Chlorine in PDB 8rny: Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]

Enzymatic activity of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]

All present enzymatic activity of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)], PDB code: 8rny was solved by M.Oszajca, M.Flejszar, A.Szura, P.Drozdz, M.Brindell, K.Kurpiewska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.13 / 1.02
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.883, 78.883, 37.026, 90, 90, 90
R / Rfree (%) 12.9 / 14.4

Other elements in 8rny:

The structure of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] (pdb code 8rny). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)], PDB code: 8rny:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8rny

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Chlorine binding site 1 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:13.8
occ:1.00
 OH A:TYR23 3.1 11.9 1.0
O A:HOH354 3.2 14.2 1.0
CE2 A:TYR23 3.7 10.4 1.0
CZ A:TYR23 3.7 10.7 1.0
C2 A:EDO202 4.0 27.0 0.8
CA A:GLY104 4.1 11.2 1.0
O A:ARG21 4.6 13.8 1.0
N A:GLY104 4.7 11.5 1.0
C1 A:EDO202 4.8 36.9 0.8
CD2 A:TYR23 4.9 10.9 1.0
CE1 A:TYR23 4.9 10.7 1.0

Chlorine binding site 2 out of 8 in 8rny

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Chlorine binding site 2 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:18.6
occ:1.00
 O A:HOH420 3.0 40.6 1.0
OG A:SER24 3.0 17.1 1.0
N A:GLY26 3.1 11.5 1.0
CB A:SER24 3.5 14.4 1.0
CA A:GLY26 3.5 11.6 1.0
CA A:GLN121 3.6 17.6 1.0
CD1 A:ILE124 3.7 22.6 1.0
CB A:GLN121 4.0 22.9 1.0
N A:GLN121 4.0 15.4 1.0
CG A:GLN121 4.1 29.2 1.0
CG1 A:ILE124 4.2 18.9 1.0
N A:LEU25 4.2 12.5 1.0
C A:VAL120 4.3 13.9 1.0
O A:VAL120 4.3 14.3 1.0
CG2 A:VAL120 4.3 15.6 1.0
C A:LEU25 4.3 11.5 1.0
C A:SER24 4.3 12.5 1.0
C A:GLY26 4.6 10.6 1.0
CA A:SER24 4.6 12.8 1.0
N A:ASN27 4.7 10.6 1.0
CA A:LEU25 4.7 12.4 1.0
O A:SER24 4.8 12.6 1.0
C A:GLN121 4.8 15.4 1.0

Chlorine binding site 3 out of 8 in 8rny

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Chlorine binding site 3 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:14.8
occ:1.00
 O A:HOH361 3.2 12.3 1.0
O A:HOH410 3.2 26.8 1.0
N A:THR69 3.3 12.1 1.0
O A:THR69 3.3 14.0 1.0
N A:ARG68 3.5 12.0 0.5
C A:GLY67 3.5 13.0 1.0
N A:ARG68 3.5 12.3 0.5
O A:HOH371 3.6 31.7 1.0
CA A:GLY67 3.6 13.2 1.0
OG A:SER72 3.6 15.7 1.0
N A:GLY67 3.7 11.8 1.0
C A:THR69 3.7 12.8 1.0
OD1 A:ASN65 3.7 13.7 1.0
CA A:THR69 3.9 12.2 1.0
O A:HOH385 4.0 15.3 1.0
O A:GLY67 4.2 15.5 1.0
C A:ARG68 4.2 13.6 0.5
CB A:THR69 4.3 12.1 1.0
OD1 A:ASP66 4.3 10.6 1.0
C A:ARG68 4.3 12.3 0.5
CA A:ARG68 4.3 14.2 0.5
CA A:ARG68 4.4 12.1 0.5
N A:PRO70 4.6 13.0 1.0
NA A:NA211 4.7 12.6 1.0
C A:ASP66 4.7 11.1 1.0
OG1 A:THR69 4.9 12.2 1.0
CB A:SER72 4.9 15.6 1.0
O A:HOH364 4.9 24.8 0.6
N A:ASP66 4.9 10.6 1.0
CG A:ASN65 4.9 13.5 1.0

Chlorine binding site 4 out of 8 in 8rny

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Chlorine binding site 4 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:31.9
occ:1.00
 O A:HOH322 3.1 43.2 1.0
N A:ASN74 3.2 15.9 1.0
NE A:ARG73 3.2 22.7 1.0
C A:ASN74 3.8 15.3 1.0
O A:ASN74 3.8 16.2 1.0
CB A:ARG73 3.8 17.1 1.0
CA A:ASN74 3.9 14.7 1.0
O A:HOH403 3.9 48.2 1.0
CA A:ARG73 3.9 16.2 1.0
CD A:ARG73 4.0 21.2 1.0
C A:ARG73 4.1 15.1 1.0
NH2 A:ARG73 4.1 22.9 1.0
O A:HOH307 4.1 46.8 1.0
CZ A:ARG73 4.2 21.6 1.0
CD2 A:LEU75 4.2 20.4 1.0
N A:LEU75 4.3 15.3 1.0
CB A:ASN74 4.3 14.5 1.0
CG A:ARG73 4.5 19.6 1.0
CA A:LEU75 4.7 16.3 1.0
CG A:LEU75 4.9 18.6 1.0
O A:HOH406 4.9 35.8 1.0

