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Chlorine in PDB 5yky: Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6

Enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6

All present enzymatic activity of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6, PDB code: 5yky was solved by H.Tabe, H.Takahashi, T.Shimoi, S.Abe, T.Ueno, Y.Yamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.48 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.458, 78.458, 36.647, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23.7

Other elements in 5yky:

The structure of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 (pdb code 5yky). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6, PDB code: 5yky:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5yky

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Chlorine binding site 1 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:34.5
occ:1.00
 OH A:TYR23 3.0 23.9 1.0
O A:HOH317 3.3 35.8 1.0
CZ A:TYR23 3.7 24.2 1.0
CE2 A:TYR23 3.7 24.2 1.0
CA A:GLY104 4.2 27.6 1.0
O A:ARG21 4.5 31.0 1.0
N A:GLY104 4.8 27.4 1.0
CE1 A:TYR23 4.9 24.1 1.0
CD2 A:TYR23 5.0 26.5 1.0

Chlorine binding site 2 out of 12 in 5yky

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Chlorine binding site 2 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:43.1
occ:0.40
 PT A:PT203 2.1 40.6 0.4
CL A:CL207 2.8 48.1 0.4
CL A:CL208 2.9 36.6 0.4
CL A:CL209 3.0 29.7 0.4
CL A:CL210 3.1 70.3 0.4
O A:HOH324 3.5 35.5 1.0
CA A:LYS1 3.8 32.6 1.0
CB A:LYS1 4.0 34.6 1.0
N A:LYS1 4.3 32.1 1.0
CG A:LYS1 4.3 34.2 1.0
CL A:CL206 4.6 33.5 0.4
CD A:LYS1 5.0 36.4 1.0

Chlorine binding site 3 out of 12 in 5yky

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Chlorine binding site 3 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:33.5
occ:0.40
 PT A:PT203 2.4 40.6 0.4
CL A:CL207 3.0 48.1 0.4
CL A:CL210 3.1 70.3 0.4
CL A:CL209 3.3 29.7 0.4
CL A:CL208 3.4 36.6 0.4
CL A:CL205 4.6 43.1 0.4

Chlorine binding site 4 out of 12 in 5yky

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Chlorine binding site 4 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:48.1
occ:0.40
 PT A:PT203 2.0 40.6 0.4
CL A:CL205 2.8 43.1 0.4
CL A:CL209 2.9 29.7 0.4
CL A:CL210 3.0 70.3 0.4
CL A:CL206 3.0 33.5 0.4
O A:HOH324 3.6 35.5 1.0
CL A:CL208 4.0 36.6 0.4

Chlorine binding site 5 out of 12 in 5yky

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Chlorine binding site 5 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:36.6
occ:0.40
 PT A:PT203 2.0 40.6 0.4
CL A:CL210 2.8 70.3 0.4
CL A:CL205 2.9 43.1 0.4
CL A:CL209 3.2 29.7 0.4
CL A:CL206 3.4 33.5 0.4
CL A:CL207 4.0 48.1 0.4

Chlorine binding site 6 out of 12 in 5yky

Go back to Chlorine Binding Sites List in 5yky
Chlorine binding site 6 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:29.7
occ:0.40
 PT A:PT203 2.3 40.6 0.4
CL A:CL207 2.9 48.1 0.4
CL A:CL205 3.0 43.1 0.4
CL A:CL208 3.2 36.6 0.4
NE2 A:GLN41 3.3 28.5 1.0
CL A:CL206 3.3 33.5 0.4
O A:HOH310 3.3 26.7 1.0
N A:LYS1 3.4 32.1 1.0
CA A:LYS1 3.8 32.6 1.0
O A:HOH324 4.3 35.5 1.0
CL A:CL210 4.3 70.3 0.4
CD A:GLN41 4.3 26.8 1.0
CB A:LYS1 4.8 34.6 1.0
C A:LYS1 4.8 33.9 1.0
CG A:GLN41 5.0 25.4 1.0

