Sodium in PDB 7jxf: E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog

All present enzymatic activity of E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog:
2.1.1.45;

The structure of E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog, PDB code: 7jxf was solved by J.Finer-Moore, S.A.Kholodar, R.M.Stroud, A.Kohen, V.Moliner, K.Swiderek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.64 / 1.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	125.442, 125.442, 67.049, 90, 90, 120
R / Rfree (%)	15.1 / 17.5

The binding sites of Sodium atom in the E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog (pdb code 7jxf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog, PDB code: 7jxf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:29.2 occ:0.87 O A:HIS108 2.3 26.9 1.0 O A:HOH617 2.4 50.1 1.0 O A:HOH522 2.4 26.2 1.0 O A:HOH571 2.5 30.5 1.0 H A:ASP110 3.3 25.1 0.5 H A:ASP110 3.3 25.1 0.5 C A:HIS108 3.4 26.9 1.0 HA A:ILE109 3.4 31.3 0.5 HA A:ILE109 3.5 31.5 0.5 HB2 A:ASP110 3.7 25.7 1.0 N A:ASP110 3.8 20.9 1.0 O A:HOH560 3.8 32.0 1.0 HB2 A:HIS108 3.9 28.9 1.0 O A:HOH600 3.9 54.1 1.0 CA A:ILE109 4.0 26.1 0.5 N A:ILE109 4.1 23.8 0.5 N A:ILE109 4.1 23.5 0.5 CA A:ILE109 4.1 26.2 0.5 H A:HIS108 4.2 30.7 1.0 HB3 A:ASP110 4.2 25.7 1.0 C A:ILE109 4.2 22.3 0.5 C A:ILE109 4.2 22.0 0.5 CB A:ASP110 4.3 21.4 1.0 CA A:HIS108 4.4 24.4 1.0 CB A:HIS108 4.4 24.0 1.0 HB3 A:HIS108 4.4 28.9 1.0 O A:HOH653 4.5 46.6 1.0 CA A:ASP110 4.7 21.9 1.0 HD13 A:ILE109 4.7 32.0 0.5 N A:HIS108 4.7 25.6 1.0 H A:ILE109 4.8 28.3 0.5 H A:ILE109 4.8 28.6 0.5 HA A:ALA100 4.9 25.0 1.0

Sodium binding site 2 out of 3 in the E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:29.1 occ:0.57 O A:HOH549 2.3 46.4 1.0 O A:PHE240 2.4 26.2 1.0 OE1 A:GLN64 2.5 33.6 1.0 O A:HOH596 2.6 39.0 1.0 O A:HOH538 2.6 35.0 1.0 HA A:ASP241 3.2 27.9 1.0 CD A:GLN64 3.3 30.0 1.0 C A:PHE240 3.6 27.3 1.0 HE22 A:GLN64 3.7 48.6 1.0 NE2 A:GLN64 3.9 40.5 1.0 O A:HOH498 3.9 28.0 1.0 O A:HOH637 3.9 52.5 1.0 CA A:ASP241 4.0 23.2 1.0 O A:HOH620 4.1 48.1 1.0 N A:ASP241 4.3 22.7 1.0 O A:TYR242 4.4 26.4 1.0 HG2 A:GLN64 4.4 31.2 1.0 OD1 A:ASP241 4.4 42.0 1.0 HB3 A:PHE240 4.4 30.0 1.0 CG A:GLN64 4.4 26.0 1.0 O A:HOH611 4.6 48.0 1.0 C A:ASP241 4.6 23.2 1.0 HE21 A:GLN64 4.6 48.6 1.0 HG3 A:GLN64 4.6 31.2 1.0 CA A:PHE240 4.7 24.4 1.0 H A:TYR242 4.8 27.8 1.0 O A:HOH508 4.8 24.3 1.0 HA A:PHE240 4.8 29.3 1.0 N A:TYR242 4.9 23.1 1.0 CB A:PHE240 5.0 25.0 1.0

Sodium binding site 3 out of 3 in the E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli Tsase Complex with A Bi-Substrate Reaction Intermediate Diastereomer Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:54.6 occ:1.00 HE2 B:LYS10 2.4 62.5 1.0 O B:HOH530 2.5 47.6 1.0 O A:HOH514 2.6 48.6 1.0 O B:GLY31 2.7 27.2 1.0 ND1 B:HIS32 2.7 28.9 1.0 HD12 B:ILE29 2.9 38.1 1.0 HA B:HIS32 3.1 26.8 1.0 HB2 B:HIS32 3.2 29.1 1.0 CE B:LYS10 3.2 52.0 1.0 HE3 B:LYS10 3.3 62.5 1.0 HD3 B:LYS10 3.4 41.2 1.0 HH21 A:ARG35 3.4 32.4 0.5 CG B:HIS32 3.6 23.8 1.0 O A:HOH625 3.6 56.2 1.0 CB B:HIS32 3.6 24.2 1.0 CA B:HIS32 3.7 22.3 1.0 CD1 B:ILE29 3.8 31.8 1.0 CE1 B:HIS32 3.8 33.0 1.0 C B:GLY31 3.8 25.4 1.0 HD11 B:ILE29 3.8 38.1 1.0 CD B:LYS10 3.9 34.3 1.0 HH22 A:ARG35 3.9 32.4 0.5 NH2 A:ARG35 3.9 27.0 0.5 HE1 B:HIS32 3.9 39.7 1.0 O A:HOH473 4.1 30.9 1.0 O B:HOH515 4.1 38.0 1.0 HH11 A:ARG35 4.2 25.1 0.6 N B:HIS32 4.2 23.7 1.0 HH12 A:ARG35 4.3 25.1 0.6 HD13 B:ILE29 4.3 38.1 1.0 HD2 B:LYS10 4.3 41.2 1.0 NZ B:LYS10 4.4 70.5 1.0 HZ2 B:LYS10 4.4 84.6 1.0 NH1 A:ARG35 4.4 20.9 0.6 HB3 B:HIS32 4.6 29.1 1.0 HZ1 B:LYS10 4.6 84.6 1.0 HG13 B:ILE29 4.7 31.8 1.0 HB B:ILE29 4.7 28.6 1.0 CG1 B:ILE29 4.8 26.4 1.0 CD2 B:HIS32 4.8 26.3 1.0 NE2 B:HIS32 4.9 29.2 1.0 HD2 A:ARG35 4.9 32.0 0.6 H B:GLN33 4.9 28.4 1.0 OE1 A:GLN33 5.0 28.6 1.0

S.A.Kholodar, J.S.Finer-Moore, K.Swiderek, K.Arafet, V.Moliner, R.M.Stroud, A.Kohen. Caught in Action: X-Ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33829766
DOI: 10.1021/ACS.BIOCHEM.1C00063