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Chlorine in PDB 5lxw: Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf

Enzymatic activity of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf

All present enzymatic activity of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf:
3.2.1.17;

Protein crystallography data

The structure of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf, PDB code: 5lxw was solved by J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.39 / 1.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.370, 79.370, 37.840, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.3

Other elements in 5lxw:

The structure of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf also contains other interesting chemical elements:

Platinum (Pt) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf (pdb code 5lxw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf, PDB code: 5lxw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5lxw

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Chlorine binding site 1 out of 5 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:29.1
occ:1.00
 HH A:TYR23 2.3 15.8 1.0
OH A:TYR23 2.9 13.1 1.0
HE2 A:TYR23 3.1 14.7 1.0
HA3 A:GLY104 3.3 15.4 1.0
O A:HOH341 3.4 21.3 1.0
CZ A:TYR23 3.6 12.8 1.0
CE2 A:TYR23 3.6 12.2 1.0
O A:HOH355 3.9 25.0 1.0
HA2 A:GLY104 4.0 15.4 1.0
CA A:GLY104 4.1 12.8 1.0
HH21 A:ARG21 4.5 38.0 0.5
H A:MET105 4.6 14.2 1.0
N A:GLY104 4.7 13.7 1.0
O A:ARG21 4.8 16.1 0.5
O A:ARG21 4.8 19.1 0.5
HE A:ARG21 4.8 38.8 0.5
CE1 A:TYR23 4.8 12.8 1.0
HB3 A:ARG21 4.8 23.7 0.5
H A:GLY104 4.9 16.4 1.0
CD2 A:TYR23 4.9 12.2 1.0
HB3 A:ARG21 5.0 22.2 0.5

Chlorine binding site 2 out of 5 in 5lxw

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Chlorine binding site 2 out of 5 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:25.5
occ:0.30
 PT A:PT205 2.3 32.4 0.3
HG23 A:THR89 2.7 25.6 1.0
HB3 A:HIS15 2.8 30.6 1.0
OD1 A:ASN93 2.9 21.7 0.5
HN1 A:NH3209 3.0 33.5 0.3
N A:NH3209 3.1 27.9 0.3
ND1 A:HIS15 3.2 35.8 1.0
HB A:VAL92 3.2 19.4 1.0
HA A:THR89 3.3 22.6 1.0
HG11 A:VAL92 3.4 20.7 1.0
HG12 A:VAL92 3.5 20.7 1.0
HN3 A:NH3209 3.5 33.5 0.3
CB A:HIS15 3.6 25.5 1.0
CG2 A:THR89 3.6 21.3 1.0
HD21 A:ASN93 3.7 28.3 0.5
CG A:ASN93 3.7 19.6 0.5
CG A:HIS15 3.7 30.9 1.0
CG1 A:VAL92 3.8 17.2 1.0
O A:THR89 3.8 16.8 1.0
HN2 A:NH3209 3.8 33.5 0.3
HG22 A:THR89 3.8 25.6 1.0
O A:HIS15 3.9 22.0 1.0
ND2 A:ASN93 4.0 23.6 0.5
CB A:VAL92 4.0 16.2 1.0
CA A:THR89 4.0 18.8 1.0
HB2 A:ASN93 4.1 30.3 0.5
HA A:HIS15 4.1 29.1 1.0
H A:ASN93 4.1 16.8 0.5
H A:ASN93 4.1 18.5 0.5
HZ1 A:LYS96 4.2 26.6 1.0
CE1 A:HIS15 4.2 39.1 1.0
HG21 A:THR89 4.2 25.6 1.0
N A:NH3210 4.3 21.4 0.3
CB A:THR89 4.3 21.6 1.0
HB2 A:HIS15 4.3 30.6 1.0
CA A:HIS15 4.3 24.2 1.0
C A:THR89 4.4 17.7 1.0
N A:ASN93 4.5 14.0 0.5
N A:ASN93 4.5 15.4 0.5
HE1 A:HIS15 4.5 46.9 1.0
OG1 A:THR89 4.5 23.9 1.0
HN3 A:NH3210 4.6 25.7 0.3
C A:HIS15 4.6 22.5 1.0
HG21 A:VAL92 4.6 19.3 1.0
HN2 A:NH3210 4.7 25.7 0.3
HD22 A:ASN93 4.7 28.3 0.5
HG13 A:VAL92 4.7 20.7 1.0
HA A:ASN93 4.7 21.6 0.5
HN1 A:NH3210 4.7 25.7 0.3
HA A:ASN93 4.8 17.9 0.5
CB A:ASN93 4.8 17.6 0.5
CD2 A:HIS15 4.8 33.3 1.0
CG2 A:VAL92 4.9 16.1 1.0
CB A:ASN93 4.9 25.3 0.5
HZ3 A:LYS96 4.9 26.6 1.0
C A:VAL92 4.9 14.3 1.0
NZ A:LYS96 4.9 22.2 1.0
HE3 A:LYS96 5.0 23.5 1.0
CA A:ASN93 5.0 18.0 0.5
CA A:ASN93 5.0 14.9 0.5

