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Sodium in PDB 2hu3: Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme

Enzymatic activity of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme

All present enzymatic activity of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme, PDB code: 2hu3 was solved by F.Frolow, S.Lagziel-Simis, N.Cohen-Hadar, Y.Wine, A.Freeman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.73 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.870, 78.870, 36.788, 90.00, 90.00, 90.00
R / Rfree (%) 10.3 / 14.5

Other elements in 2hu3:

The structure of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme (pdb code 2hu3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme, PDB code: 2hu3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2hu3

Go back to Sodium Binding Sites List in 2hu3
Sodium binding site 1 out of 5 in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9001

b:14.2
occ:1.00
 OG1 A:THR51 2.7 8.7 1.0
OD2 A:ASP66 2.7 7.7 1.0
NE A:ARG68 2.8 8.2 0.5
O A:GLY49 2.9 17.5 1.0
NE A:ARG68 3.0 7.5 0.5
OG1 A:THR69 3.1 10.1 1.0
N A:THR51 3.4 7.6 1.0
CB A:THR51 3.5 6.6 1.0
CD A:ARG68 3.5 6.7 0.5
C A:SER50 3.5 10.2 1.0
CG A:ARG68 3.5 8.1 0.5
CG A:ARG68 3.6 10.5 0.5
CG A:ASP66 3.6 7.2 1.0
CA A:SER50 3.7 10.5 1.0
NE A:ARG45 3.7 15.5 0.5
OG A:SER60 3.8 9.3 1.0
OD1 A:ASP66 3.8 8.2 1.0
CZ A:ARG68 3.8 9.6 0.5
CD A:ARG68 3.8 14.6 0.5
CZ A:ARG68 3.9 8.7 0.5
NH2 A:ARG68 3.9 8.6 0.5
NH1 A:ARG68 3.9 10.7 0.5
O A:ARG68 3.9 15.3 1.0
C A:GLY49 4.0 15.8 1.0
CA A:THR51 4.0 6.9 1.0
NE A:ARG45 4.1 13.7 0.5
O A:SER50 4.1 10.8 1.0
CZ A:ARG45 4.1 12.6 0.5
NH2 A:ARG45 4.2 17.0 0.5
NH2 A:ARG45 4.2 13.4 0.5
C A:ARG68 4.3 11.8 1.0
OH A:TYR53 4.3 7.2 1.0
N A:SER50 4.3 12.6 1.0
CB A:THR69 4.3 9.8 1.0
CD A:ARG45 4.4 15.8 0.5
CZ A:ARG45 4.5 13.1 0.5
CB A:ARG68 4.6 9.9 0.5
N A:THR69 4.6 10.2 1.0
CB A:SER60 4.7 9.1 1.0
CB A:ARG68 4.7 10.6 0.5
CA A:THR69 4.7 9.8 1.0
CG2 A:THR51 4.8 8.1 1.0
CG2 A:THR69 4.9 11.0 1.0
CD A:ARG45 4.9 10.2 0.5
CB A:ASP66 4.9 7.4 1.0
CA A:ARG68 4.9 9.7 0.5
CB A:SER50 5.0 13.3 1.0

Sodium binding site 2 out of 5 in 2hu3

Go back to Sodium Binding Sites List in 2hu3
Sodium binding site 2 out of 5 in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9002

b:11.7
occ:1.00
 O A:SER60 2.3 11.3 1.0
O A:HOH9028 2.4 13.6 1.0
O A:CYS64 2.4 9.4 1.0
O A:ARG73 2.4 13.0 1.0
CL A:CL5006 2.5 19.7 1.0
OG A:SER72 2.5 15.1 1.0
CB A:SER72 3.3 14.7 1.0
C A:SER60 3.5 9.6 1.0
C A:ARG73 3.5 12.8 1.0
C A:CYS64 3.5 8.0 1.0
N A:ARG73 3.9 15.9 1.0
CA A:ASN65 3.9 9.2 1.0
CA A:SER60 4.1 8.7 1.0
N A:ASN65 4.2 8.8 1.0
C A:SER72 4.2 14.6 1.0
CB A:SER60 4.2 9.1 1.0
CA A:ARG73 4.3 14.2 1.0
CA A:SER72 4.3 14.3 1.0
N A:ASN74 4.4 13.1 1.0
O A:HOH9106 4.5 28.0 1.0
N A:CYS64 4.5 8.7 1.0
O A:ARG61 4.5 16.2 1.0
N A:ARG61 4.5 10.7 1.0
C A:ARG61 4.6 13.4 1.0
CA A:ASN74 4.6 12.2 1.0
OD1 A:ASN65 4.6 11.8 1.0
N A:ASP66 4.6 8.4 1.0
CA A:CYS64 4.7 8.2 1.0
CB A:THR69 4.7 9.8 1.0
CL A:CL5002 4.7 13.7 1.0
CB A:ASN74 4.8 11.7 1.0
CA A:ARG61 4.8 12.6 1.0
C A:ASN65 4.8 7.6 1.0
O A:SER72 4.8 21.0 1.0
CB A:ASN65 4.8 9.6 1.0
N A:TRP62 4.9 10.2 1.0

