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Sodium in PDB 5b05: Lysozyme (Control Experiment)

Enzymatic activity of Lysozyme (Control Experiment)

All present enzymatic activity of Lysozyme (Control Experiment):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme (Control Experiment), PDB code: 5b05 was solved by A.Kita, Y.Morimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.73 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.816, 78.816, 36.800, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 5b05:

The structure of Lysozyme (Control Experiment) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme (Control Experiment) (pdb code 5b05). 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 (Control Experiment), PDB code: 5b05:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 1 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2005

b:18.8
occ:1.00
 O A:TYR53 2.9 12.2 1.0
OG A:SER91 2.9 14.2 1.0
N A:LEU56 3.0 14.6 1.0
N A:ILE55 3.4 14.0 1.0
C A:GLY54 3.4 14.0 1.0
N A:GLN57 3.5 12.5 1.0
CA A:GLY54 3.6 12.8 1.0
CA A:LEU56 3.6 14.5 1.0
CB A:SER91 3.6 14.0 1.0
CD1 A:ILE58 3.6 18.4 1.0
C A:LEU56 3.7 14.0 1.0
CB A:LEU56 3.8 15.6 1.0
CG1 A:ILE58 3.8 17.6 1.0
C A:TYR53 3.9 13.5 1.0
NA A:NA2006 3.9 27.3 1.0
N A:ILE58 4.0 13.7 1.0
O A:GLY54 4.0 13.8 1.0
C A:ILE55 4.0 15.6 1.0
CG1 A:ILE55 4.1 18.5 1.0
CA A:ILE55 4.2 16.0 1.0
N A:GLY54 4.2 13.1 1.0
CB A:ILE58 4.3 16.8 1.0
O A:LEU83 4.3 15.5 1.0
CD2 A:LEU83 4.5 19.5 1.0
CB A:LEU83 4.5 16.8 1.0
CA A:SER91 4.5 15.7 1.0
CA A:GLN57 4.5 13.2 1.0
O A:LEU56 4.6 14.7 1.0
CG A:LEU56 4.8 17.2 1.0
CB A:ILE55 4.8 18.7 1.0
C A:GLN57 4.8 13.6 1.0
CA A:ILE58 4.8 15.7 1.0
CG A:LEU83 4.9 16.9 1.0

Sodium binding site 2 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 2 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2006

b:27.3
occ:1.00
 O A:HOH2122 2.6 13.4 1.0
O A:LEU83 2.6 15.5 1.0
N A:ILE55 2.9 14.0 1.0
OG A:SER91 3.0 14.2 1.0
CG1 A:ILE55 3.4 18.5 1.0
CA A:GLY54 3.4 12.8 1.0
C A:GLY54 3.6 14.0 1.0
C A:LEU83 3.7 15.4 1.0
O A:THR40 3.8 13.7 1.0
CB A:ILE55 3.8 18.7 1.0
CA A:ILE55 3.8 16.0 1.0
CB A:SER91 3.9 14.0 1.0
CG2 A:ILE55 3.9 21.6 1.0
CA A:THR40 3.9 12.7 1.0
CB A:THR40 3.9 14.1 1.0
NA A:NA2005 3.9 18.8 1.0
CG2 A:THR40 4.2 13.9 1.0
O A:HOH2185 4.2 16.8 1.0
C A:THR40 4.3 12.0 1.0
CD1 A:ILE55 4.4 21.7 1.0
O A:SER85 4.5 16.8 1.0
N A:LEU84 4.6 14.9 1.0
CA A:LEU83 4.6 15.6 1.0
CA A:LEU84 4.6 14.6 1.0
N A:GLY54 4.8 13.1 1.0
O A:GLY54 4.8 13.8 1.0
C A:LEU84 4.9 16.1 1.0
N A:LEU56 4.9 14.6 1.0
C A:ILE55 5.0 15.6 1.0

Sodium binding site 3 out of 8 in 5b05

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Sodium binding site 3 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2007

b:22.7
occ:1.00
 O A:HOH2136 2.9 16.7 1.0
O A:HOH2188 3.6 21.4 1.0
CG2 A:VAL2 3.7 16.0 1.0
N A:VAL2 4.2 16.2 1.0
O A:HOH2229 4.3 47.1 1.0
CA A:LYS1 4.5 16.9 1.0
C A:LYS1 4.5 16.4 1.0
CB A:VAL2 4.6 15.5 1.0
N A:LYS1 4.6 16.6 1.0
NE2 A:GLN41 4.8 16.4 1.0
CA A:VAL2 5.0 15.8 1.0

Sodium binding site 4 out of 8 in 5b05

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Sodium binding site 4 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2008

