Atomistry » Platinum » PDB 5djm-5v6i » 5lxw
Atomistry »
  Platinum »
    PDB 5djm-5v6i »
      5lxw »

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: Thu Oct 10 11:37:40 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy