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Chlorine 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:

Sodium (Na) 5 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 12 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 2hu3

Go back to Chlorine Binding Sites List in 2hu3
Chlorine binding site 1 out of 12 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 Chlorine with other atoms in the Cl 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:Cl5001

b:10.8
occ:1.00
 OH A:TYR23 3.0 8.7 1.0
O A:HOH9172 3.6 29.7 0.5
CE2 A:TYR23 3.7 6.7 1.0
CZ A:TYR23 3.7 7.6 1.0
CA A:GLY104 4.1 8.7 1.0
O A:ARG21 4.6 10.4 1.0
N A:GLY104 4.7 8.7 1.0
CD2 A:TYR23 4.9 7.5 1.0
CE1 A:TYR23 4.9 7.1 1.0

Chlorine binding site 2 out of 12 in 2hu3

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Chlorine binding site 2 out of 12 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 Chlorine with other atoms in the Cl 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:Cl5002

b:13.7
occ:1.00
 O A:HOH9101 3.1 24.1 1.0
CL A:CL5006 3.1 19.7 1.0
N A:THR69 3.2 10.2 1.0
O A:THR69 3.3 12.6 1.0
CL A:CL5012 3.3 39.2 1.0
N A:ARG68 3.5 10.5 1.0
C A:GLY67 3.5 10.1 1.0
O A:HOH9037 3.6 30.1 1.0
CA A:GLY67 3.6 10.3 1.0
C A:THR69 3.6 10.0 1.0
OG A:SER72 3.6 15.1 1.0
N A:GLY67 3.7 9.5 1.0
OD1 A:ASN65 3.7 11.8 1.0
CA A:THR69 3.8 9.8 1.0
O A:HOH9028 4.0 13.6 1.0
O A:GLY67 4.1 13.6 1.0
CB A:THR69 4.2 9.8 1.0
C A:ARG68 4.2 11.8 1.0
OD1 A:ASP66 4.2 8.2 1.0
CA A:ARG68 4.2 12.2 0.5
CA A:ARG68 4.3 9.7 0.5
N A:PRO70 4.5 10.7 1.0
NA A:NA9002 4.7 11.7 1.0
C A:ASP66 4.8 8.2 1.0
O A:HOH9064 4.8 17.2 0.5
OG1 A:THR69 4.8 10.1 1.0
CB A:SER72 4.9 14.7 1.0
N A:ASP66 4.9 8.4 1.0
CG A:ASN65 5.0 11.2 1.0
O A:HOH9106 5.0 28.0 1.0

Chlorine binding site 3 out of 12 in 2hu3

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Chlorine binding site 3 out of 12 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 Chlorine with other atoms in the Cl 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:Cl5003

b:15.0
occ:1.00
 O A:HOH9069 2.9 33.5 1.0
OG A:SER24 3.1 13.6 1.0
N A:GLY26 3.2 8.4 1.0
CB A:SER24 3.5 12.0 1.0
CA A:GLY26 3.5 7.9 1.0
CA A:GLN121 3.6 12.5 1.0
CD1 A:ILE124 3.7 23.0 1.0
CB A:GLN121 3.9 18.1 1.0
N A:GLN121 3.9 12.2 1.0
CG1 A:ILE124 4.0 18.4 1.0
CG A:GLN121 4.1 20.7 1.0
C A:VAL120 4.2 11.4 1.0
N A:LEU25 4.3 9.8 1.0
O A:VAL120 4.3 10.4 1.0
CG2 A:VAL120 4.3 13.6 1.0
C A:LEU25 4.4 9.0 1.0
C A:SER24 4.4 9.0 1.0
C A:GLY26 4.5 7.3 1.0
CA A:SER24 4.6 8.9 1.0
N A:ASN27 4.6 7.3 1.0
CA A:LEU25 4.8 8.5 1.0
C A:GLN121 4.9 11.6 1.0
O A:SER24 4.9 9.7 1.0

Chlorine binding site 4 out of 12 in 2hu3

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Chlorine binding site 4 out of 12 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 Chlorine with other atoms in the Cl 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:Cl5004

b:28.9
occ:1.00
 NH1 A:ARG68 2.7 10.4 0.5
NH2 A:ARG68 3.0 12.3 0.5
CD A:ARG68 3.6 14.6 0.5
CD A:ARG68 3.8 6.7 0.5
CZ A:ARG68 3.8 8.7 0.5
CZ A:ARG68 4.1 9.6 0.5
NE A:ARG68 4.1 7.5 0.5
NE A:ARG68 4.3 8.2 0.5
NH1 A:ARG45 4.7 14.3 0.5
CG A:ARG68 4.9 10.5 0.5
CG A:ARG68 4.9 8.1 0.5
NH2 A:ARG68 4.9 8.6 0.5

Chlorine binding site 5 out of 12 in 2hu3

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Chlorine binding site 5 out of 12 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 Chlorine with other atoms in the Cl 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:Cl5005

b:20.1
occ:1.00
 O A:HOH9152 3.1 32.7 1.0
NZ A:LYS33 3.3 11.6 0.5
CE A:LYS33 3.7 10.2 0.5
CE2 A:PHE38 3.7 10.2 1.0
CZ3 A:TRP123 3.9 12.3 1.0
NZ A:LYS33 4.0 16.2 0.5
CD A:LYS33 4.0 7.7 0.5
CD A:ARG5 4.1 13.8 1.0
O A:HOH9097 4.3 25.8 1.0
CB A:ARG5 4.3 16.5 1.0
O A:HOH9150 4.3 30.6 1.0
CD A:LYS33 4.4 9.6 0.5
CZ A:PHE38 4.4 9.8 1.0
CE A:LYS33 4.5 10.9 0.5
C2 A:EDO1006 4.5 29.5 1.0
CG A:ARG5 4.7 15.9 1.0
CD2 A:PHE38 4.7 9.2 1.0
CE3 A:TRP123 4.7 10.4 1.0
NE A:ARG5 4.8 15.3 1.0
CH2 A:TRP123 4.8 13.7 1.0

Chlorine binding site 6 out of 12 in 2hu3

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Chlorine binding site 6 out of 12 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl5006

b:19.7
occ:1.00
 NA A:NA9002 2.5 11.7 1.0
OD1 A:ASP66 2.8 8.2 1.0
N A:ASP66 2.9 8.4 1.0
O A:HOH9028 3.1 13.6 1.0
CL A:CL5002 3.1 13.7 1.0
OG A:SER72 3.2 15.1 1.0
O A:CYS64 3.4 9.4 1.0
OD1 A:ASN65 3.5 11.8 1.0
CA A:ASN65 3.5 9.2 1.0
CB A:THR69 3.6 9.8 1.0
O A:SER60 3.6 11.3 1.0
CG A:ASP66 3.6 7.2 1.0
OG1 A:THR69 3.7 10.1 1.0
C A:ASN65 3.7 7.6 1.0
N A:GLY67 3.8 9.5 1.0
CA A:ASP66 3.8 8.5 1.0
CB A:SER60 3.9 9.1 1.0
N A:THR69 4.2 10.2 1.0
C A:ASP66 4.2 8.2 1.0
CB A:ASP66 4.2 7.4 1.0
C A:CYS64 4.3 8.0 1.0
CG A:ASN65 4.3 11.2 1.0
CB A:SER72 4.4 14.7 1.0
N A:ASN65 4.4 8.8 1.0
CA A:THR69 4.4 9.8 1.0
CB A:ASN65 4.5 9.6 1.0
OD2 A:ASP66 4.5 7.7 1.0
C A:SER60 4.5 9.6 1.0
OG A:SER60 4.5 9.3 1.0
O A:THR69 4.5 12.6 1.0
N A:ARG68 4.6 10.5 1.0
CA A:SER60 4.6 8.7 1.0
CA A:GLY67 4.8 10.3 1.0
CG2 A:THR69 4.8 11.0 1.0
O A:ARG73 4.8 13.0 1.0
O A:ASN65 4.9 8.0 1.0
SG A:CYS80 4.9 7.8 1.0
C A:THR69 4.9 10.0 1.0
O A:HOH9101 5.0 24.1 1.0

Chlorine binding site 7 out of 12 in 2hu3

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Chlorine binding site 7 out of 12 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl5007

b:20.7
occ:1.00
 O A:HOH9043 3.1 20.2 1.0
ND2 A:ASN65 3.3 14.1 1.0
CB A:PRO79 3.7 10.4 1.0
CA A:PRO79 3.7 10.3 1.0
CB A:ASN65 3.8 9.6 1.0
N A:PRO79 3.9 9.6 1.0
CG A:ASN65 4.0 11.2 1.0
CD A:PRO79 4.3 11.7 1.0
O A:ASN65 4.3 8.0 1.0
CG A:PRO79 4.4 15.3 1.0
C A:ILE78 4.5 10.2 1.0
O A:ILE78 4.7 10.2 1.0
ND2 A:ASN74 4.8 14.1 1.0
C A:ASN65 4.9 7.6 1.0
CA A:ASN65 4.9 9.2 1.0

Chlorine binding site 8 out of 12 in 2hu3

Go back to Chlorine Binding Sites List in 2hu3
Chlorine binding site 8 out of 12 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl5008

b:21.9
occ:1.00
 O A:HOH9155 3.0 36.6 1.0
N A:ILE88 3.3 10.7 1.0
O A:HOH9193 3.3 19.7 1.0
O A:HOH9072 3.6 26.3 1.0
CG1 A:ILE88 3.7 12.1 1.0
CA A:ASP87 3.8 11.9 1.0
CE1 A:HIS15 3.8 17.4 1.0
C A:ASP87 4.0 10.5 1.0
O A:SER86 4.1 15.0 1.0
CB A:ALA11 4.1 11.6 1.0
OD1 A:ASP87 4.1 16.5 1.0
CB A:ILE88 4.2 10.6 1.0
CA A:ILE88 4.3 9.4 1.0
CG2 A:ILE88 4.3 13.0 1.0
CZ A:PHE3 4.3 12.1 1.0
CG A:ASP87 4.4 18.1 1.0
O A:HOH9123 4.6 30.6 1.0
CD1 A:ILE88 4.6 13.3 1.0
NE2 A:HIS15 4.6 23.7 1.0
ND1 A:HIS15 4.6 18.2 1.0
CB A:ASP87 4.6 14.8 1.0
CE2 A:PHE3 4.8 11.1 1.0
N A:ASP87 4.8 11.1 1.0
C A:SER86 4.9 12.6 1.0
N A:THR89 5.0 9.3 1.0

Chlorine binding site 9 out of 12 in 2hu3

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Chlorine binding site 9 out of 12 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl5009

b:20.6
occ:1.00
 NE A:ARG114 2.9 8.7 1.0
O A:HOH9045 2.9 10.3 0.8
NH2 A:ARG114 3.5 10.1 1.0
CZ A:ARG114 3.6 9.2 1.0
CB A:ARG114 3.7 8.4 1.0
CG A:ARG114 3.8 9.5 1.0
CD A:ARG114 3.9 9.4 1.0
CZ A:PHE34 4.0 11.0 1.0
CE1 A:PHE34 4.2 9.8 1.0
CE2 A:PHE34 4.3 12.3 1.0
CA A:ARG114 4.4 8.2 1.0
O A:HOH9231 4.4 10.1 0.2
O A:ARG114 4.4 10.1 1.0
CD1 A:PHE34 4.8 8.2 1.0
CD2 A:PHE34 4.9 10.1 1.0
NH1 A:ARG114 4.9 9.4 1.0
C A:ARG114 4.9 7.9 1.0
O A:HOH9095 4.9 18.5 1.0

Chlorine binding site 10 out of 12 in 2hu3

Go back to Chlorine Binding Sites List in 2hu3
Chlorine binding site 10 out of 12 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl5010

b:26.3
occ:1.00
 O A:HOH9206 3.0 44.0 1.0
O A:HOH9151 3.1 35.5 1.0
N A:ASN74 3.2 13.1 1.0
NE A:ARG73 3.2 17.5 1.0
O A:HOH9103 3.7 34.7 1.0
O A:HOH9180 3.8 36.8 1.0
C A:ASN74 3.8 13.1 1.0
CB A:ARG73 3.8 13.3 1.0
O A:ASN74 3.8 13.5 1.0
CD A:ARG73 3.9 17.6 1.0
CA A:ARG73 3.9 14.2 1.0
CA A:ASN74 3.9 12.2 1.0
O A:HOH9191 4.0 46.4 1.0
C A:ARG73 4.0 12.8 1.0
CZ A:ARG73 4.2 15.4 1.0
CD2 A:LEU75 4.2 19.6 1.0
CB A:ASN74 4.2 11.7 1.0
NH2 A:ARG73 4.2 21.1 1.0
N A:LEU75 4.3 11.7 1.0
CG A:ARG73 4.4 14.4 1.0
CA A:LEU75 4.7 12.8 1.0
CG A:LEU75 4.9 14.9 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: Sat Jul 20 07:56:32 2024

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