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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

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