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Sodium in PDB 5b07: Lysozyme (Denatured By Dcl and Refolded)

Enzymatic activity of Lysozyme (Denatured By Dcl and Refolded)

All present enzymatic activity of Lysozyme (Denatured By Dcl and Refolded):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme (Denatured By Dcl and Refolded), PDB code: 5b07 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 5b07:

The structure of Lysozyme (Denatured By Dcl and Refolded) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme (Denatured By Dcl and Refolded) (pdb code 5b07). 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 (Denatured By Dcl and Refolded), PDB code: 5b07:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5b07

Go back to Sodium Binding Sites List in 5b07
Sodium binding site 1 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:19.1
occ:1.00
 O A:TYR53 2.8 12.2 1.0
OG A:SER91 3.0 14.7 1.0
N A:LEU56 3.0 13.9 1.0
N A:ILE55 3.4 13.7 1.0
C A:GLY54 3.4 13.7 1.0
N A:GLN57 3.5 12.5 1.0
CA A:GLY54 3.5 12.9 1.0
CA A:LEU56 3.6 14.1 1.0
CB A:SER91 3.6 14.0 1.0
C A:LEU56 3.7 13.7 1.0
CD1 A:ILE58 3.7 16.6 1.0
CB A:LEU56 3.8 14.7 1.0
CG1 A:ILE58 3.8 17.6 1.0
C A:TYR53 3.9 13.3 1.0
N A:ILE58 4.0 13.0 1.0
NA A:NA2006 4.0 28.1 1.0
O A:GLY54 4.0 13.6 1.0
C A:ILE55 4.1 15.5 1.0
CG1 A:ILE55 4.2 19.0 1.0
N A:GLY54 4.2 13.2 1.0
CA A:ILE55 4.2 15.7 1.0
CB A:ILE58 4.3 16.0 1.0
O A:LEU83 4.4 15.4 1.0
CD2 A:LEU83 4.4 17.7 1.0
CB A:LEU83 4.4 15.3 1.0
CA A:GLN57 4.5 12.5 1.0
CA A:SER91 4.5 14.6 1.0
O A:LEU56 4.5 14.1 1.0
CG A:LEU56 4.7 16.5 1.0
C A:GLN57 4.8 12.9 1.0
CA A:ILE58 4.8 14.7 1.0
CB A:ILE55 4.8 19.7 1.0
CG A:LEU83 4.9 15.7 1.0

Sodium binding site 2 out of 8 in 5b07

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Sodium binding site 2 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:28.1
occ:1.00
 O A:HOH2115 2.5 13.2 1.0
O A:LEU83 2.6 15.4 1.0
N A:ILE55 2.9 13.7 1.0
OG A:SER91 3.0 14.7 1.0
CA A:GLY54 3.4 12.9 1.0
CG1 A:ILE55 3.4 19.0 1.0
C A:GLY54 3.6 13.7 1.0
C A:LEU83 3.7 14.7 1.0
O A:THR40 3.8 13.5 1.0
CB A:ILE55 3.8 19.7 1.0
CB A:THR40 3.8 14.8 1.0
CA A:THR40 3.8 12.6 1.0
CB A:SER91 3.9 14.0 1.0
CA A:ILE55 3.9 15.7 1.0
CG2 A:ILE55 3.9 22.4 1.0
NA A:NA2005 4.0 19.1 1.0
CG2 A:THR40 4.1 13.7 1.0
O A:HOH2184 4.3 16.1 1.0
C A:THR40 4.3 12.1 1.0
CD1 A:ILE55 4.5 22.8 1.0
O A:SER85 4.5 15.5 1.0
N A:LEU84 4.6 14.3 1.0
CA A:LEU83 4.6 15.2 1.0
CA A:LEU84 4.6 13.9 1.0
N A:GLY54 4.8 13.2 1.0
O A:GLY54 4.8 13.6 1.0
C A:LEU84 4.9 15.5 1.0
N A:LEU56 5.0 13.9 1.0
CB A:LEU83 5.0 15.3 1.0

Sodium binding site 3 out of 8 in 5b07

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Sodium binding site 3 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:20.7
occ:1.00
 O A:HOH2129 3.0 15.7 1.0
O A:HOH2187 3.5 20.7 1.0
CG2 A:VAL2 3.7 16.4 1.0
N A:VAL2 4.2 15.8 1.0
O A:HOH2227 4.3 47.4 1.0
CA A:LYS1 4.5 16.5 1.0
CB A:VAL2 4.5 15.6 1.0
C A:LYS1 4.6 16.2 1.0
N A:LYS1 4.6 16.4 1.0
NE2 A:GLN41 4.8 16.0 1.0
CA A:VAL2 5.0 15.6 1.0

Sodium binding site 4 out of 8 in 5b07

Go back to Sodium Binding Sites List in 5b07
Sodium binding site 4 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:23.6
occ:1.00
 OG1 A:THR51 2.7 13.1 1.0
OD2 A:ASP66 2.8 13.4 1.0
NE A:ARG68 2.9 26.3 1.0
O A:GLY49 2.9 23.8 1.0
OG1 A:THR69 3.1 15.3 1.0
N A:THR51 3.4 12.5 1.0
CB A:THR51 3.5 11.9 1.0
C A:SER50 3.5 14.2 1.0
CG A:ARG68 3.5 19.4 1.0
CD A:ARG68 3.6 23.1 1.0
CG A:ASP66 3.7 13.3 1.0
NE A:ARG45 3.7 41.5 1.0
CA A:SER50 3.8 15.6 1.0
O A:ARG68 3.8 20.0 1.0
OG A:SER60 3.8 12.9 1.0
CZ A:ARG68 3.8 32.0 1.0
OD1 A:ASP66 3.8 13.2 1.0
NH2 A:ARG68 3.9 23.3 1.0
NH2 A:ARG45 4.0 28.7 1.0
C A:GLY49 4.0 20.0 1.0
CA A:THR51 4.1 12.4 1.0
CZ A:ARG45 4.1 36.9 1.0
O A:SER50 4.1 15.3 1.0
C A:ARG68 4.2 17.1 1.0
N A:SER50 4.4 15.6 1.0
CB A:THR69 4.4 17.1 1.0
OH A:TYR53 4.4 13.5 1.0
CD A:ARG45 4.5 27.2 1.0
CB A:ARG68 4.6 18.5 1.0
N A:THR69 4.6 15.7 1.0
CA A:THR69 4.7 15.8 1.0
CB A:SER60 4.8 14.4 1.0
CG2 A:THR51 4.8 13.0 1.0
CG2 A:THR69 4.9 17.1 1.0
CA A:ARG68 5.0 16.6 1.0
CB A:ASP66 5.0 13.9 1.0

Sodium binding site 5 out of 8 in 5b07

Go back to Sodium Binding Sites List in 5b07
Sodium binding site 5 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:22.5
occ:1.00
 O A:ARG21 2.8 16.0 1.0
CL A:CL2013 3.3 17.5 1.0
CE2 A:TYR23 3.6 12.5 1.0
CA A:GLY22 3.8 15.9 1.0
CZ A:TYR23 3.9 13.6 1.0
C A:ARG21 3.9 16.2 1.0
C A:GLY22 3.9 15.8 1.0
O A:GLY22 4.0 16.5 1.0
CD2 A:TYR23 4.0 12.0 1.0
OH A:TYR23 4.3 14.2 1.0
N A:GLY22 4.3 16.9 1.0
CE1 A:TYR23 4.4 13.4 1.0
N A:TYR23 4.5 12.9 1.0
CG A:TYR23 4.6 12.0 1.0
CD1 A:TYR23 4.8 13.3 1.0

Sodium binding site 6 out of 8 in 5b07

Go back to Sodium Binding Sites List in 5b07
Sodium binding site 6 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:26.9
occ:1.00
 O A:HOH2152 2.8 29.1 1.0
ND2 A:ASN44 3.4 26.2 1.0
CB A:ALA42 3.5 13.4 1.0
CA A:ALA42 4.0 13.9 1.0
CG A:ASN44 4.3 25.9 1.0
OD1 A:ASN44 4.3 22.8 1.0
O A:THR43 4.4 18.2 1.0
N A:THR43 4.5 13.8 1.0
C A:ALA42 4.7 13.7 1.0
O A:GLU35 4.9 11.8 1.0
O A:SER36 4.9 13.0 1.0

Sodium binding site 7 out of 8 in 5b07

Go back to Sodium Binding Sites List in 5b07
Sodium binding site 7 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:25.3
occ:1.00
 O A:HOH2101 2.5 8.3 1.0
O A:HOH2209 2.6 39.1 1.0
OD1 A:ASN65 2.9 17.9 1.0
O A:HOH2146 3.1 12.6 1.0
OG A:SER72 3.4 18.6 1.0
CA A:ASN65 3.4 14.5 1.0
O A:ARG73 3.4 19.6 1.0
CB A:ASN65 3.5 14.9 1.0
CG A:ASN65 3.6 17.4 1.0
O A:CYS64 3.7 14.8 1.0
CB A:ASN74 3.8 17.7 1.0
C A:ARG73 3.8 18.5 1.0
O A:HOH2208 4.0 28.1 1.0
CL A:CL2014 4.0 18.2 1.0
N A:ASN65 4.1 14.5 1.0
N A:ASN74 4.2 17.7 1.0
C A:CYS64 4.2 12.5 1.0
O A:SER72 4.3 22.5 1.0
CA A:ASN74 4.3 17.2 1.0
O A:HOH2203 4.3 19.0 1.0
O A:HOH2124 4.4 28.6 1.0
C A:SER72 4.5 22.2 1.0
CA A:ARG73 4.5 18.7 1.0
C A:ASN65 4.6 12.0 1.0
CB A:SER72 4.6 17.0 1.0
N A:ASP66 4.6 13.1 1.0
N A:ARG73 4.6 18.2 1.0
CG A:ASN74 4.7 17.1 1.0
O A:SER60 4.7 16.4 1.0
ND2 A:ASN65 4.9 18.2 1.0

Sodium binding site 8 out of 8 in 5b07

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Sodium binding site 8 out of 8 in the Lysozyme (Denatured By Dcl and Refolded)


Mono view


Stereo pair view

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

b:21.6
occ:1.00
 O A:GLN41 2.7 15.3 1.0
OG1 A:THR43 2.8 16.5 1.0
N A:THR43 3.2 13.8 1.0
CB A:THR43 3.5 15.2 1.0
CG2 A:THR43 3.5 15.6 1.0
C A:ALA42 3.8 13.7 1.0
C A:GLN41 3.8 13.7 1.0
CA A:THR43 3.8 15.6 1.0
CA A:ALA42 4.0 13.9 1.0
O A:THR43 4.3 18.2 1.0
N A:ALA42 4.4 12.5 1.0
C A:THR43 4.5 16.6 1.0
O A:ALA42 4.6 11.7 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 19:58:52 2024

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