Chlorine binding site 7 out of 12 in 5yky

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Chlorine binding site 7 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:70.3
occ:0.40
 PT A:PT203 2.1 40.6 0.4
CL A:CL208 2.8 36.6 0.4
CL A:CL207 3.0 48.1 0.4
CL A:CL205 3.1 43.1 0.4
CL A:CL206 3.1 33.5 0.4
CL A:CL209 4.3 29.7 0.4

Chlorine binding site 8 out of 12 in 5yky

Go back to Chlorine Binding Sites List in 5yky
Chlorine binding site 8 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:27.9
occ:0.30
 PT A:PT202 2.5 51.0 0.3
CL A:CL213 2.8 46.6 0.3
CL A:CL212 3.3 41.4 0.3
CL A:CL214 3.3 39.2 0.3
N A:ILE88 3.4 31.4 1.0
NE2 A:HIS15 3.6 46.9 1.0
CG1 A:ILE88 3.6 35.0 1.0
O A:SER86 3.9 35.2 1.0
CA A:ASP87 3.9 37.7 1.0
CG2 A:ILE88 4.0 33.1 1.0
CZ A:PHE3 4.1 37.9 1.0
CB A:ILE88 4.1 32.3 1.0
C A:ASP87 4.1 35.0 1.0
CB A:ALA11 4.2 31.7 1.0
CD2 A:HIS15 4.2 40.7 1.0
CA A:ILE88 4.3 32.5 1.0
OD1 A:ASP87 4.4 41.6 1.0
CD1 A:ILE88 4.5 34.8 1.0
CL A:CL215 4.6 45.5 0.3
CE2 A:PHE3 4.6 33.7 1.0
CE1 A:HIS15 4.7 46.4 1.0
C A:SER86 4.8 35.7 1.0
N A:ASP87 4.8 33.0 1.0
CB A:ASP87 4.9 41.8 1.0
CG A:ASP87 4.9 46.7 1.0

Chlorine binding site 9 out of 12 in 5yky

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Chlorine binding site 9 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:41.4
occ:0.30
 PT A:PT202 2.1 51.0 0.3
CL A:CL213 2.5 46.6 0.3
CL A:CL215 3.0 45.5 0.3
CL A:CL211 3.3 27.9 0.3
CL A:CL214 3.3 39.2 0.3
NE2 A:HIS15 4.9 46.9 1.0

Chlorine binding site 10 out of 12 in 5yky

Go back to Chlorine Binding Sites List in 5yky
Chlorine binding site 10 out of 12 in the Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Cross-Linked Tetragonal Hen Egg White Lysozyme Soaked with 10 Mm Rose Bengal and 10MM H2PTCL6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:46.6
occ:0.30
 PT A:PT202 1.9 51.0 0.3
CL A:CL212 2.5 41.4 0.3
CL A:CL211 2.8 27.9 0.3
CL A:CL215 3.1 45.5 0.3
OD1 A:ASP87 3.4 41.6 1.0
CG A:ASP87 3.5 46.7 1.0
NE2 A:HIS15 3.8 46.9 1.0
CB A:ASP87 3.9 41.8 1.0
CL A:CL214 3.9 39.2 0.3
CA A:ASP87 3.9 37.7 1.0
OD2 A:ASP87 4.0 53.2 1.0
CE1 A:HIS15 4.3 46.4 1.0
N A:ILE88 4.5 31.4 1.0
C A:ASP87 4.7 35.0 1.0

Reference:

H.Tabe, H.Takahashi, T.Shimoi, Y.Yamada. Photocatalytic Hydrogen Evolution Systems Constructed in Cross-Linked Porous Protein Crystals Appl Catal B V. 237 1124 2018.
ISSN: ISSN 0926-3373
DOI: 10.1016/J.APCATB.2018.01.046
Page generated: Fri Jul 26 21:30:40 2024

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