Sodium binding site 3 out of 5 in 2hu3

Go back to Sodium Binding Sites List in 2hu3
Sodium binding site 3 out of 5 in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9003

b:18.4
occ:1.00
 O A:HOH9201 2.9 28.3 1.0
O A:HOH9223 2.9 9.7 1.0
O A:HOH9134 3.4 36.8 1.0
O A:HOH9013 3.5 24.9 1.0
CG2 A:VAL2 3.7 10.9 1.0
N A:VAL2 4.1 10.1 1.0
O A:HOH9125 4.2 33.6 1.0
CA A:LYS1 4.4 11.4 0.5
CA A:LYS1 4.5 11.3 0.5
C A:LYS1 4.5 9.8 1.0
CB A:VAL2 4.6 10.5 1.0
N A:LYS1 4.6 10.8 1.0
NE2 A:GLN41 4.8 8.4 1.0
CA A:VAL2 5.0 9.1 1.0

Sodium binding site 4 out of 5 in 2hu3

Go back to Sodium Binding Sites List in 2hu3
Sodium binding site 4 out of 5 in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9004

b:14.7
occ:1.00
 OH A:TYR53 2.8 7.2 1.0
NH2 A:ARG68 3.0 8.6 0.5
CZ A:ARG68 3.1 8.7 0.5
NE A:ARG68 3.5 7.5 0.5
NH1 A:ARG68 3.5 10.4 0.5
NH2 A:ARG45 3.7 13.4 0.5
CZ A:TYR53 3.8 6.7 1.0
CD A:ARG68 3.9 6.7 0.5
CE2 A:TYR53 3.9 7.5 1.0
CD A:ARG68 4.3 14.6 0.5
OG1 A:THR51 4.4 8.7 1.0
CG2 A:THR51 4.4 8.1 1.0
OD2 A:ASP66 4.4 7.7 1.0
CG A:ARG68 4.6 10.5 0.5
CB A:THR51 4.6 6.6 1.0
NE A:ARG68 4.7 8.2 0.5
CB A:ASP66 4.8 7.4 1.0
CG A:ARG68 5.0 8.1 0.5
CG A:ASP66 5.0 7.2 1.0
CE1 A:TYR53 5.0 7.7 1.0

Sodium binding site 5 out of 5 in 2hu3

Go back to Sodium Binding Sites List in 2hu3
Sodium binding site 5 out of 5 in the Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Parent Structure of Hen Egg White Lysozyme Grown in Acidic pH 4.8. Refinement For Comparison with Crosslinked Molecules of Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na9005

b:18.2
occ:1.00
 O A:HOH9006 2.8 11.1 1.0
O A:ASP87 3.0 11.1 1.0
O A:ALA82 3.0 11.4 1.0
N A:SER91 3.1 8.1 1.0
OG A:SER91 3.5 8.7 1.0
O A:HOH9009 3.5 13.9 1.0
N A:ALA90 3.6 9.5 1.0
CA A:ILE88 3.7 9.4 1.0
C A:ILE88 3.7 8.5 1.0
CB A:ALA90 3.7 11.6 1.0
CB A:SER91 3.7 9.6 1.0
O A:ILE88 3.8 9.1 1.0
CA A:LEU83 3.9 10.0 1.0
CA A:ALA90 3.9 10.3 1.0
C A:ALA90 3.9 8.7 1.0
CA A:SER91 4.0 9.1 1.0
C A:ASP87 4.0 10.5 1.0
C A:LEU83 4.1 9.0 1.0
C A:ALA82 4.1 10.5 1.0
N A:THR89 4.2 9.3 1.0
O A:LEU83 4.2 11.1 1.0
O A:HOH9015 4.2 7.2 0.5
CB A:SER85 4.2 13.3 1.0
O A:HOH9068 4.3 17.2 1.0
N A:ILE88 4.3 10.7 1.0
O A:SER85 4.4 11.1 1.0
N A:LEU83 4.4 9.2 1.0
N A:SER85 4.4 10.2 1.0
C A:THR89 4.5 10.5 1.0
O A:HOH9229 4.5 16.8 0.5
N A:LEU84 4.7 9.9 1.0
CB A:ILE88 4.8 10.6 1.0
CA A:SER85 4.8 10.9 1.0
CD2 A:LEU83 4.8 17.9 1.0
CA A:THR89 4.9 10.6 1.0
CB A:LEU83 5.0 9.8 1.0
C A:SER85 5.0 10.7 1.0

Reference:

S.Lagziel-Simis, Y.Wine, N.Cohen-Hadar, A.Freeman, F.Frolow. Monitoring Influence of pH on the Molecular and Crystal Structure of Hen Egg-White Tetragonal Lysozyme To Be Published.
Page generated: Tue Dec 15 05:50:47 2020

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