Atomistry » Sodium » PDB 5fje-5g3f » 5fnk
Atomistry »
  Sodium »
    PDB 5fje-5g3f »
      5fnk »

Sodium in PDB 5fnk: Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination

Enzymatic activity of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination

All present enzymatic activity of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination:
4.2.1.1;

Protein crystallography data

The structure of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination, PDB code: 5fnk was solved by L.A.Woods, O.Dolezal, B.Ren, J.H.Ryan, T.S.Peat, S.A.Poulsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.88 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.350, 41.516, 72.157, 90.00, 104.42, 90.00
R / Rfree (%) 14.7 / 19.5

Other elements in 5fnk:

The structure of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination (pdb code 5fnk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination, PDB code: 5fnk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5fnk

Go back to Sodium Binding Sites List in 5fnk
Sodium binding site 1 out of 2 in the Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1265

b:37.1
occ:1.00
 OD1 A:ASP34 2.1 14.4 0.4
O A:HOH2065 2.4 31.3 1.0
O A:HOH2062 2.5 18.5 1.0
O A:HOH2068 2.7 16.6 1.0
OD1 A:ASP110 2.9 13.2 1.0
OD2 A:ASP34 3.2 16.5 0.6
CG A:ASP34 3.3 14.5 0.4
CG A:ASP34 3.4 13.3 0.6
CG A:ASP110 3.5 10.4 1.0
OD1 A:ASP34 3.6 11.8 0.6
CB A:ASP110 3.7 10.1 1.0
CA A:ASP110 3.7 8.4 1.0
ND1 A:HIS36 3.9 21.6 1.0
O A:HOH2066 3.9 16.3 1.0
O A:HOH2160 4.0 31.4 1.0
OD2 A:ASP34 4.1 13.2 0.4
CB A:ASP34 4.3 11.4 0.6
CB A:ASP34 4.3 11.9 0.4
CE1 A:HIS36 4.4 23.2 1.0
CA A:ASP34 4.4 11.1 0.4
CA A:ASP34 4.4 10.6 0.6
C A:ASP110 4.4 9.0 1.0
OD2 A:ASP110 4.4 16.4 1.0
O A:ASP110 4.7 10.5 1.0
N A:ASP110 4.8 8.1 1.0
N A:THR35 4.9 11.2 1.0

Sodium binding site 2 out of 2 in 5fnk

Go back to Sodium Binding Sites List in 5fnk
Sodium binding site 2 out of 2 in the Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1266

b:23.7
occ:1.00
 O A:HOH2126 2.3 29.1 1.0
O A:LEU90 2.7 9.9 1.0
O A:HOH2106 2.9 12.2 1.0
O A:ASP71 3.1 15.8 1.0
O A:ALA77 3.5 15.7 1.0
N A:ALA77 3.7 17.7 1.0
C A:LEU90 3.7 8.1 1.0
CB A:ALA77 3.8 14.6 1.0
N A:LEU90 3.8 8.5 1.0
CG A:ARG89 3.9 22.2 1.0
CA A:ASP72 3.9 15.0 1.0
CB A:LEU90 4.0 9.6 1.0
C A:ASP71 4.0 13.3 1.0
CA A:LEU90 4.1 8.9 1.0
CA A:ALA77 4.1 15.2 1.0
CB A:ASP72 4.2 16.6 1.0
CB A:PHE70 4.3 11.0 1.0
C A:ALA77 4.3 13.6 1.0
N A:ASP72 4.3 15.1 1.0
CB A:LYS76 4.3 23.0 1.0
O A:GLN74 4.5 21.8 1.0
C A:LYS76 4.6 19.2 1.0
C A:ARG89 4.6 9.1 1.0
N A:LYS76 4.7 22.4 1.0
CA A:LYS76 4.8 19.4 1.0
CD A:ARG89 4.8 19.0 1.0
CB A:ARG89 4.9 14.1 1.0
CG A:LEU90 4.9 9.1 1.0
N A:ILE91 4.9 7.4 1.0
CA A:ARG89 5.0 9.9 1.0

Reference:

L.Woods, O.Dolezal, B.Ren, J.H.Ryan, T.S.Peat, S.Poulsen. Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly As A Fragment Screening Combination. J.Med.Chem. V. 59 2192 2016.
ISSN: ISSN 0022-2623
PubMed: 26882437
DOI: 10.1021/ACS.JMEDCHEM.5B01940
Page generated: Mon Oct 7 21:03:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy