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Sodium in PDB 3rt5: Lysozyme in 30% Propanol

Enzymatic activity of Lysozyme in 30% Propanol

All present enzymatic activity of Lysozyme in 30% Propanol:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme in 30% Propanol, PDB code: 3rt5 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) 25.36 / 1.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.935, 77.935, 36.961, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.4

Other elements in 3rt5:

The structure of Lysozyme in 30% Propanol also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme in 30% Propanol (pdb code 3rt5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Lysozyme in 30% Propanol, PDB code: 3rt5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3rt5

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Sodium binding site 1 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na130

b:39.3
occ:1.00
 O X:HOH230 2.4 40.1 1.0
O X:SER81 3.0 21.7 1.0
N X:SER85 3.5 21.1 1.0
C X:LEU84 3.7 21.4 1.0
CA X:SER85 3.8 24.1 1.0
CB X:LEU84 4.0 21.0 1.0
O X:LEU84 4.1 21.5 1.0
C X:SER81 4.1 20.9 1.0
CB X:SER85 4.1 25.7 1.0
CA X:LEU84 4.3 20.5 1.0
O X:HOH170 4.4 28.0 1.0
N X:LEU84 4.4 19.3 1.0
O X:HOH179 4.5 32.3 1.0
O X:HOH189 4.6 31.3 1.0
CA X:ALA82 4.8 23.5 1.0
N X:ALA82 4.8 19.5 1.0
CB X:SER81 4.9 22.5 1.0
CA X:SER81 5.0 19.0 1.0
C X:ALA82 5.0 23.1 1.0
OG X:SER85 5.0 25.7 1.0

Sodium binding site 2 out of 8 in 3rt5

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Sodium binding site 2 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na131

b:32.1
occ:1.00
 O X:ARG114 2.5 22.5 1.0
NA X:NA134 3.3 30.6 1.0
C X:ARG114 3.6 19.9 1.0
CE2 X:PHE34 4.1 26.5 1.0
CA X:ARG114 4.1 20.2 1.0
CB X:ARG114 4.3 21.8 1.0
CG2 X:THR118 4.3 25.2 1.0
CZ X:PHE34 4.3 23.7 1.0
O X:HOH164 4.5 24.0 1.0
N X:CYS115 4.8 20.2 1.0
OG1 X:THR118 4.9 23.8 1.0
CB X:THR118 4.9 23.9 1.0

Sodium binding site 3 out of 8 in 3rt5

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Sodium binding site 3 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na132

b:35.8
occ:1.00
 OD1 X:ASN27 2.5 19.0 1.0
CL X:CL154 2.5 41.0 1.0
CG X:ASN27 3.5 18.3 1.0
N X:GLY117 3.6 23.2 1.0
O X:CYS115 3.7 21.1 1.0
CA X:LYS116 3.8 19.6 1.0
ND2 X:ASN27 3.8 21.0 1.0
CZ2 X:TRP111 3.8 21.1 1.0
CG1 X:VAL120 4.0 22.4 1.0
C X:LYS116 4.2 19.8 1.0
NE1 X:TRP111 4.2 17.9 1.0
CG2 X:VAL120 4.3 25.5 1.0
CE2 X:TRP111 4.3 20.1 1.0
C X:CYS115 4.3 21.0 1.0
N X:LYS116 4.4 18.8 1.0
CA X:GLY117 4.6 27.2 1.0
O X:THR118 4.6 22.6 1.0
N X:THR118 4.7 24.6 1.0
CB X:VAL120 4.8 21.8 1.0
CH2 X:TRP111 4.8 19.3 1.0
CB X:ASN27 4.9 20.3 1.0
CB X:LYS116 4.9 20.3 1.0

Sodium binding site 4 out of 8 in 3rt5

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Sodium binding site 4 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na133

b:28.9
occ:1.00
 O X:HOH214 2.4 24.6 1.0
O X:SER85 2.5 24.0 1.0
O X:HOH211 2.7 20.8 1.0
CA X:ILE88 3.5 22.3 1.0
O X:ASP87 3.5 24.7 1.0
C X:SER85 3.6 27.1 1.0
O X:LEU83 3.7 22.2 1.0
CG2 X:ILE88 3.7 23.1 1.0
OG X:SER91 3.8 21.8 1.0
CG2 X:THR40 3.9 19.7 1.0
CB X:THR40 3.9 21.9 1.0
N X:SER85 3.9 21.1 1.0
C X:ASP87 3.9 24.8 1.0
CB X:ILE88 3.9 20.3 1.0
N X:ILE88 4.0 26.0 1.0
C X:LEU83 4.2 22.5 1.0
CA X:SER85 4.2 24.1 1.0
CB X:SER91 4.3 20.2 1.0
C X:LEU84 4.3 21.4 1.0
C X:ILE88 4.5 21.8 1.0
CB X:SER85 4.6 25.7 1.0
N X:LEU84 4.7 19.3 1.0
N X:ASP87 4.7 23.5 1.0
N X:SER86 4.7 24.9 1.0
C X:SER86 4.8 24.9 1.0
CA X:LEU84 4.8 20.5 1.0
CG2 X:ILE55 4.8 24.7 1.0
CA X:THR40 4.8 17.6 1.0
O X:ILE88 4.8 20.8 1.0
O X:ALA82 4.8 24.6 1.0
O X:LEU84 4.9 21.5 1.0
OG1 X:THR40 4.9 21.1 1.0
CA X:LEU83 4.9 19.8 1.0

Sodium binding site 5 out of 8 in 3rt5

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Sodium binding site 5 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na134

b:30.6
occ:1.00
 NE X:ARG114 2.6 19.8 1.0
NA X:NA131 3.3 32.1 1.0
NH2 X:ARG114 3.4 21.3 1.0
CZ X:ARG114 3.4 20.5 1.0
CB X:ARG114 3.5 21.8 1.0
CG X:ARG114 3.6 21.0 1.0
CD X:ARG114 3.7 22.4 1.0
CZ X:PHE34 3.9 23.7 1.0
CE2 X:PHE34 4.1 26.5 1.0
CE1 X:PHE34 4.2 24.6 1.0
CA X:ARG114 4.3 20.2 1.0
O X:ARG114 4.4 22.5 1.0
CD2 X:PHE34 4.7 21.2 1.0
NH1 X:ARG114 4.7 19.3 1.0
CD1 X:PHE34 4.8 20.8 1.0
O X:HOH161 4.8 27.6 1.0
C X:ARG114 4.9 19.9 1.0

Sodium binding site 6 out of 8 in 3rt5

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Sodium binding site 6 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na135

b:30.9
occ:1.00
 O X:HOH215 2.4 32.6 1.0
O X:ASP87 2.6 24.7 1.0
N X:ALA90 3.1 22.7 1.0
O X:HOH211 3.5 20.8 1.0
CB X:ALA90 3.5 24.7 1.0
N X:THR89 3.6 23.6 1.0
C X:ASP87 3.6 24.8 1.0
OD1 X:ASP87 3.7 27.7 1.0
CG X:ASP87 3.7 31.5 1.0
CB X:THR89 3.9 27.1 1.0
CA X:ALA90 3.9 23.5 1.0
CB X:ASP87 3.9 28.9 1.0
CA X:THR89 4.0 25.1 1.0
C X:THR89 4.0 22.5 1.0
CB X:SER85 4.1 25.7 1.0
OG X:SER85 4.1 25.7 1.0
O X:ALA82 4.1 24.6 1.0
C X:ILE88 4.2 21.8 1.0
OD2 X:ASP87 4.3 33.8 1.0
CA X:ASP87 4.4 23.7 1.0
N X:ILE88 4.4 26.0 1.0
CA X:ILE88 4.6 22.3 1.0
OG1 X:THR89 4.7 27.3 1.0
CG2 X:THR89 4.9 31.0 1.0
O X:ILE88 4.9 20.8 1.0

Sodium binding site 7 out of 8 in 3rt5

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Sodium binding site 7 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na136

b:34.5
occ:1.00
 O X:HOH172 2.6 24.3 1.0
O X:ASN37 2.6 19.6 1.0
OD1 X:ASN37 3.3 25.0 1.0
CG X:ASN37 3.6 25.0 1.0
C X:ASN37 3.7 21.7 1.0
CD2 X:PHE38 3.7 20.6 1.0
CG1 X:VAL2 3.8 22.5 1.0
CB X:PHE38 3.9 18.2 1.0
ND2 X:ASN37 3.9 30.3 1.0
CG X:PHE38 4.2 19.1 1.0
O X:PHE3 4.3 19.4 1.0
CB X:ASN37 4.4 20.8 1.0
CA X:ASN37 4.4 19.5 1.0
NZ X:LYS33 4.5 26.5 1.0
N X:PHE38 4.6 19.3 1.0
CE2 X:PHE38 4.6 21.3 1.0
CA X:PHE38 4.8 18.1 1.0

Sodium binding site 8 out of 8 in 3rt5

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Sodium binding site 8 out of 8 in the Lysozyme in 30% Propanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Lysozyme in 30% Propanol within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Na137

b:27.9
occ:1.00
 ND2 X:ASN65 3.2 25.4 1.0
CA X:GLY67 3.6 23.2 1.0
N X:GLY67 4.0 21.3 1.0
CG X:ASN65 4.2 22.5 1.0
OD1 X:ASN65 4.3 23.7 1.0
C X:ASP66 4.6 20.2 1.0
O X:ASP66 4.9 22.3 1.0
C X:GLY67 5.0 24.8 1.0

Reference:

P.Sharma, A.K.Solanki, Ashish. Crystal Structure of Lysozyme in 30% Propanol To Be Published.
Page generated: Mon Oct 7 12:51:54 2024

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