b:22.5
occ:1.00
 OG1 A:THR51 2.7 13.3 1.0
OD2 A:ASP66 2.8 14.9 1.0
NE A:ARG68 2.9 23.6 1.0
O A:GLY49 2.9 23.5 1.0
OG1 A:THR69 3.1 16.0 1.0
N A:THR51 3.4 12.0 1.0
C A:SER50 3.5 14.1 1.0
CB A:THR51 3.5 11.9 1.0
CG A:ARG68 3.5 18.0 1.0
CD A:ARG68 3.7 21.1 1.0
CG A:ASP66 3.7 13.3 1.0
NE A:ARG45 3.7 37.6 1.0
CA A:SER50 3.7 15.7 1.0
OG A:SER60 3.8 13.3 1.0
CZ A:ARG68 3.8 26.1 1.0
OD1 A:ASP66 3.9 13.7 1.0
NH2 A:ARG68 3.9 21.2 1.0
O A:ARG68 3.9 21.1 1.0
C A:GLY49 4.0 19.4 1.0
O A:SER50 4.0 15.5 1.0
CA A:THR51 4.0 12.8 1.0
NH2 A:ARG45 4.1 26.0 1.0
CZ A:ARG45 4.1 31.0 1.0
C A:ARG68 4.3 17.9 1.0
N A:SER50 4.3 16.4 1.0
CB A:THR69 4.4 17.2 1.0
CD A:ARG45 4.4 26.9 1.0
OH A:TYR53 4.4 12.8 1.0
N A:THR69 4.7 17.1 1.0
CB A:ARG68 4.7 18.2 1.0
CA A:THR69 4.7 17.3 1.0
CG2 A:THR51 4.8 13.2 1.0
CB A:SER60 4.8 14.4 1.0
CG2 A:THR69 4.9 18.3 1.0
CB A:SER50 5.0 16.8 1.0
CB A:ASP66 5.0 14.0 1.0

Sodium binding site 5 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 5 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2009

b:23.3
occ:1.00
 O A:ARG21 2.8 15.7 1.0
CL A:CL2013 3.3 18.2 1.0
CE2 A:TYR23 3.6 12.8 1.0
C A:ARG21 3.9 15.9 1.0
CZ A:TYR23 3.9 13.8 1.0
CA A:GLY22 3.9 15.9 1.0
C A:GLY22 4.0 16.9 1.0
CD2 A:TYR23 4.0 12.2 1.0
O A:GLY22 4.0 16.8 1.0
OH A:TYR23 4.3 13.7 1.0
N A:GLY22 4.3 17.3 1.0
CE1 A:TYR23 4.4 13.1 1.0
N A:TYR23 4.5 13.6 1.0
CG A:TYR23 4.6 12.3 1.0
CD1 A:TYR23 4.8 13.3 1.0

Sodium binding site 6 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 6 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2010

b:28.2
occ:1.00
 O A:HOH2128 2.8 25.9 1.0
CB A:ALA42 3.5 13.9 1.0
ND2 A:ASN44 3.6 24.6 1.0
CA A:ALA42 4.1 14.5 1.0
OD1 A:ASN44 4.4 20.9 1.0
CG A:ASN44 4.4 24.0 1.0
O A:THR43 4.5 16.9 1.0
N A:THR43 4.6 14.9 1.0
C A:ALA42 4.8 14.2 1.0
O A:SER36 4.9 13.0 1.0
CA A:SER36 5.0 11.9 1.0
O A:GLU35 5.0 11.5 1.0

Sodium binding site 7 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 7 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2011

b:26.9
occ:1.00
 O A:HOH2101 2.4 11.2 1.0
O A:HOH2163 2.5 44.0 1.0
OD1 A:ASN65 2.9 18.6 1.0
O A:HOH2152 3.1 11.9 1.0
OG A:SER72 3.3 21.1 1.0
O A:ARG73 3.4 21.4 1.0
CA A:ASN65 3.5 14.7 1.0
CB A:ASN65 3.5 15.4 1.0
CG A:ASN65 3.6 18.5 1.0
O A:CYS64 3.7 13.4 1.0
C A:ARG73 3.8 19.6 1.0
CB A:ASN74 3.8 17.7 1.0
CL A:CL2014 4.0 19.5 1.0
O A:HOH2206 4.0 29.9 1.0
N A:ASN65 4.1 14.8 1.0
N A:ASN74 4.1 17.3 1.0
C A:CYS64 4.2 12.1 1.0
CA A:ASN74 4.4 17.6 1.0
O A:SER72 4.4 26.4 1.0
O A:HOH2191 4.4 23.4 1.0
O A:HOH2118 4.5 32.2 1.0
CA A:ARG73 4.5 19.7 1.0
C A:SER72 4.5 24.4 1.0
CB A:SER72 4.5 21.3 1.0
N A:ARG73 4.6 20.2 1.0
C A:ASN65 4.6 12.5 1.0
N A:ASP66 4.7 13.7 1.0
CG A:ASN74 4.7 17.2 1.0
O A:SER60 4.7 17.9 1.0
ND2 A:ASN65 4.9 19.5 1.0

Sodium binding site 8 out of 8 in 5b05

Go back to Sodium Binding Sites List in 5b05
Sodium binding site 8 out of 8 in the Lysozyme (Control Experiment)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Lysozyme (Control Experiment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2012

b:21.3
occ:1.00
 O A:GLN41 2.7 15.5 1.0
OG1 A:THR43 2.8 15.6 1.0
N A:THR43 3.1 14.9 1.0
CB A:THR43 3.5 14.7 1.0
CG2 A:THR43 3.5 14.9 1.0
C A:ALA42 3.8 14.2 1.0
C A:GLN41 3.8 14.0 1.0
CA A:THR43 3.8 15.2 1.0
CA A:ALA42 3.9 14.5 1.0
O A:THR43 4.2 16.9 1.0
N A:ALA42 4.3 13.0 1.0
C A:THR43 4.5 16.0 1.0
O A:ALA42 4.6 12.9 1.0

Reference:

A.Kita, Y.Morimoto. An Effective Deuterium Exchange Method For Neutron Crystal Structure Analysis with Unfolding-Refolding Processes Mol Biotechnol. V. 58 130 2016.
ISSN: ESSN 1559-0305
PubMed: 26718545
DOI: 10.1007/S12033-015-9908-8
Page generated: Mon Oct 7 19:58:30 2024

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