Atomistry » Magnesium » PDB 6ind-6izw » 6iq4
Atomistry »
  Magnesium »
    PDB 6ind-6izw »
      6iq4 »

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

Protein crystallography data

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

Other elements in 6iq4:

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

Magnesium Binding Sites:

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 6iq4

Go back to Magnesium Binding Sites List in 6iq4
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 6iq4

Go back to Magnesium Binding Sites List in 6iq4
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 6iq4

Go back to Magnesium Binding Sites List in 6iq4
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 6iq4

Go back to Magnesium Binding Sites List in 6iq4
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

Reference:

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
Page generated: Mon Dec 14 22:58:35 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy