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Chlorine 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:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution, PDB code: 2z18:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2z18

Go back to Chlorine Binding Sites List in 2z18
Chlorine binding site 1 out of 4 in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl132

b:7.4
occ:1.00
ND2 A:ASN59 3.2 10.3 1.0
NE1 A:TRP63 3.2 5.1 1.0
O A:HOH139 3.3 6.5 1.0
CD1 A:TRP62 3.7 7.9 1.0
CB A:ASN59 3.7 6.5 1.0
CD1 A:TRP63 3.8 6.3 1.0
CG A:ASN59 3.9 7.6 1.0
CE2 A:TRP63 4.4 4.8 1.0
NE1 A:TRP62 4.6 7.7 1.0
CG A:TRP62 4.6 5.2 1.0
CB A:TRP62 4.7 5.5 1.0
CZ2 A:TRP63 4.9 6.5 1.0
O A:HOH145 5.0 7.7 1.0

Chlorine binding site 2 out of 4 in 2z18

Go back to Chlorine Binding Sites List in 2z18
Chlorine binding site 2 out of 4 in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 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:Cl133

b:20.6
occ:1.00
NH2 A:ARG21 3.1 10.6 1.0
CA A:ARG21 3.5 4.2 1.0
N A:GLY22 3.6 6.1 1.0
NE A:ARG21 3.6 10.9 1.0
C A:ARG21 3.7 4.6 1.0
CZ A:ARG21 3.7 9.9 1.0
N A:ARG21 4.0 5.1 1.0
CA A:GLY22 4.4 6.4 1.0
O A:ARG21 4.4 5.6 1.0
CB A:ARG21 4.7 5.8 1.0
O A:ASN19 4.7 7.6 1.0
CD A:ARG21 4.8 8.1 1.0
NH1 A:ARG21 5.0 13.0 1.0

Chlorine binding site 3 out of 4 in 2z18

Go back to Chlorine Binding Sites List in 2z18
Chlorine binding site 3 out of 4 in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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:Cl134

b:21.7
occ:1.00
O A:HOH226 3.0 20.9 1.0
O A:HOH250 3.6 32.8 1.0
CE2 A:PHE38 3.8 7.7 1.0
CD A:LYS33 3.8 8.7 1.0
CE A:LYS33 3.9 15.1 1.0
NZ A:LYS33 4.3 21.8 1.0
CB A:ARG5 4.4 5.6 1.0
CZ A:PHE38 4.4 6.5 1.0
CZ3 A:TRP123 4.6 9.7 1.0
CD A:ARG5 4.7 5.3 1.0
CD2 A:PHE38 4.7 6.4 1.0
O A:HOH178 4.8 11.5 1.0
NE A:ARG5 5.0 6.3 1.0

Chlorine binding site 4 out of 4 in 2z18

Go back to Chlorine Binding Sites List in 2z18
Chlorine binding site 4 out of 4 in the Phase Transition of Monoclinic Lysozyme Crystal Soaked in A 10% Nacl Solution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 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:Cl135

b:13.8
occ:1.00
OD1 A:ASN65 2.7 17.9 1.0
O A:HOH141 3.0 7.3 1.0
N A:GLY67 3.2 7.2 1.0
O A:THR69 3.3 9.6 1.0
N A:THR69 3.3 9.7 1.0
O A:HOH142 3.4 6.3 1.0
CA A:GLY67 3.4 7.0 1.0
C A:GLY67 3.4 10.4 1.0
N A:ARG68 3.6 7.9 1.0
C A:THR69 3.7 13.4 1.0
O A:HOH278 3.7 22.5 1.0
OG A:SER72 3.8 7.8 1.0
CG A:ASN65 3.9 17.9 1.0
O A:GLY67 4.0 9.9 1.0
CA A:THR69 4.1 10.0 1.0
OG1 A:THR69 4.1 10.4 1.0
O A:HOH293 4.2 27.2 0.8
N A:ASP66 4.3 6.5 1.0
OD1 A:ASP66 4.3 6.8 1.0
C A:ARG68 4.3 9.3 1.0
C A:ASP66 4.4 6.2 1.0
NA A:NA131 4.4 5.4 1.0
N A:PRO70 4.4 15.5 1.0
CA A:ARG68 4.6 8.1 1.0
CA A:ASN65 4.7 4.9 1.0
CB A:THR69 4.7 10.3 1.0
ND2 A:ASN65 4.8 20.0 1.0
O A:HOH158 4.8 9.4 1.0
CA A:PRO70 4.8 15.8 1.0
O A:HOH214 4.8 16.3 1.0
CB A:ASN65 4.9 8.0 1.0
CA A:ASP66 4.9 6.2 1.0
C A:ASN65 4.9 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: Sat Dec 12 09:29:57 2020

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