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Sodium 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
Platinum (Pt) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 4yem

Go back to Sodium Binding Sites List in 4yem
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na219

b:10.6
occ:1.00
 O A:SER60 2.3 9.7 1.0
O A:CYS64 2.4 8.6 1.0
O A:ARG73 2.4 13.1 1.0
O A:HOH419 2.5 12.7 1.0
O A:HOH412 2.5 10.4 1.0
OG A:SER72 2.5 11.5 1.0
CB A:SER72 3.2 10.8 1.0
C A:CYS64 3.5 8.6 1.0
C A:ARG73 3.5 11.6 1.0
C A:SER60 3.5 8.8 1.0
N A:ARG73 3.9 12.5 1.0
CA A:ASN65 3.9 8.8 1.0
N A:ASN65 4.1 8.1 1.0
C A:SER72 4.1 13.5 1.0
CA A:SER60 4.1 7.5 1.0
CB A:SER60 4.3 6.9 1.0
CA A:ARG73 4.3 14.2 1.0
CA A:SER72 4.3 12.0 1.0
N A:ASN74 4.4 11.1 1.0
N A:CYS64 4.4 9.3 1.0
O A:ARG61 4.4 13.6 1.0
C A:ARG61 4.5 12.2 1.0
N A:ARG61 4.6 9.7 1.0
CA A:CYS64 4.6 8.4 1.0
CA A:ASN74 4.6 11.6 1.0
N A:ASP66 4.6 7.8 1.0
O A:SER72 4.7 14.4 1.0
CA A:ARG61 4.7 11.2 1.0
CB A:ASN74 4.8 12.2 1.0
OD1 A:ASN65 4.8 15.9 1.0
BR A:BR208 4.8 19.3 0.8
CB A:THR69 4.8 9.5 1.0
C A:ASN65 4.8 8.5 1.0
CB A:ASN65 4.8 9.6 1.0
O A:HOH427 4.9 29.3 1.0
N A:TRP62 5.0 11.6 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 Oct 7 19:30:01 2024

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