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Sodium in PDB 3t6u: Crystal Structure of Lysozyme in 40% Sucrose

Enzymatic activity of Crystal Structure of Lysozyme in 40% Sucrose

All present enzymatic activity of Crystal Structure of Lysozyme in 40% Sucrose:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Lysozyme in 40% Sucrose, PDB code: 3t6u was solved by P.Sharma, S.Singh, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.53 / 2.21
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.614, 77.614, 37.483, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.8

Other elements in 3t6u:

The structure of Crystal Structure of Lysozyme in 40% Sucrose also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lysozyme in 40% Sucrose (pdb code 3t6u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Lysozyme in 40% Sucrose, PDB code: 3t6u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 1 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na136

b:37.0
occ:1.00
 O A:ASP87 2.7 35.2 1.0
O A:ALA82 3.1 33.9 1.0
O A:HOH148 3.3 34.8 1.0
OG A:SER91 3.3 29.2 1.0
N A:SER91 3.5 27.9 1.0
CA A:ILE88 3.5 32.8 1.0
C A:ILE88 3.7 32.7 1.0
C A:ASP87 3.7 35.7 1.0
N A:ALA90 3.9 33.5 1.0
CB A:ALA90 3.9 29.5 1.0
CA A:LEU83 3.9 30.1 1.0
CB A:SER91 3.9 28.8 1.0
C A:LEU83 4.0 34.1 1.0
O A:ILE88 4.0 32.9 1.0
O A:LEU83 4.0 31.2 1.0
N A:ILE88 4.1 33.1 1.0
N A:THR89 4.1 30.9 1.0
CA A:ALA90 4.2 34.9 1.0
O A:SER85 4.2 33.5 1.0
C A:ALA82 4.2 32.4 1.0
C A:ALA90 4.2 30.1 1.0
CA A:SER91 4.3 30.0 1.0
N A:SER85 4.3 33.4 1.0
O A:HOH160 4.3 38.5 1.0
CB A:SER85 4.5 34.6 1.0
N A:LEU84 4.5 33.5 1.0
N A:LEU83 4.6 30.1 1.0
CB A:ILE88 4.7 34.2 1.0
C A:THR89 4.7 31.8 1.0
CA A:SER85 4.7 32.1 1.0
C A:SER85 4.8 32.3 1.0
OG A:SER85 4.9 36.1 1.0
CD2 A:LEU83 5.0 33.2 1.0
CA A:ASP87 5.0 37.3 1.0

Sodium binding site 2 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 2 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na137

b:49.9
occ:0.50
 N A:GLY71 3.3 42.1 1.0
CA A:GLY71 4.0 46.7 1.0
C A:PRO70 4.2 45.6 1.0
CA A:PRO70 4.3 43.1 1.0
N A:SER72 4.4 40.2 1.0
C A:GLY71 4.7 46.6 1.0
O A:THR69 4.8 38.8 1.0

Sodium binding site 3 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 3 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na138

b:33.1
occ:1.00
 O A:ARG21 2.7 34.7 1.0
CA A:GLY22 3.6 32.3 1.0
C A:GLY22 3.7 29.2 1.0
CE2 A:TYR23 3.8 31.4 1.0
C A:ARG21 3.8 34.2 1.0
O A:GLY22 3.9 29.3 1.0
CZ A:TYR23 4.0 30.8 1.0
CD2 A:TYR23 4.1 29.0 1.0
N A:GLY22 4.2 34.0 1.0
N A:TYR23 4.4 29.6 1.0
OH A:TYR23 4.4 30.6 1.0
CE1 A:TYR23 4.5 26.9 1.0
CG A:TYR23 4.6 30.1 1.0
CD1 A:TYR23 4.8 28.6 1.0

