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Platinum in PDB 5l3i: Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

Enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15

All present enzymatic activity of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15:
3.2.1.17;

Protein crystallography data

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i 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) 18.39 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.016, 78.016, 37.071, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5l3i:

The structure of Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 (pdb code 5l3i). 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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15, PDB code: 5l3i:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 5l3i

Go back to Platinum Binding Sites List in 5l3i
Platinum binding site 1 out of 5 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:27.7
occ:0.60
 N A:NH3207 2.0 18.4 0.6
N A:NH3206 2.0 14.7 0.6
ND1 A:HIS15 2.2 19.9 1.0
HN3 A:NH3206 2.3 17.6 0.6
HN1 A:NH3206 2.3 17.6 0.6
CL A:CL205 2.3 20.0 0.6
HN3 A:NH3207 2.3 22.1 0.6
HN1 A:NH3207 2.5 22.1 0.6
HN2 A:NH3207 2.6 22.1 0.6
HN2 A:NH3206 2.8 17.6 0.6
HA A:HIS15 2.9 19.9 1.0
CE1 A:HIS15 3.1 20.9 1.0
CG A:HIS15 3.2 15.6 1.0
HB3 A:HIS15 3.2 17.5 1.0
HE1 A:HIS15 3.3 25.0 1.0
CB A:HIS15 3.5 14.6 1.0
HG23 A:THR89 3.5 23.4 1.0
CA A:HIS15 3.6 16.6 1.0
O A:HIS15 3.9 18.1 1.0
C A:HIS15 4.2 16.3 1.0
NE2 A:HIS15 4.2 19.3 1.0
CD2 A:HIS15 4.3 21.0 1.0
HB2 A:HIS15 4.4 17.5 1.0
CG2 A:THR89 4.4 19.5 1.0
HD21 A:ASN93 4.5 33.6 1.0
HA A:THR89 4.5 16.2 1.0
HZ1 A:LYS96 4.6 25.4 1.0
HG22 A:THR89 4.7 23.4 1.0
N A:HIS15 4.8 18.3 1.0
HG12 A:VAL92 4.8 16.1 1.0
ND2 A:ASN93 4.9 28.0 1.0
HG21 A:THR89 5.0 23.4 1.0
OG1 A:THR89 5.0 20.1 1.0

Platinum binding site 2 out of 5 in 5l3i

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Platinum binding site 2 out of 5 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:17.2
occ:0.50
 HH22 A:ARG14 1.3 26.0 1.0
N A:NH3208 2.0 11.4 0.5
NH2 A:ARG14 2.1 21.7 1.0
HN3 A:NH3208 2.1 13.7 0.5
CL A:CL212 2.2 14.4 0.5
HH12 A:ARG14 2.2 26.1 1.0
HN2 A:NH3208 2.3 13.7 0.5
NE2 A:HIS15 2.4 19.3 1.0
HH21 A:ARG14 2.7 26.0 1.0
CZ A:ARG14 2.7 20.4 1.0
NH1 A:ARG14 2.8 21.8 1.0
HN1 A:NH3208 2.9 13.7 0.5
HD2 A:HIS15 3.1 25.1 1.0
CD2 A:HIS15 3.1 21.0 1.0
CE1 A:HIS15 3.5 20.9 1.0
HH11 A:ARG14 3.6 26.1 1.0
HB2 A:ALA11 3.6 16.8 1.0
HG12 A:ILE88 3.8 14.3 1.0
HE1 A:HIS15 3.8 25.0 1.0
NE A:ARG14 4.0 19.8 1.0
HG13 A:ILE88 4.3 14.3 1.0
H A:ILE88 4.3 22.3 1.0
HE A:ARG14 4.3 23.8 1.0
CG A:HIS15 4.4 15.6 1.0
CB A:ALA11 4.4 14.0 1.0
HA A:ALA11 4.4 19.4 1.0
HB1 A:ALA11 4.4 16.8 1.0
CG1 A:ILE88 4.5 11.9 1.0
ND1 A:HIS15 4.5 19.9 1.0
HD12 A:ILE88 4.6 20.2 1.0
HA A:ASP87 4.9 19.1 1.0
OG1 A:THR89 4.9 20.1 1.0
CA A:ALA11 4.9 16.2 1.0
O A:ALA11 4.9 12.0 1.0

Platinum binding site 3 out of 5 in 5l3i

Go back to Platinum Binding Sites List in 5l3i
Platinum binding site 3 out of 5 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt215

b:19.1
occ:0.15
 H1 A:LYS1 1.5 14.0 1.0
N A:LYS1 2.4 11.7 1.0
H2 A:LYS1 2.7 14.0 1.0
H3 A:LYS1 2.9 14.0 1.0
HB2 A:LYS1 3.0 20.6 1.0
CA A:LYS1 3.2 14.0 1.0
HA A:LYS1 3.2 16.8 1.0
HB3 A:SER86 3.3 28.4 1.0
CB A:LYS1 3.5 17.2 1.0
HE22 A:GLN41 3.6 16.1 1.0
HB3 A:LYS1 3.7 20.6 1.0
HG1 A:THR40 3.8 14.2 0.0
HG3 A:GLN41 3.9 14.3 1.0
NE2 A:GLN41 3.9 13.4 1.0
OG1 A:THR40 4.2 11.8 1.0
HE21 A:GLN41 4.2 16.1 1.0
CB A:SER86 4.3 23.7 1.0
O A:HOH311 4.3 9.9 1.0
CD A:GLN41 4.5 13.1 1.0
HA A:SER86 4.5 20.7 1.0
CG A:GLN41 4.5 12.0 1.0
C A:LYS1 4.6 14.4 1.0
HG2 A:GLN41 4.6 14.3 1.0
H A:SER86 4.6 20.1 1.0
HB2 A:SER86 4.7 28.4 1.0
CA A:SER86 4.8 17.2 1.0
N A:SER86 4.8 16.8 1.0
CG A:LYS1 4.9 16.9 1.0

Platinum binding site 4 out of 5 in 5l3i

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Platinum binding site 4 out of 5 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt216

b:24.8
occ:0.15
 HZ3 A:LYS96 1.5 25.4 1.0
NZ A:LYS96 2.3 21.1 1.0
HZ1 A:LYS96 2.5 25.4 1.0
HZ2 A:LYS96 2.8 25.4 1.0
HD3 A:LYS96 3.0 15.3 1.0
CE A:LYS96 3.3 15.3 1.0
CD A:LYS96 3.5 12.7 1.0
HD2 A:LYS96 3.6 15.3 1.0
HE2 A:LYS96 3.6 18.3 1.0
HN2 A:NH3207 3.8 22.1 0.6
HE1 A:TYR20 3.9 17.5 1.0
HE3 A:LYS96 4.1 18.3 1.0
HN1 A:NH3207 4.4 22.1 0.6
HA3 A:GLY16 4.5 20.8 1.0
N A:NH3207 4.5 18.4 0.6
O A:HIS15 4.6 18.1 1.0
CE1 A:TYR20 4.6 14.6 1.0
HD1 A:TYR20 4.9 16.6 1.0
HH A:TYR20 4.9 19.7 0.0
CG A:LYS96 4.9 10.6 1.0

Platinum binding site 5 out of 5 in 5l3i

Go back to Platinum Binding Sites List in 5l3i
Platinum binding site 5 out of 5 in the Re-Refinement of 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15


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 4DD6; Cisplatin Coordination Chemistry Determination at Hen Egg White Lysozyme HIS15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt218

b:28.9
occ:0.10
 HZ1 A:LYS33 1.9 34.5 1.0
HZ2 A:LYS33 2.2 34.5 1.0
HZ3 A:LYS33 2.2 34.5 1.0
NZ A:LYS33 2.2 28.8 1.0
O A:HOH339 3.4 20.4 1.0
OD1 A:ASN37 3.6 23.8 1.0
CE A:LYS33 3.7 25.5 1.0
HD21 A:ASN37 3.9 27.6 1.0
CL A:CL209 3.9 34.5 1.0
HE2 A:LYS33 4.0 30.6 1.0
HE3 A:LYS33 4.1 30.6 1.0
CG A:ASN37 4.5 19.1 1.0
ND2 A:ASN37 4.5 23.0 1.0
HD2 A:LYS33 4.6 24.2 1.0
CD A:LYS33 4.7 20.2 1.0
HD3 A:LYS33 4.7 24.2 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: Thu Oct 10 11:37:29 2024

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