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Platinum in PDB 4yem: Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement

Enzymatic activity of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement

All present enzymatic activity of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement:
3.2.1.17;

Protein crystallography data

The structure of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement, PDB code: 4yem was solved by I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.29 / 1.47
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.580, 78.580, 37.290, 90.00, 90.00, 90.00
R / Rfree (%) 10.5 / 15.6

Other elements in 4yem:

The structure of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement also contains other interesting chemical elements:

Bromine (Br) 19 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Platinum Binding Sites:

The binding sites of Platinum atom in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement (pdb code 4yem). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement, PDB code: 4yem:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 4yem

Go back to Platinum Binding Sites List in 4yem
Platinum binding site 1 out of 3 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:17.3
occ:0.85
 ND1 A:HIS15 2.1 19.3 1.0
CL A:CL223 2.3 29.6 0.8
BR A:BR202 2.5 19.4 0.8
BR A:BR203 2.5 23.9 0.8
BR A:BR204 3.1 23.3 0.1
CE1 A:HIS15 3.1 18.6 1.0
CG A:HIS15 3.1 13.5 1.0
CB A:HIS15 3.4 12.8 1.0
CA A:HIS15 3.5 12.7 1.0
O A:HIS15 4.1 15.7 1.0
NE2 A:HIS15 4.2 18.5 1.0
O A:HOH321 4.2 28.9 1.0
CD2 A:HIS15 4.2 14.0 1.0
C A:HIS15 4.3 13.8 1.0
N A:HIS15 4.6 12.3 1.0
CG2 A:THR89 4.7 11.8 1.0
OG1 A:THR89 4.8 14.1 1.0
O A:ARG14 4.8 16.1 1.0

Platinum binding site 2 out of 3 in 4yem

Go back to Platinum Binding Sites List in 4yem
Platinum binding site 2 out of 3 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt218

b:17.0
occ:0.10
 BR A:BR214 2.3 26.8 0.2
NZ A:LYS96 2.4 18.2 1.0
O A:HOH301 2.5 26.9 1.0
CE A:LYS96 3.3 14.6 1.0
CD A:LYS96 3.5 13.8 1.0
BR A:BR204 3.7 23.3 0.1
O A:HOH447 3.8 34.1 1.0
O A:HIS15 4.5 15.7 1.0
OD1 A:ASN93 4.9 18.0 0.6
CE2 A:TYR20 4.9 13.1 1.0
CG A:LYS96 4.9 10.5 1.0

Platinum binding site 3 out of 3 in 4yem

Go back to Platinum Binding Sites List in 4yem
Platinum binding site 3 out of 3 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt224

b:21.1
occ:0.15
 NH2 A:ARG14 2.1 27.4 1.0
BR A:BR205 2.1 19.9 0.6
O A:HOH318 2.4 26.4 0.7
NE2 A:HIS15 2.7 18.5 1.0
CZ A:ARG14 3.1 23.4 1.0
NE A:ARG14 3.5 25.5 1.0
CE1 A:HIS15 3.5 18.6 1.0
CD2 A:HIS15 3.6 14.0 1.0
O A:HOH358 3.6 43.4 1.0
OD1 A:ASP87 4.1 18.2 1.0
NH1 A:ARG14 4.2 26.3 1.0
ND1 A:HIS15 4.6 19.3 1.0
CG A:HIS15 4.7 13.5 1.0
CG A:ASP87 4.8 20.5 1.0
CB A:ALA11 4.8 11.6 1.0
OG1 A:THR89 4.9 14.1 1.0
CD A:ARG14 4.9 23.3 1.0
CG1 A:ILE88 4.9 12.8 1.0
N A:ILE88 4.9 10.9 1.0

Reference:

I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer. Crystallography and Chemistry Should Always Go Together: A Cautionary Tale of Protein Complexes with Cisplatin and Carboplatin To Be Published.
Page generated: Mon Aug 18 23:47:25 2025

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