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Sodium in PDB 6rnb: Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time

Enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time

All present enzymatic activity of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time:
3.2.1.17;

Protein crystallography data

The structure of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time, PDB code: 6rnb was solved by P.Mehrabi, E.C.Schulz, R.J.D.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.65 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.700, 78.700, 37.900, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.6

Other elements in 6rnb:

The structure of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time (pdb code 6rnb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time, PDB code: 6rnb:

Sodium binding site 1 out of 1 in 6rnb

Go back to Sodium Binding Sites List in 6rnb
Sodium binding site 1 out of 1 in the Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Liquid Application Method For Time-Resolved Analyses (Lama) By Serial Synchrotron Crystallography, Lysozyme with GLCNAC3 50MS Diffusion Time within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:68.0
occ:1.00
 O A:SER60 2.4 25.3 1.0
N A:TRP63 2.4 22.0 1.0
O A:ARG73 2.5 42.0 1.0
O A:CYS64 2.5 23.1 1.0
N A:CYS64 2.5 21.3 1.0
O A:HOH302 2.5 28.4 1.0
C A:TRP62 2.8 28.9 1.0
C A:SER60 2.9 22.8 1.0
N A:TRP62 3.2 27.7 1.0
C A:TRP63 3.2 24.8 1.0
C A:CYS64 3.2 23.7 1.0
CA A:TRP63 3.3 21.3 1.0
CA A:SER60 3.4 18.1 1.0
C A:ARG61 3.4 37.9 1.0
CA A:CYS64 3.5 24.2 1.0
CA A:TRP62 3.5 29.4 1.0
O A:TRP62 3.5 29.3 1.0
O A:ASN59 3.6 24.4 1.0
C A:ARG73 3.6 36.6 1.0
O A:ASN59 3.7 24.3 0.0
N A:ARG61 3.7 21.0 1.0
O A:ARG61 3.9 34.2 1.0
CA A:ARG61 4.0 27.8 1.0
CA A:ASN74 4.2 29.3 1.0
O A:TRP63 4.3 27.2 1.0
N A:SER60 4.4 19.3 1.0
N A:ASN74 4.4 33.7 1.0
C A:ASN59 4.4 22.8 1.0
CB A:TRP63 4.4 22.7 1.0
C A:ASN59 4.4 23.3 0.0
N A:ASN65 4.4 25.3 1.0
CB A:SER60 4.4 21.8 1.0
OG A:SER72 4.5 43.4 1.0
N A:ARG73 4.6 37.2 1.0
CB A:CYS64 4.6 20.6 1.0
CB A:SER72 4.7 40.3 1.0
SG A:CYS64 4.7 22.9 1.0
O A:HOH355 4.7 29.4 1.0
O A:HOH360 4.7 39.2 1.0
CA A:ARG73 4.7 37.3 1.0
CB A:TRP62 4.8 29.4 1.0

Reference:

P.Mehrabi, E.C.Schulz, M.Agthe, S.Horrell, G.Bourenkov, D.Von Stetten, J.P.Leimkohl, H.Schikora, T.R.Schneider, A.R.Pearson, F.Tellkamp, R.J.D.Miller. Liquid Application Method For Time-Resolved Analyses By Serial Synchrotron Crystallography. Nat.Methods V. 16 979 2019.
ISSN: ESSN 1548-7105
PubMed: 31527838
DOI: 10.1038/S41592-019-0553-1
Page generated: Tue Oct 8 13:16:45 2024

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