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Platinum in PDB 5l3h: Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

Enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties

All present enzymatic activity of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h was solved by J.R.Helliwell, S.W.M.Tanley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.832, 78.832, 37.021, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.8

Other elements in 5l3h:

The structure of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties (pdb code 5l3h). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties, PDB code: 5l3h:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 5l3h

Go back to Platinum Binding Sites List in 5l3h
Platinum binding site 1 out of 5 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:22.3
occ:0.70
N A:NH3208 2.0 19.5 0.7
N A:NH3207 2.0 17.1 0.7
HN2 A:NH3208 2.2 23.4 0.7
ND1 A:HIS15 2.3 16.7 1.0
HN1 A:NH3207 2.3 20.5 0.7
CL A:CL205 2.3 16.6 0.7
HN3 A:NH3208 2.4 23.4 0.7
HN2 A:NH3207 2.5 20.5 0.7
HN3 A:NH3207 2.6 20.5 0.7
HN1 A:NH3208 2.7 23.4 0.7
HA A:HIS15 2.8 18.2 1.0
CE1 A:HIS15 3.2 17.1 1.0
CG A:HIS15 3.2 15.8 1.0
HB3 A:HIS15 3.2 17.6 1.0
HE1 A:HIS15 3.4 20.6 1.0
CB A:HIS15 3.5 14.7 1.0
CA A:HIS15 3.5 15.2 1.0
HG23 A:THR89 3.7 17.1 1.0
O A:HIS15 4.0 15.1 1.0
C A:HIS15 4.2 15.1 1.0
O A:HOH323 4.2 16.7 1.0
NE2 A:HIS15 4.3 16.9 1.0
CD2 A:HIS15 4.4 15.4 1.0
HB2 A:HIS15 4.5 17.6 1.0
HA A:THR89 4.5 14.8 1.0
OG1 A:THR89 4.6 14.3 1.0
CG2 A:THR89 4.6 14.3 1.0
N A:HIS15 4.7 14.7 1.0
O A:ARG14 4.7 16.6 1.0
HG11 A:VAL92 4.8 14.0 1.0
HG21 A:THR89 4.9 17.1 1.0
HZ2 A:LYS96 4.9 17.2 1.0

Platinum binding site 2 out of 5 in 5l3h

Go back to Platinum Binding Sites List in 5l3h
Platinum binding site 2 out of 5 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:16.4
occ:0.52
HH11 A:ARG14 1.8 22.2 1.0
N A:NH3209 2.0 13.9 0.5
HH12 A:ARG14 2.1 22.2 1.0
NH1 A:ARG14 2.2 18.5 1.0
CL A:CL206 2.3 12.9 0.5
NE2 A:HIS15 2.4 16.9 1.0
HN1 A:NH3209 2.4 16.7 0.5
HN2 A:NH3209 2.5 16.7 0.5
HN3 A:NH3209 2.5 16.7 0.5
CE1 A:HIS15 3.3 17.1 1.0
HD3 A:ARG14 3.4 21.7 1.0
CD2 A:HIS15 3.4 15.4 1.0
HE1 A:HIS15 3.4 20.6 1.0
CZ A:ARG14 3.5 17.8 1.0
HD2 A:HIS15 3.5 18.4 1.0
OD1 A:ASP87 4.1 15.6 1.0
CD A:ARG14 4.1 18.1 1.0
HG12 A:ILE88 4.1 15.1 1.0
HB1 A:ALA11 4.2 16.0 1.0
NE A:ARG14 4.2 18.9 1.0
H A:ILE88 4.3 15.9 1.0
O A:HOH373 4.3 19.1 1.0
HH22 A:ARG14 4.3 23.3 1.0
HD2 A:ARG14 4.4 21.7 1.0
NH2 A:ARG14 4.4 19.4 1.0
OD2 A:ASP87 4.4 17.9 1.0
CG A:ASP87 4.4 16.1 1.0
ND1 A:HIS15 4.4 16.7 1.0
HG1 A:THR89 4.4 17.1 1.0
CG A:HIS15 4.5 15.8 1.0
HA A:ASP87 4.5 16.6 1.0
HA A:ALA11 4.7 15.2 1.0
HB3 A:ARG14 4.9 18.2 1.0
HG13 A:ILE88 4.9 15.1 1.0
OG1 A:THR89 5.0 14.3 1.0
CB A:ALA11 5.0 13.3 1.0
CG1 A:ILE88 5.0 12.6 1.0
HB2 A:ALA11 5.0 16.0 1.0

