 45.4 1.0 C A:VAL203 5.0 41.6 1.0 O A:LEU136 5.0 50.6 1.0 CD A:ARG137 5.0 75.2 1.0

Sodium binding site 2 out of 4 in the Structure of the Estg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Estg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:53.9 occ:1.00 OE2 A:GLU102 2.4 55.3 1.0 O A:TRP403 2.8 42.0 1.0 O A:GLY416 3.1 40.2 1.0 CD A:GLU102 3.2 48.0 1.0 OE1 A:GLU102 3.3 44.1 1.0 SD A:MET417 3.4 45.1 1.0 C A:TRP403 3.5 40.4 1.0 CG1 A:VAL415 3.5 46.1 1.0 N A:TRP403 3.7 38.9 1.0 N A:GLY416 3.8 39.3 1.0 CE A:MET417 3.8 46.6 1.0 C A:GLY416 3.9 39.9 1.0 CB A:THR402 4.0 37.9 1.0 CG A:MET417 4.1 46.6 1.0 CB A:PHE404 4.2 35.3 1.0 CA A:TRP403 4.2 40.4 1.0 CA A:VAL415 4.3 42.9 1.0 N A:PHE404 4.3 33.5 1.0 CB A:VAL415 4.4 42.8 1.0 C A:VAL415 4.4 40.9 1.0 C A:THR402 4.4 42.2 1.0 CA A:GLY416 4.4 39.6 1.0 CA A:THR402 4.6 39.2 1.0 CD2 A:PHE310 4.6 38.3 1.0 OG1 A:THR402 4.7 36.4 1.0 CA A:PHE404 4.7 35.2 1.0 CG A:GLU102 4.7 44.9 1.0 N A:MET417 4.7 39.1 1.0 CG2 A:THR402 4.8 38.1 1.0 CG A:PHE310 4.8 36.5 1.0 CG2 A:VAL415 4.9 42.0 1.0 CA A:MET417 5.0 42.7 1.0

Sodium binding site 3 out of 4 in the Structure of the Estg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Estg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:61.6 occ:1.00 OD1 A:ASP407 2.7 35.8 1.0 O A:PRO391 2.7 50.8 1.0 N A:THR393 3.1 36.8 1.0 N A:ALA409 3.2 44.1 1.0 OG1 A:THR393 3.2 40.0 1.0 CD A:PRO408 3.3 43.9 1.0 N A:PRO408 3.3 45.0 1.0 C A:GLY392 3.3 39.4 1.0 O A:GLY390 3.4 56.5 1.0 C A:PRO391 3.5 46.5 1.0 C A:ASP407 3.5 41.0 1.0 CB A:ALA409 3.6 41.0 1.0 CA A:THR393 3.6 39.8 1.0 CA A:ASP407 3.6 37.8 1.0 CG A:ASP407 3.7 34.2 1.0 O A:GLY392 3.7 44.1 1.0 C A:GLY390 3.8 52.9 1.0 CA A:GLY392 3.8 41.0 1.0 CA A:ALA409 3.9 42.9 1.0 N A:GLY392 4.0 45.1 1.0 CA A:PRO408 4.0 46.9 1.0 CB A:THR393 4.0 44.5 1.0 C A:PRO408 4.1 47.5 1.0 CG A:PRO408 4.1 41.7 1.0 CA A:GLY390 4.2 46.5 1.0 CB A:ASP407 4.2 36.6 1.0 CB A:PRO408 4.2 42.0 1.0 O A:ASP407 4.3 45.7 1.0 N A:PRO391 4.4 57.6 1.0 OD2 A:ASP407 4.6 37.4 1.0 CA A:PRO391 4.6 50.6 1.0 N A:GLY390 4.7 42.0 1.0 N A:ASN410 4.8 43.8 1.0 O A:ILE406 4.9 34.2 1.0 N A:ASP407 4.9 35.7 1.0 C A:ALA409 4.9 43.3 1.0

Sodium binding site 4 out of 4 in the Structure of the Estg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Estg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:59.7 occ:1.00 OE1 A:GLN315 2.6 35.9 1.0 N A:GLY73 3.0 51.3 1.0 CD1 A:LEU318 3.4 37.1 1.0 CD A:GLN315 3.5 39.9 1.0 O A:ASN411 3.5 44.5 1.0 N A:HIS72 3.6 52.9 1.0 CA A:GLY73 3.6 52.5 1.0 C A:ARG71 3.6 50.4 1.0 CA A:ARG71 3.7 48.1 1.0 N A:ARG71 3.7 48.3 1.0 NE2 A:GLN315 3.7 39.2 1.0 C A:ALA70 3.7 42.3 1.0 O A:ALA70 3.8 45.9 1.0 CB A:ALA70 4.0 42.5 1.0 CE2 A:PHE413 4.1 46.2 1.0 C A:HIS72 4.1 56.1 1.0 CD2 A:PHE413 4.1 41.8 1.0 O A:ARG71 4.2 53.3 1.0 C A:GLY73 4.3 49.1 1.0 CA A:HIS72 4.4 56.0 1.0 N A:ARG74 4.4 54.4 1.0 CA A:ALA70 4.4 44.4 1.0 CA A:LEU412 4.5 46.7 1.0 C A:ASN411 4.5 45.9 1.0 CG A:LEU318 4.8 38.6 1.0 CG A:GLN315 4.9 41.5 1.0 N A:PHE413 4.9 40.6 1.0 N A:LEU412 5.0 44.7 1.0 C A:LEU412 5.0 46.0 1.0

A.K.Daitch, B.C.Orsburn, Z.Chen, L.Alvarez, C.D.Eberhard, K.Sundararajan, R.Zeinert, D.F.Kreitler, J.Jakoncic, P.Chien, F.Cava, S.B.Gabelli, E.D.Goley. Estg Is A Novel Esterase Required For Cell Envelope Integrity in Caulobacter. Curr.Biol. 2022.
ISSN: ISSN 0960-9822
PubMed: 36516849
DOI: 10.1016/J.CUB.2022.11.037