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Sodium in PDB 4r6c: X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6

Enzymatic activity of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6

All present enzymatic activity of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6, PDB code: 4r6c was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.36 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.070, 79.070, 37.235, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23

Other elements in 4r6c:

The structure of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6 also contains other interesting chemical elements:

Bromine (Br) 31 atoms
Platinum (Pt) 2 atoms
Tantalum (Ta) 12 atoms
Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6 (pdb code 4r6c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6, PDB code: 4r6c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4r6c

Go back to Sodium Binding Sites List in 4r6c
Sodium binding site 1 out of 2 in the X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:22.4
occ:1.00
 O A:CYS64 2.3 14.6 1.0
O A:SER60 2.3 17.1 1.0
O A:ARG73 2.3 27.0 1.0
O A:HOH309 2.3 16.1 1.0
O A:HOH311 2.3 25.9 1.0
OG A:SER72 2.6 31.6 1.0
CB A:SER72 3.2 34.0 1.0
C A:CYS64 3.3 13.1 1.0
C A:SER60 3.5 15.8 1.0
C A:ARG73 3.5 24.0 1.0
NA A:NA213 3.6 28.6 1.0
CA A:ASN65 3.8 16.9 1.0
N A:ASN65 3.9 14.2 1.0
N A:ARG73 4.1 28.4 1.0
C A:SER72 4.1 29.4 1.0
CA A:SER60 4.2 13.3 1.0
CA A:SER72 4.3 35.1 1.0
CB A:SER60 4.4 13.0 1.0
N A:CYS64 4.4 13.2 1.0
N A:ASN74 4.4 20.6 1.0
O A:ARG61 4.4 23.5 1.0
CA A:ARG73 4.5 25.6 1.0
O A:SER72 4.5 31.3 1.0
CA A:CYS64 4.5 13.2 1.0
OD1 A:ASN65 4.5 22.0 1.0
N A:ARG61 4.5 16.5 1.0
C A:ARG61 4.6 22.9 1.0
N A:ASP66 4.6 12.4 1.0
CA A:ASN74 4.6 16.9 1.0
CB A:THR69 4.6 17.7 1.0
CB A:ASN74 4.6 16.8 1.0
CB A:ASN65 4.7 18.5 1.0
CA A:ARG61 4.7 21.5 1.0
C A:ASN65 4.8 12.5 1.0
CL A:CL208 4.8 31.6 1.0
O A:THR69 4.9 22.6 1.0
OG1 A:THR69 5.0 15.2 1.0

Sodium binding site 2 out of 2 in 4r6c

Go back to Sodium Binding Sites List in 4r6c
Sodium binding site 2 out of 2 in the X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science: the X-Ray Crystal Structure of Hen Egg White Lysozyme Cocrystallized with TA6BR12 and Then A Crystal Soaked in K2PTBR6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:28.6
occ:1.00
 CL A:CL208 1.9 31.6 1.0
O A:HOH311 2.3 25.9 1.0
OD1 A:ASN65 2.3 22.0 1.0
O A:HOH309 2.4 16.1 1.0
OG A:SER72 3.2 31.6 1.0
CG A:ASN65 3.5 20.7 1.0
NA A:NA209 3.6 22.4 1.0
N A:GLY67 4.0 14.1 1.0
O A:THR69 4.0 22.6 1.0
CA A:ASN65 4.2 16.9 1.0
CB A:ASN65 4.3 18.5 1.0
N A:ASP66 4.3 12.4 1.0
CA A:GLY67 4.4 14.8 1.0
ND2 A:ASN65 4.5 26.4 1.0
N A:THR69 4.5 17.6 1.0
CB A:SER72 4.6 34.0 1.0
O A:SER72 4.7 31.3 1.0
C A:GLY67 4.7 16.0 1.0
C A:ASN65 4.8 12.5 1.0
N A:ARG68 4.8 16.9 1.0
OD1 A:ASP66 4.8 14.9 1.0
C A:THR69 4.8 22.5 1.0
CB A:THR69 4.9 17.7 1.0

Reference:

J.R.Helliwell, A.Brink, S.Kaenket, V.L.Starkey, S.W.Tanley. X-Ray Diffraction in Temporally and Spatially Resolved Biomolecular Science. Faraday Discuss 2015.
PubMed: 25605312
DOI: 10.1039/C4FD00166D
Page generated: Mon Oct 7 18:13:28 2024

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