Magnesium in PDB 6kvo: Crystal Structure of Chloroplast Resolvase in Complex with Holliday Junction

The structure of Crystal Structure of Chloroplast Resolvase in Complex with Holliday Junction, PDB code: 6kvo was solved by J.J.Yan, S.X.Hong, Z.Y.Guan, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.02 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.316, 92.155, 65.894, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of Chloroplast Resolvase in Complex with Holliday Junction (pdb code 6kvo). 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 Chloroplast Resolvase in Complex with Holliday Junction, PDB code: 6kvo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Chloroplast Resolvase in Complex with Holliday Junction


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 Chloroplast Resolvase in Complex with Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:89.2 occ:1.00 OD2 A:ASP118 2.4 0.3 1.0 OE2 A:GLU175 2.8 0.3 1.0 OP1 F:DA10 3.1 0.8 1.0 OE2 A:GLU258 3.2 0.3 1.0 C5' F:DA10 3.6 75.2 1.0 CG A:ASP118 3.6 99.1 1.0 OD1 A:ASP116 3.7 77.7 1.0 CD A:GLU175 3.8 96.8 1.0 O3' F:DC9 3.9 0.7 1.0 P F:DA10 4.0 0.5 1.0 OD1 A:ASP118 4.1 0.3 1.0 OE1 A:GLU175 4.1 0.3 1.0 CD A:GLU258 4.1 0.2 1.0 OD2 A:ASP116 4.1 80.2 1.0 CG A:ASP116 4.2 66.3 1.0 OE1 A:GLU258 4.2 0.3 1.0 O5' F:DA10 4.3 99.5 1.0 CB A:ASP118 4.8 75.1 1.0 CB A:SER177 4.8 0.6 1.0 C4' F:DA10 4.8 71.6 1.0 OG A:SER177 4.9 0.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Chloroplast Resolvase in Complex with Holliday Junction


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 Chloroplast Resolvase in Complex with Holliday Junction within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:0.7 occ:1.00 OP1 E:DA10 2.2 98.9 1.0 OE1 B:GLU175 2.7 0.6 1.0 OE2 B:GLU175 3.0 0.8 1.0 CD B:GLU175 3.2 0.7 1.0 OE1 B:GLU258 3.3 0.2 1.0 OD1 B:ASP116 3.4 72.9 1.0 OD2 B:ASP116 3.5 82.5 1.0 P E:DA10 3.6 0.9 1.0 OD2 B:ASP118 3.6 0.3 1.0 CG B:GLU258 3.6 80.6 1.0 CG B:ASP116 3.7 68.5 1.0 CD B:GLU258 3.8 0.3 1.0 O3' E:DC9 3.9 0.4 1.0 NE2 B:HIS254 4.0 88.4 1.0 C5' E:DA10 4.1 55.9 1.0 O5' E:DA10 4.3 95.3 1.0 CB B:GLU258 4.5 75.9 1.0 CD2 B:HIS254 4.7 84.1 1.0 CG B:ASP118 4.7 0.8 1.0 CG B:GLU175 4.7 81.7 1.0 OP2 E:DA10 4.8 86.0 1.0 OE2 B:GLU258 4.9 0.0 1.0

J.Yan, S.Hong, Z.Guan, W.He, D.Zhang, P.Yin. Structural Insights Into Sequence-Dependent Holliday Junction Resolution By the Chloroplast Resolvase MOC1. Nat Commun V. 11 1417 2020.
ISSN: ESSN 2041-1723
PubMed: 32184398
DOI: 10.1038/S41467-020-15242-8