Platinum binding site 3 out of 5 in 5l3h

Go back to Platinum Binding Sites List in 5l3h
Platinum binding site 3 out of 5 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt215

b:18.4
occ:0.15
H1 A:LYS1 1.9 11.7 1.0
H2 A:LYS1 2.2 11.7 1.0
N A:LYS1 2.4 9.7 1.0
HB2 A:LYS1 2.8 13.0 1.0
H3 A:LYS1 3.1 11.7 1.0
CA A:LYS1 3.2 9.9 1.0
HA A:LYS1 3.2 11.9 1.0
HB3 A:SER86 3.2 18.8 1.0
CB A:LYS1 3.4 10.8 1.0
O A:HOH305 3.5 11.3 1.0
HE21 A:GLN41 3.7 11.9 1.0
HB3 A:LYS1 3.7 13.0 1.0
HG3 A:GLN41 4.0 10.2 1.0
NE2 A:GLN41 4.0 9.9 1.0
CB A:SER86 4.2 15.7 1.0
OG1 A:THR40 4.2 9.1 1.0
HG1 A:THR40 4.2 11.0 1.0
HA A:SER86 4.3 15.5 1.0
HE22 A:GLN41 4.3 11.9 1.0
O A:HOH329 4.3 9.2 1.0
CD A:GLN41 4.5 10.0 1.0
HB2 A:SER86 4.5 18.8 1.0
CG A:GLN41 4.6 8.5 1.0
C A:LYS1 4.6 10.8 1.0
CA A:SER86 4.6 12.9 1.0
H A:SER86 4.7 14.5 1.0
HG2 A:GLN41 4.7 10.2 1.0
CG A:LYS1 4.8 11.9 1.0
N A:SER86 4.8 12.1 1.0
O A:HOH351 4.8 17.4 1.0
HG3 A:LYS1 4.9 14.3 1.0

Platinum binding site 4 out of 5 in 5l3h

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Platinum binding site 4 out of 5 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt216

b:30.5
occ:0.15
HZ3 A:LYS96 1.5 17.2 1.0
NZ A:LYS96 2.3 14.4 1.0
HZ2 A:LYS96 2.3 17.2 1.0
HZ1 A:LYS96 2.8 17.2 1.0
HD3 A:LYS96 3.1 14.9 1.0
CE A:LYS96 3.4 13.8 1.0
CD A:LYS96 3.5 12.4 1.0
HD2 A:LYS96 3.5 14.9 1.0
HE2 A:LYS96 3.7 16.6 1.0
HE3 A:LYS96 4.1 16.6 1.0
HN1 A:NH3208 4.2 23.4 0.7
HA3 A:GLY16 4.4 19.1 1.0
HE1 A:TYR20 4.4 13.7 1.0
O A:HIS15 4.6 15.1 1.0
N A:NH3208 4.9 19.5 0.7
CE1 A:TYR20 5.0 11.4 1.0
HN3 A:NH3208 5.0 23.4 0.7

Platinum binding site 5 out of 5 in 5l3h

Go back to Platinum Binding Sites List in 5l3h
Platinum binding site 5 out of 5 in the Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Re-Refinement of 4DD4; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Standard Uncertainties within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt217

b:20.7
occ:0.10
HZ3 A:LYS33 2.3 15.7 1.0
HZ1 A:LYS33 2.3 15.7 1.0
HZ2 A:LYS33 2.5 15.7 1.0
NZ A:LYS33 2.5 13.1 1.0
O A:HOH359 3.3 13.2 1.0
OD1 A:ASN37 3.7 12.5 1.0
CL A:CL211 3.7 23.4 1.0
HD21 A:ASN37 3.8 15.3 1.0
CE A:LYS33 4.0 12.2 1.0
HE2 A:LYS33 4.3 14.7 1.0
ND2 A:ASN37 4.5 12.8 1.0
HE3 A:LYS33 4.5 14.7 1.0
CG A:ASN37 4.5 12.5 1.0
HD3 A:LYS33 4.8 14.2 1.0
O A:HOH315 4.8 13.6 1.0
HD2 A:LYS33 4.8 14.2 1.0
CD A:LYS33 4.8 11.8 1.0
HD2 A:PHE38 5.0 13.4 1.0

Reference:

J.R.Helliwell, A.M.M.Schreurs, L.M.J.Kroon-Batenburg, S.Tanley. Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 with Ligand Distances and Angles, and Their Standard Uncertainties, and Also Reporting A Split Occupancy Effect Arxiv 2016.
DOI: 10.3927/45371856
Page generated: Wed Dec 16 02:05:20 2020

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