Sodium in PDB 6tx4: Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone

All present enzymatic activity of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone:
5.2.1.8;

The structure of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone, PDB code: 6tx4 was solved by D.Fiegen, S.W.Draxler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.97 / 1.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.432, 54.387, 56.689, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 13

The structure of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone (pdb code 6tx4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone, PDB code: 6tx4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:15.4 occ:1.00 HG21 A:THR17 2.7 11.3 1.0 O A:HOH377 2.9 15.4 0.8 HG1 A:THR17 3.4 11.8 1.0 HZ3 A:LYS38 3.5 15.7 1.0 CG2 A:THR17 3.7 9.4 1.0 HZ2 A:LYS38 3.9 15.7 1.0 NZ A:LYS38 4.0 13.1 1.0 HZ1 A:LYS38 4.0 15.7 1.0 HG22 A:THR17 4.0 11.3 1.0 HB A:THR17 4.0 10.2 1.0 OG1 A:THR17 4.1 9.8 1.0 CB A:THR17 4.2 8.5 1.0 HG23 A:THR17 4.3 11.3 1.0 HA A:ALA14 4.7 11.9 1.0 O A:HOH382 4.9 10.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Pyridone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:23.1 occ:1.00 HZ2 A:LYS98 2.5 28.6 0.7 O A:HOH455 2.6 19.2 0.7 OE1 A:GLU101 2.7 9.1 1.0 HD2 A:LYS98 2.7 24.5 0.3 O A:THR96 2.7 9.3 1.0 HZ3 A:LYS98 2.8 31.4 0.3 HZ2 A:LYS98 2.9 31.4 0.3 HZ3 A:LYS98 3.0 28.6 0.7 HZ1 A:LYS35 3.0 10.0 1.0 HA A:MET97 3.2 9.3 1.0 NZ A:LYS98 3.2 23.8 0.7 HD3 A:LYS98 3.2 24.5 0.3 NZ A:LYS98 3.2 26.1 0.3 HZ3 A:LYS35 3.2 10.0 1.0 CD A:LYS98 3.3 20.4 0.3 NZ A:LYS35 3.5 8.3 1.0 CD A:GLU101 3.5 8.7 1.0 HG3 A:LYS98 3.5 19.2 0.7 HZ1 A:LYS98 3.6 28.6 0.7 OE2 A:GLU101 3.6 9.2 1.0 HZ2 A:LYS35 3.7 10.0 1.0 H A:LYS98 3.7 10.5 0.7 H A:LYS98 3.7 10.9 0.3 O A:HOH369 3.7 18.3 1.0 C A:THR96 3.8 8.4 1.0 O A:HOH350 3.8 23.0 1.0 CE A:LYS98 3.9 23.7 0.3 O A:HOH341 3.9 13.6 1.0 HD2 A:LYS98 3.9 25.5 0.7 HZ1 A:LYS98 4.0 31.4 0.3 CA A:MET97 4.0 7.8 1.0 HG21 A:VAL37 4.1 12.0 1.0 O A:HOH484 4.2 29.2 1.0 HG22 A:VAL37 4.2 12.0 1.0 N A:LYS98 4.2 8.7 0.7 N A:LYS98 4.2 9.1 0.3 CE A:LYS98 4.3 23.9 0.7 CG A:LYS98 4.3 16.0 0.7 CD A:LYS98 4.4 21.3 0.7 N A:MET97 4.4 7.7 1.0 C A:MET97 4.4 8.0 1.0 HB A:THR96 4.4 10.1 1.0 HE2 A:LYS98 4.4 28.4 0.3 O A:HOH409 4.4 31.1 0.7 HB2 A:LYS98 4.5 16.3 0.3 HE3 A:LYS98 4.5 28.4 0.3 CG2 A:VAL37 4.6 10.0 1.0 CG A:LYS98 4.7 18.0 0.3 HG22 A:THR46 4.7 14.7 1.0 HB2 A:LYS98 4.7 13.0 0.7 HE3 A:LYS98 4.7 28.6 0.7 CE A:LYS35 4.8 8.4 1.0 O A:HOH491 4.9 27.8 0.9 CG A:GLU101 4.9 8.2 1.0 HE2 A:LYS35 4.9 10.1 1.0 OG1 A:THR96 4.9 8.2 1.0 HG2 A:MET97 4.9 9.5 1.0 HG3 A:LYS98 5.0 21.6 0.3 CB A:LYS98 5.0 10.8 0.7 CB A:THR96 5.0 8.4 1.0 CB A:LYS98 5.0 13.6 0.3 CA A:THR96 5.0 8.0 1.0

S.W.Draxler, M.Bauer, C.Eickmeier, S.Nadal, H.Nar, D.Rangel, D.Seeliger, M.Zeeb, D.Fiegen. A Hybrid Screening Approach For Very Small Fragments - X-Ray and Computational Screening on FKBP51. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32420743
DOI: 10.1021/ACS.JMEDCHEM.0C00120