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Sodium in PDB 3sp3: Lysozyme in 20% Sucrose

Enzymatic activity of Lysozyme in 20% Sucrose

All present enzymatic activity of Lysozyme in 20% Sucrose:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme in 20% Sucrose, PDB code: 3sp3 was solved by P.Sharma, A.K.Solanki, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.41 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.847, 76.847, 37.600, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.9

Other elements in 3sp3:

The structure of Lysozyme in 20% Sucrose also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme in 20% Sucrose (pdb code 3sp3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Lysozyme in 20% Sucrose, PDB code: 3sp3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3sp3

Go back to Sodium Binding Sites List in 3sp3
Sodium binding site 1 out of 4 in the Lysozyme in 20% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme in 20% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na135

b:35.9
occ:1.00
N A:SER24 3.0 32.8 1.0
O A:GLY22 3.1 32.3 1.0
ND2 A:ASN27 3.4 29.4 1.0
O A:HOH168 3.5 32.3 1.0
OG A:SER24 3.5 29.5 1.0
CB A:SER24 3.5 32.9 1.0
CA A:TYR23 3.8 28.8 1.0
CA A:SER24 3.8 28.8 1.0
C A:TYR23 3.9 28.9 1.0
C A:GLY22 4.1 28.7 1.0
O A:HOH171 4.3 37.6 1.0
ND2 A:ASN19 4.3 42.8 1.0
N A:TYR23 4.5 31.6 1.0
CG A:ASN27 4.7 28.8 1.0
CB A:TYR23 5.0 26.5 1.0

Sodium binding site 2 out of 4 in 3sp3

Go back to Sodium Binding Sites List in 3sp3
Sodium binding site 2 out of 4 in the Lysozyme in 20% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme in 20% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na136

b:38.6
occ:1.00
OD1 A:ASN39 2.8 27.5 1.0
OE1 A:GLN41 2.9 34.8 1.0
N A:LYS1 3.0 30.2 1.0
CG A:GLN41 3.4 29.2 1.0
CD A:GLN41 3.6 34.5 1.0
C A:LYS1 3.6 32.5 1.0
CG A:ASN39 3.7 27.7 1.0
CA A:LYS1 3.7 35.7 1.0
O A:LYS1 3.9 30.2 1.0
CB A:GLN41 3.9 32.3 1.0
N A:VAL2 4.0 29.5 1.0
ND2 A:ASN39 4.0 31.6 1.0
CG2 A:VAL2 4.0 33.9 1.0
N A:GLN41 4.5 28.3 1.0
OG1 A:THR40 4.7 35.9 1.0
CA A:VAL2 4.8 31.0 1.0
CA A:GLN41 4.8 31.0 1.0
NE2 A:GLN41 4.9 31.5 1.0
N A:THR40 4.9 27.4 1.0
CB A:ASN39 4.9 28.5 1.0

Sodium binding site 3 out of 4 in 3sp3

Go back to Sodium Binding Sites List in 3sp3
Sodium binding site 3 out of 4 in the Lysozyme in 20% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme in 20% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na137

b:35.5
occ:1.00
OG1 A:THR51 2.7 29.3 1.0
OD2 A:ASP66 2.8 27.8 1.0
O A:GLY49 2.9 35.0 1.0
NE A:ARG68 3.1 30.6 1.0
OG1 A:THR69 3.1 31.2 1.0
N A:THR51 3.4 29.1 1.0
CG A:ARG68 3.4 33.4 1.0
C A:SER50 3.5 27.4 1.0
CB A:THR51 3.5 25.1 1.0
OG A:SER60 3.6 28.3 1.0
CA A:SER50 3.7 28.9 1.0
NH1 A:ARG45 3.7 39.9 1.0
CG A:ASP66 3.7 30.6 1.0
CD A:ARG68 3.8 32.2 1.0
OD1 A:ASP66 3.9 28.6 1.0
C A:GLY49 4.0 35.4 1.0
CZ A:ARG68 4.0 31.4 1.0
CA A:THR51 4.0 28.1 1.0
O A:SER50 4.0 30.3 1.0
NH2 A:ARG68 4.1 28.1 1.0
N A:SER50 4.3 31.8 1.0
O A:ARG68 4.3 33.6 1.0
CD A:ARG45 4.3 41.0 1.0
CZ A:ARG45 4.4 42.9 1.0
CB A:THR69 4.4 31.2 1.0
OH A:TYR53 4.4 27.3 1.0
C A:ARG68 4.5 33.4 1.0
CB A:SER60 4.5 26.9 1.0
NE A:ARG45 4.6 47.2 1.0
CB A:ARG68 4.7 34.9 1.0
N A:THR69 4.8 33.9 1.0
CG2 A:THR51 4.8 26.4 1.0
CG2 A:THR69 4.8 31.2 1.0
CA A:THR69 4.9 33.3 1.0
CB A:SER50 4.9 29.7 1.0

Sodium binding site 4 out of 4 in 3sp3

Go back to Sodium Binding Sites List in 3sp3
Sodium binding site 4 out of 4 in the Lysozyme in 20% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Lysozyme in 20% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na138

b:36.7
occ:1.00
O A:HOH139 3.0 30.7 1.0
N A:GLU7 3.2 30.3 1.0
CA A:GLY4 3.5 29.8 1.0
N A:CYS6 3.6 29.2 1.0
C A:GLY4 3.6 30.2 1.0
CB A:GLU7 3.6 32.7 1.0
CB A:CYS6 3.8 32.3 1.0
N A:ARG5 3.8 31.5 1.0
CA A:CYS6 4.0 30.8 1.0
CA A:GLU7 4.0 28.3 1.0
C A:CYS6 4.0 29.0 1.0
O A:GLY4 4.1 30.9 1.0
N A:GLY4 4.4 30.5 1.0
C A:ARG5 4.4 33.5 1.0
CA A:ARG5 4.7 32.0 1.0
OE1 A:GLU7 4.9 35.2 1.0
CG A:GLU7 5.0 32.5 1.0

Reference:

P.Sharma, A.K.Solanki, Ashish. Lysozyme in 20% Sucrose To Be Published.
Page generated: Tue Dec 15 06:24:55 2020

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