Magnesium in PDB 6iq4: Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups.

The structure of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups., PDB code: 6iq4 was solved by L.Defalco, L.K.Batchelor, Z.Adhireksan, P.J.Dyson, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.307, 109.741, 183.254, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 25.7

The structure of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. also contains other interesting chemical elements:

Gold	(Au)	1 atom
Ruthenium	(Ru)	1 atom

The binding sites of Magnesium atom in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. (pdb code 6iq4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups., PDB code: 6iq4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:51.2 occ:1.00 O D:VAL45 2.0 52.7 1.0 O D:HOH301 2.2 51.8 1.0 C D:VAL45 3.1 47.7 1.0 CA D:VAL45 3.6 48.6 1.0 OE2 C:GLU64 3.9 56.1 1.0 N D:HIS46 4.2 50.9 1.0 O D:GLN44 4.2 51.6 1.0 CB D:VAL45 4.3 54.7 1.0 ND1 D:HIS46 4.7 56.7 1.0 CA D:HIS46 4.7 52.8 1.0 N D:VAL45 4.7 52.3 1.0 OE1 C:GLU64 4.8 72.1 1.0 CD C:GLU64 4.8 56.4 1.0 CD D:PRO47 4.8 58.1 1.0 C D:GLN44 4.9 52.8 1.0 CE1 D:HIS46 4.9 57.7 1.0

Magnesium binding site 2 out of 4 in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg101 b:84.5 occ:1.00 O6 I:DG60 3.2 0.2 1.0 N7 I:DG60 3.6 0.3 1.0 C6 I:DG60 4.0 0.7 1.0 C5 I:DG60 4.2 0.5 1.0 O6 I:DG61 4.3 0.8 1.0 N7 I:DA59 4.5 0.3 1.0 N4 J:DC-61 4.7 96.7 1.0 C8 I:DG60 4.8 0.1 1.0 C8 I:DA59 4.8 0.8 1.0

Magnesium binding site 3 out of 4 in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg102 b:74.1 occ:1.00 O I:HOH202 2.2 67.2 1.0 N3 I:DA3 3.6 0.1 1.0 C2 I:DA3 4.1 97.4 1.0 N2 J:DG-2 4.1 0.4 1.0 O4' I:DG4 4.2 94.3 1.0 C4' I:DG4 4.4 0.4 1.0 O4' J:DA-1 4.6 92.0 1.0 O4' I:DA3 4.7 0.0 1.0 C5' I:DG4 4.7 0.9 1.0 C4 I:DA3 4.8 0.6 1.0 C1' I:DA3 4.8 0.6 1.0

Magnesium binding site 4 out of 4 in the Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nucleosome Core Particle Cross-Linked with A Hetero-Binuclear Molecule Possessing Rapta and Gold(I) 4-(Diphenylphosphino)Benzoic Acid Groups. within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg101 b:75.9 occ:1.00 N7 J:DG60 2.7 0.3 1.0 O6 J:DG60 3.1 0.5 1.0 C5 J:DG60 3.5 0.7 1.0 C6 J:DG60 3.6 0.3 1.0 C8 J:DG60 3.8 0.6 1.0 N7 J:DA59 4.0 0.7 1.0 C8 J:DA59 4.1 0.3 1.0 O6 J:DG61 4.3 0.1 1.0 C4 J:DG60 4.7 0.5 1.0 N9 J:DG60 4.9 0.2 1.0 N9 J:DA59 5.0 0.5 1.0

L.K.Batchelor, L.De Falco, T.Von Erlach, D.Sharma, Z.Adhireksan, U.Roethlisberger, C.A.Davey, P.J.Dyson. Crosslinking Allosteric Sites on the Nucleosome. Angew.Chem.Int.Ed.Engl. V. 58 15660 2019.
ISSN: ESSN 1521-3773
PubMed: 31478581
DOI: 10.1002/ANIE.201906423