Sodium in PDB 6tx6: Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with Nicotinamide

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

The structure of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with Nicotinamide, PDB code: 6tx6 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 / 0.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.407, 54.372, 56.738, 90.00, 90.00, 90.00
R / Rfree (%)	11.1 / 12.1

The structure of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with Nicotinamide 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 Nicotinamide (pdb code 6tx6). 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 Nicotinamide, PDB code: 6tx6:
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 Nicotinamide


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 Nicotinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:13.9 occ:1.00 HG21 A:THR17 2.7 9.6 1.0 O A:HOH369 2.8 18.3 1.0 HZ3 A:LYS38 3.5 18.5 1.0 CG2 A:THR17 3.6 8.0 1.0 HZ1 A:LYS38 3.7 18.5 1.0 HG22 A:THR17 4.0 9.6 1.0 HB A:THR17 4.0 8.9 1.0 NZ A:LYS38 4.0 15.4 1.0 OG1 A:THR17 4.1 8.3 1.0 CB A:THR17 4.2 7.4 1.0 HZ2 A:LYS38 4.2 18.5 1.0 HG23 A:THR17 4.3 9.6 1.0 HG1 A:THR17 4.4 9.9 1.0 HA A:ALA14 4.7 10.4 1.0 O A:HOH393 4.9 8.8 1.0

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


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 Nicotinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:21.4 occ:1.00 HZ3 A:LYS98 2.5 27.8 0.7 O A:HOH458 2.7 19.4 0.8 OE1 A:GLU101 2.7 7.6 1.0 HZ2 A:LYS98 2.7 24.6 0.3 O A:THR96 2.7 8.0 1.0 HD2 A:LYS98 2.8 19.7 0.3 HZ3 A:LYS98 2.8 24.6 0.3 HD3 A:LYS98 3.0 19.7 0.3 HZ1 A:LYS35 3.0 8.4 1.0 HZ1 A:LYS98 3.1 27.8 0.7 NZ A:LYS98 3.1 20.5 0.3 HA A:MET97 3.1 7.8 1.0 NZ A:LYS98 3.2 23.1 0.7 HG3 A:LYS98 3.2 17.0 0.7 CD A:LYS98 3.2 16.4 0.3 HZ3 A:LYS35 3.3 8.4 1.0 CD A:GLU101 3.5 7.2 1.0 NZ A:LYS35 3.5 7.0 1.0 HZ2 A:LYS98 3.6 27.8 0.7 OE2 A:GLU101 3.6 7.6 1.0 H A:LYS98 3.7 8.8 0.7 H A:LYS98 3.7 9.7 0.3 HZ2 A:LYS35 3.7 8.4 1.0 CE A:LYS98 3.8 18.9 0.3 O A:HOH377 3.8 16.1 1.0 C A:THR96 3.8 7.1 1.0 HZ1 A:LYS98 3.9 24.6 0.3 O A:HOH359 4.0 11.9 1.0 CA A:MET97 4.0 6.5 1.0 HG21 A:VAL37 4.1 9.4 1.0 O A:HOH399 4.1 20.6 1.0 CG A:LYS98 4.1 14.2 0.7 N A:LYS98 4.1 7.4 0.7 N A:LYS98 4.1 8.1 0.3 HD2 A:LYS98 4.2 21.2 0.7 HG22 A:VAL37 4.2 9.4 1.0 O A:HOH486 4.3 13.7 0.8 C A:MET97 4.4 6.8 1.0 HE3 A:LYS98 4.4 22.7 0.3 CE A:LYS98 4.4 21.1 0.7 N A:MET97 4.4 6.5 1.0 HB2 A:LYS98 4.4 14.0 0.3 HE2 A:LYS98 4.4 22.7 0.3 HB A:THR96 4.5 8.3 1.0 CD A:LYS98 4.5 17.7 0.7 CG2 A:VAL37 4.6 7.8 1.0 CG A:LYS98 4.6 14.2 0.3 HB2 A:LYS98 4.7 11.3 0.7 HG22 A:THR46 4.7 11.4 1.0 HE3 A:LYS98 4.7 25.3 0.7 HG2 A:LYS98 4.7 17.0 0.7 O A:HOH495 4.9 20.8 0.6 CE A:LYS35 4.9 7.0 1.0 CG A:GLU101 4.9 6.9 1.0 CB A:LYS98 4.9 9.4 0.7 CB A:LYS98 4.9 11.7 0.3 HG2 A:MET97 4.9 8.0 1.0 HE2 A:LYS35 4.9 8.4 1.0 OG1 A:THR96 5.0 6.9 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