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Manganese in PDB 3rek: 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin

Protein crystallography data

The structure of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin, PDB code: 3rek was solved by B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.001, 109.436, 176.357, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 28.1

Other elements in 3rek:

The structure of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin also contains other interesting chemical elements:

Platinum (Pt) 40 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin (pdb code 3rek). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin, PDB code: 3rek:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3rek

Go back to Manganese Binding Sites List in 3rek
Manganese binding site 1 out of 2 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:53.2
occ:1.00
OD1 A:ASP77 2.0 57.8 1.0
CG A:ASP77 3.1 54.5 1.0
OD2 A:ASP77 3.6 56.7 1.0
OE1 A:GLN76 4.3 53.8 1.0
O A:GLU73 4.3 45.8 1.0
N A:ASP77 4.4 52.2 1.0
CB A:ASP77 4.4 52.8 1.0
O B:LEU22 4.4 52.2 1.0
CA A:ASP77 4.6 53.2 1.0
CB A:GLN76 4.8 50.6 1.0
CG A:GLU73 4.9 45.8 1.0
C A:GLN76 5.0 51.6 1.0

Manganese binding site 2 out of 2 in 3rek

Go back to Manganese Binding Sites List in 3rek
Manganese binding site 2 out of 2 in the 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) Derivatized with Oxaliplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1007

b:0.9
occ:1.00
O D:VAL45 2.5 80.8 1.0
C D:VAL45 3.3 80.8 1.0
CA D:VAL45 3.6 80.7 1.0
OE1 C:GLU64 4.1 77.3 1.0
O D:GLN44 4.3 81.2 1.0
CB D:VAL45 4.4 80.9 1.0
N D:HIS46 4.5 80.9 1.0
O3 D:SO41101 4.7 83.3 1.0
CD D:PRO47 4.7 82.5 1.0
N D:VAL45 4.7 80.7 1.0
CA D:HIS46 5.0 81.7 1.0
CG1 D:VAL45 5.0 81.2 1.0
C D:GLN44 5.0 80.8 1.0

Reference:

B.Wu, G.E.Davey, A.A.Nazarov, P.J.Dyson, C.A.Davey. Specific Dna Structural Attributes Modulate Platinum Anticancer Drug Site Selection and Cross-Link Generation. Nucleic Acids Res. V. 39 8200 2011.
ISSN: ISSN 0305-1048
PubMed: 21724603
DOI: 10.1093/NAR/GKR491
Page generated: Tue Dec 15 04:14:43 2020

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