Sodium binding site 4 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 4 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na139

b:33.9
occ:1.00
 OD1 A:ASN39 2.8 29.9 1.0
N A:LYS1 2.9 35.7 1.0
NE2 A:GLN41 2.9 32.8 1.0
CG A:GLN41 3.4 31.3 1.0
C A:LYS1 3.6 35.9 1.0
CA A:LYS1 3.6 34.4 1.0
CD A:GLN41 3.6 30.8 1.0
O A:LYS1 3.9 33.8 1.0
CG A:ASN39 3.9 30.3 1.0
CB A:GLN41 3.9 25.9 1.0
N A:VAL2 4.0 36.2 1.0
CG2 A:VAL2 4.1 27.7 1.0
ND2 A:ASN39 4.4 28.5 1.0
N A:GLN41 4.5 27.7 1.0
OG1 A:THR40 4.8 32.0 1.0
OE1 A:GLN41 4.9 29.6 1.0
CA A:VAL2 4.9 31.6 1.0
CA A:GLN41 4.9 30.8 1.0
N A:THR40 5.0 29.3 1.0
O A:HOH144 5.0 30.6 1.0

Sodium binding site 5 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 5 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na140

b:36.7
occ:1.00
 OD2 A:ASP66 2.8 30.2 1.0
OG1 A:THR51 2.9 33.0 1.0
OG1 A:THR69 2.9 32.0 1.0
O A:GLY49 3.1 34.2 1.0
NE A:ARG68 3.2 40.9 1.0
N A:THR51 3.3 32.7 1.0
CB A:THR51 3.5 33.2 1.0
C A:SER50 3.5 31.8 1.0
OG A:SER60 3.6 30.0 1.0
CG A:ARG68 3.6 36.1 1.0
CA A:SER50 3.6 31.6 1.0
CG A:ASP66 3.7 30.9 1.0
OD1 A:ASP66 3.8 27.8 1.0
CD A:ARG68 3.9 40.6 1.0
O A:ARG68 4.0 42.7 1.0
CA A:THR51 4.0 31.5 1.0
CZ A:ARG68 4.1 41.0 1.0
NH2 A:ARG68 4.1 37.3 1.0
C A:GLY49 4.1 36.7 1.0
NH1 A:ARG45 4.2 42.1 1.0
O A:SER50 4.2 31.4 1.0
CB A:THR69 4.2 35.3 1.0
OH A:TYR53 4.3 29.4 1.0
C A:ARG68 4.3 38.0 1.0
N A:SER50 4.4 31.8 1.0
CD A:ARG45 4.6 36.1 1.0
CZ A:ARG45 4.6 44.4 1.0
CB A:SER60 4.6 29.6 1.0
N A:THR69 4.7 38.3 1.0
CA A:THR69 4.7 39.2 1.0
CG2 A:THR69 4.7 34.8 1.0
NE A:ARG45 4.8 43.6 1.0
CB A:ARG68 4.8 38.9 1.0
CB A:SER50 4.8 31.1 1.0
CG2 A:THR51 4.9 30.5 1.0

Sodium binding site 6 out of 6 in 3t6u

Go back to Sodium Binding Sites List in 3t6u
Sodium binding site 6 out of 6 in the Crystal Structure of Lysozyme in 40% Sucrose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Lysozyme in 40% Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na141

b:48.1
occ:1.00
 OG A:SER72 3.0 44.7 1.0
OD1 A:ASN65 3.3 36.7 1.0
O A:ARG73 3.6 36.9 1.0
CB A:ASN65 3.7 36.4 1.0
CB A:ASN74 3.8 34.5 1.0
CA A:ASN65 3.8 31.7 1.0
C A:ARG73 3.8 38.6 1.0
CG A:ASN65 3.9 38.4 1.0
CL A:CL135 4.0 45.9 1.0
O A:SER72 4.0 43.2 1.0
O A:CYS64 4.1 32.1 1.0
N A:ASN74 4.2 36.0 1.0
C A:SER72 4.3 44.7 1.0
CB A:SER72 4.4 41.7 1.0
CA A:ASN74 4.4 38.1 1.0
N A:ASN65 4.4 33.1 1.0
CA A:ARG73 4.5 44.1 1.0
C A:CYS64 4.5 35.0 1.0
N A:ARG73 4.5 43.6 1.0
CG A:ASN74 4.7 34.6 1.0
O A:SER60 4.7 35.0 1.0
CA A:SER72 4.9 42.6 1.0
ND2 A:ASN74 4.9 35.8 1.0
C A:ASN65 5.0 28.6 1.0

Reference:

P.Sharma, S.Singh, Ashish. Crystal Structure of Lysozyme in 40% Sucrose To Be Published.
Page generated: Mon Oct 7 13:11:26 2024

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