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Sodium in PDB 6tx7: Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone

Enzymatic activity of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone

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

Protein crystallography data

The structure of Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone, PDB code: 6tx7 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) 39.28 / 1.13
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.411, 54.482, 56.690, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 15.2

Other elements in 6tx7:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone (pdb code 6tx7). 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-Piperidone, PDB code: 6tx7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6tx7

Go back to Sodium Binding Sites List in 6tx7
Sodium binding site 1 out of 2 in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone


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-Piperidone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.5
occ:1.00
HG21 A:THR17 2.7 13.9 1.0
O A:HOH329 2.8 34.1 1.0
HZ3 A:LYS38 3.5 20.0 1.0
CG2 A:THR17 3.7 11.6 1.0
HZ2 A:LYS38 3.9 20.0 1.0
HG22 A:THR17 4.0 13.9 1.0
NZ A:LYS38 4.0 16.7 1.0
HZ1 A:LYS38 4.0 20.0 1.0
HB A:THR17 4.0 12.4 1.0
OG1 A:THR17 4.1 12.7 1.0
CB A:THR17 4.2 10.4 1.0
HG23 A:THR17 4.3 13.9 1.0
HG1 A:THR17 4.6 15.2 1.0
HA A:ALA14 4.8 15.1 1.0
O A:HOH362 5.0 13.0 1.0

Sodium binding site 2 out of 2 in 6tx7

Go back to Sodium Binding Sites List in 6tx7
Sodium binding site 2 out of 2 in the Crystal Structure of Human FKBP51 FK1 Domain A19T Mutant in Complex with 2-Piperidone


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-Piperidone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:26.6
occ:1.00
HZ2 A:LYS98 2.6 29.2 0.3
O A:HOH434 2.7 26.8 0.8
OE1 A:GLU101 2.7 11.7 1.0
HZ3 A:LYS98 2.7 33.2 0.7
HZ1 A:LYS98 2.7 29.2 0.3
O A:THR96 2.7 11.8 1.0
HD2 A:LYS98 2.8 22.8 0.3
HZ1 A:LYS35 3.0 13.2 1.0
NZ A:LYS98 3.0 24.3 0.3
HD3 A:LYS98 3.0 22.8 0.3
HZ1 A:LYS98 3.0 33.2 0.7
HA A:MET97 3.2 11.3 1.0
HZ3 A:LYS35 3.2 13.2 1.0
NZ A:LYS98 3.3 27.7 0.7
CD A:LYS98 3.3 19.0 0.3
HG3 A:LYS98 3.3 23.8 0.7
NZ A:LYS35 3.4 11.0 1.0
CD A:GLU101 3.5 10.7 1.0
OE2 A:GLU101 3.6 11.8 1.0
HZ2 A:LYS35 3.7 13.2 1.0
H A:LYS98 3.7 13.6 0.3
H A:LYS98 3.7 13.1 0.7
HZ2 A:LYS98 3.7 33.2 0.7
CE A:LYS98 3.7 21.9 0.3
O A:HOH364 3.8 20.9 1.0
HZ3 A:LYS98 3.8 29.2 0.3
C A:THR96 3.8 10.5 1.0
O A:HOH328 3.9 17.4 1.0
CA A:MET97 4.0 9.4 1.0
O A:HOH363 4.0 21.5 1.0
HG21 A:VAL37 4.1 16.6 1.0
O A:HOH448 4.2 26.6 1.0
HG22 A:VAL37 4.2 16.6 1.0
N A:LYS98 4.2 11.3 0.3
N A:LYS98 4.2 10.9 0.7
HD2 A:LYS98 4.2 27.8 0.7
CG A:LYS98 4.2 19.8 0.7
HE2 A:LYS98 4.3 26.2 0.3
HB A:THR96 4.4 12.6 1.0
N A:MET97 4.4 9.6 1.0
HE3 A:LYS98 4.4 26.2 0.3
C A:MET97 4.4 10.2 1.0
CE A:LYS98 4.4 26.7 0.7
CD A:LYS98 4.5 23.1 0.7
HB2 A:LYS98 4.5 18.7 0.3
CG2 A:VAL37 4.6 13.9 1.0
CG A:LYS98 4.7 17.9 0.3
HG22 A:THR46 4.8 17.1 1.0
HB2 A:LYS98 4.8 18.7 0.7
CE A:LYS35 4.8 10.7 1.0
HG2 A:LYS98 4.8 23.8 0.7
CG A:GLU101 4.9 10.9 1.0
HE2 A:LYS35 4.9 12.8 1.0
HE3 A:LYS98 4.9 32.1 0.7
O A:HOH450 4.9 40.1 1.0
OG1 A:THR96 4.9 10.4 1.0
HG2 A:MET97 4.9 11.5 1.0
CB A:THR96 4.9 10.5 1.0
CA A:THR96 5.0 9.8 1.0
CB A:LYS98 5.0 15.6 0.7
CB A:LYS98 5.0 15.6 0.3

Reference:

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
Page generated: Tue Dec 15 14:27:51 2020

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