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Platinum 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:

Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 3 binding sites of Platinum 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 Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 5lxw

Go back to Platinum Binding Sites List in 5lxw
Platinum binding site 1 out of 3 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 Platinum with other atoms in the Pt 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:Pt204

b:27.6
occ:0.50
NH2 A:ARG14 2.0 27.4 1.0
HH21 A:ARG14 2.3 32.9 1.0
NE2 A:HIS15 2.4 35.4 1.0
CZ A:ARG14 3.1 26.1 1.0
CD2 A:HIS15 3.3 33.3 1.0
PT A:PT207 3.4 17.9 0.2
HD2 A:HIS15 3.4 40.0 1.0
CE1 A:HIS15 3.4 39.1 1.0
NH1 A:ARG14 3.5 27.2 1.0
HE1 A:HIS15 3.6 46.9 1.0
HB1 A:ALA11 4.0 28.7 1.0
OD1 A:ASP87 4.2 28.6 1.0
NE A:ARG14 4.2 25.5 1.0
HG12 A:ILE88 4.3 26.1 1.0
HG1 A:THR89 4.3 28.7 1.0
HE A:ARG14 4.3 30.6 1.0
HH11 A:ARG14 4.4 32.6 1.0
H A:ILE88 4.4 22.7 1.0
CG A:HIS15 4.5 30.9 1.0
ND1 A:HIS15 4.5 35.8 1.0
CG A:ASP87 4.6 29.1 1.0
HA A:ALA11 4.6 27.9 1.0
OD2 A:ASP87 4.7 34.1 1.0
O A:HOH353 4.7 34.3 1.0
OG1 A:THR89 4.8 23.9 1.0
CB A:ALA11 4.8 23.9 1.0
HB2 A:ALA11 4.8 28.7 1.0
HA A:ASP87 4.8 27.6 1.0
HG13 A:ILE88 4.8 26.1 1.0
CG1 A:ILE88 5.0 21.7 1.0

Platinum binding site 2 out of 3 in 5lxw

Go back to Platinum Binding Sites List in 5lxw
Platinum binding site 2 out of 3 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 Platinum with other atoms in the Pt 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:Pt205

b:32.4
occ:0.30
N A:NH3210 1.9 21.4 0.3
N A:NH3209 2.0 27.9 0.3
ND1 A:HIS15 2.1 35.8 1.0
HN2 A:NH3209 2.3 33.5 0.3
HN3 A:NH3210 2.3 25.7 0.3
CL A:CL206 2.3 25.5 0.3
HN2 A:NH3210 2.4 25.7 0.3
HN1 A:NH3210 2.5 25.7 0.3
HN1 A:NH3209 2.5 33.5 0.3
HN3 A:NH3209 2.6 33.5 0.3
HA A:HIS15 2.9 29.1 1.0
CE1 A:HIS15 3.1 39.1 1.0
CG A:HIS15 3.1 30.9 1.0
HB3 A:HIS15 3.1 30.6 1.0
HE1 A:HIS15 3.3 46.9 1.0
CB A:HIS15 3.4 25.5 1.0
HG23 A:THR89 3.5 25.6 1.0
CA A:HIS15 3.6 24.2 1.0
O A:HIS15 4.1 22.0 1.0
NE2 A:HIS15 4.2 35.4 1.0
CD2 A:HIS15 4.3 33.3 1.0
C A:HIS15 4.3 22.5 1.0
CG2 A:THR89 4.4 21.3 1.0
HB2 A:HIS15 4.4 30.6 1.0
HA A:THR89 4.5 22.6 1.0
HG21 A:THR89 4.6 25.6 1.0
OG1 A:THR89 4.6 23.9 1.0
N A:HIS15 4.7 23.4 1.0
PT A:PT207 4.8 17.9 0.2
OD1 A:ASN93 4.8 21.7 0.5
HG11 A:VAL92 4.9 20.7 1.0
HD21 A:ASN93 4.9 28.3 0.5
O A:ARG14 4.9 26.7 1.0
HG22 A:THR89 5.0 25.6 1.0

Platinum binding site 3 out of 3 in 5lxw

Go back to Platinum Binding Sites List in 5lxw
Platinum binding site 3 out of 3 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 Platinum with other atoms in the Pt 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:Pt207

b:17.9
occ:0.20
HE1 A:HIS15 2.0 46.9 1.0
NH1 A:ARG14 2.3 27.2 1.0
CE1 A:HIS15 2.6 39.1 1.0
HH11 A:ARG14 2.7 32.6 1.0
NE2 A:HIS15 3.0 35.4 1.0
CZ A:ARG14 3.3 26.1 1.0
PT A:PT204 3.4 27.6 0.5
HN2 A:NH3210 3.4 25.7 0.3
NH2 A:ARG14 3.5 27.4 1.0
ND1 A:HIS15 3.7 35.8 1.0
HN3 A:NH3210 4.1 25.7 0.3
N A:NH3210 4.1 21.4 0.3
OG1 A:THR89 4.2 23.9 1.0
CD2 A:HIS15 4.2 33.3 1.0
HG1 A:THR89 4.2 28.7 1.0
HH21 A:ARG14 4.3 32.9 1.0
O A:HOH382 4.4 40.1 1.0
NE A:ARG14 4.5 25.5 1.0
CG A:HIS15 4.5 30.9 1.0
HG2 A:ARG14 4.7 30.8 1.0
HD2 A:ARG14 4.7 31.6 1.0
PT A:PT205 4.8 32.4 0.3
HN1 A:NH3210 4.8 25.7 0.3
HD2 A:HIS15 4.9 40.0 1.0
OD2 A:ASP87 5.0 34.1 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: Wed Dec 16 02:05:21 2020

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