Chlorine binding site 3 out of 5 in 5lxw

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Chlorine binding site 3 out of 5 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:28.5
occ:1.00
 H A:GLY26 2.5 16.9 1.0
HG3 A:GLN121 2.7 34.0 0.5
HG A:SER24 2.7 21.6 1.0
HA3 A:GLY26 2.9 16.7 1.0
HA A:GLN121 2.9 25.0 0.5
HA A:GLN121 2.9 30.5 0.5
HB2 A:SER24 3.1 19.8 1.0
OG A:SER24 3.1 18.0 1.0
HD11 A:ILE124 3.2 32.7 1.0
N A:GLY26 3.2 14.1 1.0
HG2 A:GLN121 3.4 50.2 0.5
HD13 A:ILE124 3.5 32.7 1.0
CG A:GLN121 3.5 28.3 0.5
CA A:GLY26 3.5 13.9 1.0
HG23 A:VAL120 3.6 21.7 1.0
CB A:SER24 3.6 16.5 1.0
HG12 A:ILE124 3.6 30.7 1.0
CD1 A:ILE124 3.7 27.2 1.0
CA A:GLN121 3.7 20.9 0.5
HG2 A:GLN121 3.8 34.0 0.5
CA A:GLN121 3.8 25.4 0.5
CB A:GLN121 4.1 26.2 0.5
HA2 A:GLY26 4.1 16.7 1.0
N A:GLN121 4.2 21.4 0.5
N A:GLN121 4.2 19.4 0.5
HB3 A:GLN121 4.2 31.5 0.5
HB3 A:SER24 4.2 19.8 1.0
CG A:GLN121 4.2 41.9 0.5
CG1 A:ILE124 4.2 25.6 1.0
H A:ASN27 4.3 14.8 1.0
HG3 A:GLN121 4.3 50.2 0.5
H A:LEU25 4.3 17.4 1.0
N A:LEU25 4.4 14.5 1.0
CB A:GLN121 4.4 34.1 0.5
C A:LEU25 4.4 14.6 1.0
O A:VAL120 4.4 18.6 1.0
HB3 A:LEU25 4.5 18.7 1.0
C A:VAL120 4.5 19.0 1.0
C A:SER24 4.5 14.8 1.0
H A:GLN121 4.5 25.6 0.5
CG2 A:VAL120 4.5 18.1 1.0
H A:GLN121 4.5 23.2 0.5
HB3 A:GLN121 4.5 40.9 0.5
C A:GLY26 4.6 12.6 1.0
HD12 A:ILE124 4.6 32.7 1.0
CD A:GLN121 4.7 27.9 0.5
CA A:SER24 4.7 14.8 1.0
HG13 A:ILE124 4.7 30.7 1.0
HG21 A:VAL120 4.7 21.7 1.0
N A:ASN27 4.7 12.3 1.0
CA A:LEU25 4.9 14.5 1.0
HG21 A:ILE124 4.9 26.4 1.0
C A:GLN121 4.9 22.3 0.5
C A:GLN121 5.0 20.0 0.5
O A:SER24 5.0 13.5 1.0
HB A:VAL120 5.0 21.9 1.0
HB2 A:GLN121 5.0 31.5 0.5
HG23 A:ILE124 5.0 26.4 1.0

Chlorine binding site 4 out of 5 in 5lxw

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Chlorine binding site 4 out of 5 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:16.5
occ:1.00
 H A:THR69 2.4 15.6 1.0
O A:HOH356 3.2 13.3 1.0
HA2 A:GLY67 3.2 16.4 1.0
O A:HOH389 3.2 26.5 1.0
O A:HOH369 3.2 24.2 1.0
N A:THR69 3.3 13.0 1.0
O A:THR69 3.3 13.4 1.0
H A:GLY67 3.3 15.2 1.0
HG A:SER72 3.4 17.5 0.0
H A:ARG68 3.5 16.2 1.0
O A:HOH347 3.5 30.8 1.0
OG A:SER72 3.6 14.6 1.0
N A:ARG68 3.6 13.5 1.0
C A:GLY67 3.6 13.6 1.0
CA A:GLY67 3.6 13.7 1.0
C A:THR69 3.7 12.9 1.0
HB A:THR69 3.7 14.8 1.0
N A:GLY67 3.7 12.7 1.0
OD1 A:ASN65 3.8 14.7 1.0
CA A:THR69 3.9 12.4 1.0
O A:HOH351 4.0 17.3 1.0
O A:GLY67 4.2 15.6 1.0
CB A:THR69 4.3 12.3 1.0
C A:ARG68 4.3 13.7 1.0
H A:ASP66 4.4 13.6 0.5
H A:ASP66 4.4 13.6 0.5
OD1 A:ASP66 4.4 11.6 1.0
CA A:ARG68 4.4 13.5 1.0
HA A:PRO70 4.4 19.1 1.0
HA A:ARG68 4.5 16.2 1.0
N A:PRO70 4.5 14.6 1.0
HG1 A:THR69 4.6 15.1 1.0
HA3 A:GLY67 4.6 16.4 1.0
H A:SER72 4.6 19.2 1.0
NA A:NA203 4.8 13.3 1.0
O A:HOH397 4.8 30.5 1.0
HA A:THR69 4.8 14.9 1.0
CB A:SER72 4.8 14.3 1.0
C A:ASP66 4.8 12.1 1.0
HB3 A:SER72 4.9 17.2 1.0
HA A:ASN65 5.0 14.6 1.0
O A:HOH330 5.0 14.1 0.5
OG1 A:THR69 5.0 12.6 1.0
CA A:PRO70 5.0 15.9 1.0

Chlorine binding site 5 out of 5 in 5lxw

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Chlorine binding site 5 out of 5 in the Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years on the Shelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:33.5
occ:1.00
 H A:ARG45 2.1 16.5 1.0
HA A:ASN44 2.7 16.6 1.0
O A:HOH349 2.9 20.1 1.0
N A:ARG45 2.9 13.7 1.0
HB3 A:ARG45 3.3 21.3 1.0
CA A:ASN44 3.5 13.8 1.0
HB2 A:ARG45 3.7 21.3 1.0
C A:ASN44 3.7 13.0 1.0
CB A:ARG45 3.8 17.7 1.0
OD1 A:ASN44 3.9 22.2 1.0
CA A:ARG45 3.9 14.7 1.0
O A:THR43 4.1 14.8 1.0
O A:ARG45 4.3 15.3 1.0
CG A:ASN44 4.4 18.8 1.0
N A:ASN44 4.4 13.0 1.0
CB A:ASN44 4.5 15.8 1.0
C A:ARG45 4.6 14.4 1.0
C A:THR43 4.7 13.4 1.0
HA A:ARG45 4.7 17.6 1.0
HB2 A:ASN44 4.7 18.9 1.0
O A:ASN44 4.9 12.1 1.0

Reference:

J.R.Helliwell, T.Simon. Atomic Resolution X-Ray Crystal Structure of Cisplatin Bound to Hen Egg White Lysozyme Stored For 5 Years 'on the Shelf' Zenodo 2016.
DOI: 10.5281/ZENODO.155068
Page generated: Fri Jul 26 12:19:20 2024

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