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Sodium in PDB 2z18: Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution

Enzymatic activity of Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution

All present enzymatic activity of Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution:
3.2.1.17;

Protein crystallography data

The structure of Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution, PDB code: 2z18 was solved by K.Harata, T.Akiba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 26.622, 60.588, 31.223, 90.00, 111.44, 90.00
R / Rfree (%) 15.6 / 17.6

Other elements in 2z18:

The structure of Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution (pdb code 2z18). 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 Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution, PDB code: 2z18:

Sodium binding site 1 out of 1 in 2z18

Go back to Sodium Binding Sites List in 2z18
Sodium binding site 1 out of 1 in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na131

b:5.4
occ:1.00
O A:CYS64 2.3 5.2 1.0
O A:SER60 2.4 5.2 1.0
O A:HOH142 2.4 6.3 1.0
O A:ARG73 2.4 6.0 1.0
O A:HOH141 2.5 7.3 1.0
OG A:SER72 2.6 7.8 1.0
CB A:SER72 3.4 5.9 1.0
C A:ARG73 3.4 6.1 1.0
C A:CYS64 3.5 4.4 1.0
C A:SER60 3.5 4.0 1.0
N A:ARG73 3.9 6.2 1.0
CA A:ASN65 4.0 4.9 1.0
N A:ASN65 4.1 4.8 1.0
CA A:SER60 4.2 3.6 1.0
C A:SER72 4.3 6.9 1.0
CA A:ARG73 4.3 7.9 1.0
N A:ASN74 4.3 6.4 1.0
N A:CYS64 4.4 4.7 1.0
CL A:CL135 4.4 13.8 1.0
CB A:SER60 4.4 7.8 1.0
C A:ARG61 4.4 4.7 1.0
CA A:SER72 4.5 6.0 1.0
O A:ARG61 4.5 4.7 1.0
O A:HOH214 4.5 16.3 1.0
CA A:ASN74 4.6 5.5 1.0
N A:ARG61 4.6 4.6 1.0
CA A:CYS64 4.6 4.0 1.0
OG1 A:THR69 4.7 10.4 1.0
CB A:ASN74 4.7 7.0 1.0
CA A:ARG61 4.7 4.6 1.0
OD1 A:ASN65 4.7 17.9 1.0
N A:TRP62 4.8 4.8 1.0
N A:ASP66 4.9 6.5 1.0
CB A:ASN65 4.9 8.0 1.0
O A:HOH158 4.9 9.4 1.0
O A:SER72 4.9 7.8 1.0
N A:TRP63 4.9 3.6 1.0
C A:ASN65 5.0 5.5 1.0

Reference:

K.Harata, T.Akiba. Effect of A Sodium Ion on the Dehydration-Induced Phase Transition of Monoclinic Lysozyme Crystals. Acta Crystallogr.,Sect.D V. 63 1016 2007.
ISSN: ISSN 0907-4449
PubMed: 17704571
DOI: 10.1107/S0907444907031319
Page generated: Tue Dec 15 06:00:51 2020

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