Sodium in PDB 6nnr: High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase

All present enzymatic activity of High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase:
2.1.1.45;

The structure of High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase, PDB code: 6nnr was solved by R.M.Stroud, J.Finer-Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.77 / 1.05
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	125.530, 125.530, 66.757, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 13.2

The binding sites of Sodium atom in the High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase (pdb code 6nnr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase, PDB code: 6nnr:

Sodium binding site 1 out of 1 in the High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of Wild-Type E. Coli Thymidylate Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:19.8 occ:0.74 O A:HOH1275 2.3 24.0 1.0 O A:ASN76 2.3 15.5 1.0 O A:HOH1342 2.4 27.9 1.0 O A:HOH1214 2.5 22.6 1.0 O A:HOH1173 2.7 14.1 1.0 HE1 A:HIS51 2.7 16.4 0.6 HA A:VAL77 3.1 11.8 1.0 O A:HOH1420 3.1 21.8 1.0 CE1 A:HIS51 3.2 13.7 0.6 HH11 A:ARG53 3.5 25.3 1.0 C A:ASN76 3.5 12.2 1.0 HG A:SER54 3.8 16.6 1.0 NE2 A:HIS51 3.8 19.0 0.6 H A:THR78 3.8 11.6 1.0 HE2 A:HIS51 3.9 22.8 0.6 HH12 A:ARG53 3.9 25.3 1.0 CA A:VAL77 4.0 9.9 1.0 ND1 A:HIS51 4.0 11.5 0.6 NH1 A:ARG53 4.0 21.1 1.0 OG A:SER54 4.1 13.8 1.0 HB3 A:ASN76 4.1 22.9 1.0 O A:HOH1143 4.1 29.1 1.0 N A:VAL77 4.2 10.7 1.0 HG22 A:VAL77 4.2 14.1 1.0 O A:HOH1250 4.4 31.9 1.0 OE2 A:CB3902 4.4 15.6 1.0 N A:THR78 4.4 9.7 1.0 OG1 A:THR78 4.5 13.3 1.0 HG23 A:THR78 4.5 17.6 1.0 HD3 A:ARG53 4.7 22.2 1.0 CA A:ASN76 4.7 14.9 1.0 CB A:ASN76 4.7 19.0 1.0 HB2 A:ASN76 4.7 22.9 1.0 C A:VAL77 4.7 9.8 1.0 OE1 A:CB3902 4.8 19.6 1.0 HG1 A:THR78 4.8 15.9 1.0 CD2 A:HIS51 4.8 18.8 0.6 CG2 A:VAL77 4.8 11.7 1.0 HG23 A:VAL77 4.9 14.1 1.0 HG13 A:VAL77 4.9 12.3 1.0 CG A:HIS51 4.9 14.4 0.6 HG3 A:ARG53 5.0 21.8 1.0 CB A:VAL77 5.0 10.9 1.0

Z.Wang, P.J.Sapienza, T.Abeysinghe, C.Luzum, A.L.Lee, J.S.Finer-Moore, R.M.Stroud, A.Kohen. MG2+ Binds to the Surface of Thymidylate Synthase and Affects Hydride Transfer at the Interior Active Site. J. Am. Chem. Soc. V. 135 7583 2013.
ISSN: ESSN 1520-5126
PubMed: 23611499
DOI: 10.1021/JA400761X