Chlorine binding site 5 out of 8 in 8rny

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Chlorine binding site 5 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:25.5
occ:1.00
 NA A:NA213 2.8 64.0 1.0
O A:HOH373 2.9 54.5 1.0
O A:HOH390 3.4 34.7 1.0
N A:ILE88 3.4 13.2 1.0
O A:HOH343 3.5 28.2 1.0
CG1 A:ILE88 3.7 13.9 1.0
CA A:ASP87 3.9 14.8 1.0
CE1 A:HIS15 3.9 24.0 1.0
O A:SER86 4.0 16.7 1.0
C A:ASP87 4.1 13.8 1.0
OD1 A:ASP87 4.2 20.5 1.0
CB A:ALA11 4.2 14.5 1.0
CZ A:PHE3 4.3 14.9 1.0
CB A:ILE88 4.3 13.2 1.0
CG2 A:ILE88 4.3 14.2 1.0
CA A:ILE88 4.3 12.2 1.0
CG A:ASP87 4.6 21.5 1.0
CD1 A:ILE88 4.6 15.3 1.0
ND1 A:HIS15 4.7 22.2 1.0
CE2 A:PHE3 4.7 14.2 1.0
CB A:ASP87 4.8 17.8 1.0
NE2 A:HIS15 4.8 26.0 1.0
N A:ASP87 4.9 14.1 1.0
C A:SER86 4.9 14.4 1.0

Chlorine binding site 6 out of 8 in 8rny

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Chlorine binding site 6 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:31.5
occ:1.00
 NZ A:LYS33 3.7 22.7 1.0
CE2 A:PHE38 3.7 12.8 1.0
CZ3 A:TRP123 4.0 19.4 1.0
O A:HOH362 4.1 46.5 1.0
CE A:LYS33 4.1 20.3 1.0
O A:HOH395 4.1 44.3 1.0
CD A:LYS33 4.2 16.5 1.0
CD A:ARG5 4.3 18.2 1.0
CB A:ARG5 4.4 16.9 1.0
CZ A:PHE38 4.4 12.1 1.0
CD2 A:PHE38 4.6 11.8 1.0
CG A:ARG5 4.7 17.4 1.0
CE3 A:TRP123 4.8 17.1 1.0
CH2 A:TRP123 4.9 19.6 1.0
NE A:ARG5 4.9 19.5 1.0

Chlorine binding site 7 out of 8 in 8rny

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Chlorine binding site 7 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:21.4
occ:1.00
 O A:HOH412 3.0 21.5 1.0
O A:HOH431 3.1 43.2 1.0
ND2 A:ASN65 3.3 15.2 1.0
CB A:PRO79 3.7 12.5 1.0
CA A:PRO79 3.7 12.0 1.0
CB A:ASN65 3.9 13.3 1.0
N A:PRO79 3.9 12.7 1.0
CG A:ASN65 4.1 13.5 1.0
CD A:PRO79 4.3 15.5 1.0
O A:ASN65 4.3 11.3 1.0
CG A:PRO79 4.4 16.5 1.0
C A:ILE78 4.5 13.1 1.0
O A:ILE78 4.6 13.2 1.0
ND2 A:ASN74 4.9 16.2 1.0
C A:ASN65 4.9 10.4 1.0
CA A:ASN65 5.0 11.3 1.0

Chlorine binding site 8 out of 8 in 8rny

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Chlorine binding site 8 out of 8 in the Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Hen Egg White Lysozyme Soaked with with [H2IND][Trans-RUCL4(Dmso) (Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:34.6
occ:1.00
 ND2 A:ASN74 3.2 16.2 1.0
CB A:ASN74 3.8 14.5 1.0
CB A:ASN65 3.8 13.3 1.0
CG A:ASN65 4.0 13.5 1.0
O A:HOH406 4.0 35.8 1.0
CG A:ASN74 4.0 14.5 1.0
OD1 A:ASN65 4.3 13.7 1.0
O A:HOH307 4.4 46.8 1.0
O A:HOH385 4.4 15.3 1.0
ND2 A:ASN65 4.5 15.2 1.0
O A:HOH412 4.8 21.5 1.0
O A:HOH371 5.0 31.7 1.0

Reference:

M.Oszajca, M.Flejszar, A.Szura, P.Drozdz, M.Brindell, K.Kurpiewska. Exploring the Coordination Chemistry of Ruthenium Complexes with Lysozymes: Structural and in Solution Studies To Be Published.
Page generated: Tue Jul 30 12:16:00 2024

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