Magnesium in PDB 6ryk: Crystal Structure of the Parb-Like Protein Padc

The structure of Crystal Structure of the Parb-Like Protein Padc, PDB code: 6ryk was solved by F.Altegoer, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.74 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.850, 42.440, 49.530, 108.54, 99.15, 89.28
R / Rfree (%)	18.5 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of the Parb-Like Protein Padc (pdb code 6ryk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Parb-Like Protein Padc, PDB code: 6ryk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Parb-Like Protein Padc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Parb-Like Protein Padc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.3 occ:1.00 O1A A:CTP502 2.0 31.2 1.0 O2B A:CTP502 2.2 26.2 1.0 O2G A:CTP502 2.2 29.5 1.0 O A:HOH665 2.2 35.5 1.0 O A:HOH690 2.3 33.2 1.0 O A:HOH671 2.3 28.8 1.0 PB A:CTP502 3.2 26.6 1.0 PA A:CTP502 3.2 28.7 1.0 PG A:CTP502 3.3 29.5 1.0 O3A A:CTP502 3.6 25.6 1.0 O3B A:CTP502 3.7 26.0 1.0 O5' A:CTP502 3.8 26.7 1.0 O3G A:CTP502 3.9 26.5 1.0 NH2 A:ARG311 3.9 37.4 1.0 O B:HOH686 4.2 52.0 1.0 O A:HOH696 4.2 45.8 1.0 OE2 A:GLU382 4.2 37.7 0.5 O A:HOH663 4.2 36.6 1.0 OE1 A:GLU382 4.2 42.3 0.5 NH2 A:ARG350 4.2 25.0 1.0 O2A A:CTP502 4.5 35.9 1.0 O1B A:CTP502 4.6 24.8 1.0 O1G A:CTP502 4.6 32.6 1.0 O A:HOH668 4.7 43.2 1.0 CD A:GLU382 4.7 49.0 0.5 CD A:GLU382 4.8 44.5 0.5 OE2 A:GLU382 4.9 59.9 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of the Parb-Like Protein Padc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Parb-Like Protein Padc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:27.3 occ:1.00 O2A B:CTP502 1.9 28.5 1.0 O1G B:CTP502 2.1 27.9 1.0 O1B B:CTP502 2.1 25.1 1.0 O B:HOH608 2.2 30.4 1.0 O B:HOH680 2.3 35.2 1.0 O B:HOH609 2.4 39.4 1.0 PA B:CTP502 3.2 29.2 1.0 PB B:CTP502 3.2 26.7 1.0 PG B:CTP502 3.3 29.1 1.0 O3A B:CTP502 3.5 27.6 1.0 O3B B:CTP502 3.7 24.8 1.0 NH2 B:ARG311 3.8 32.3 1.0 O5' B:CTP502 3.9 27.9 1.0 O3G B:CTP502 3.9 27.3 1.0 O B:HOH663 4.1 33.5 1.0 OE1 B:GLU382 4.1 34.6 0.4 OE2 B:GLU382 4.2 39.4 0.6 O B:HOH689 4.3 51.1 1.0 NH2 B:ARG350 4.3 24.0 1.0 OE1 B:GLU382 4.3 27.7 0.6 O B:HOH678 4.4 40.9 1.0 O1A B:CTP502 4.4 39.0 1.0 CD B:GLU382 4.5 31.8 0.6 O2B B:CTP502 4.5 20.9 1.0 O2G B:CTP502 4.6 32.9 1.0 O B:HOH627 4.9 40.5 1.0

M.Osorio-Valeriano, F.Altegoer, W.Steinchen, S.Urban, Y.Liu, G.Bange, M.Thanbichler. Parb-Type Dna Segregation Proteins Are Ctp-Dependent Molecular Switches. Cell V. 179 1512 2019.
ISSN: ISSN 1097-4172
PubMed: 31835030
DOI: 10.1016/J.CELL.2019.11.015