Magnesium in PDB 6rqy: Structure of % Reduced Kpdyp

The structure of Structure of % Reduced Kpdyp, PDB code: 6rqy was solved by V.Pfanzagl, J.Beale, S.Hofbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.889, 76.647, 76.579, 90.00, 108.01, 90.00
R / Rfree (%)	17.2 / 19.9

The structure of Structure of % Reduced Kpdyp also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Structure of % Reduced Kpdyp (pdb code 6rqy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of % Reduced Kpdyp, PDB code: 6rqy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of % Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of % Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:22.1 occ:1.00 O A:HOH649 1.9 26.5 1.0 O A:HOH516 1.9 13.4 1.0 O A:HOH734 1.9 25.2 1.0 O A:HOH817 2.1 24.3 1.0 O A:HOH545 2.2 12.9 1.0 OD2 A:ASP220 2.3 14.2 1.0 CG A:ASP220 3.2 11.3 1.0 OD1 A:ASP220 3.5 11.1 1.0 O A:HOH506 3.9 31.6 1.0 O1D A:HEM401 4.1 5.2 0.1 O2D A:HEM401 4.1 5.5 0.1 O1D A:HEM401 4.1 6.2 0.9 O2D A:HEM401 4.1 6.5 0.9 OE1 A:GLU204 4.3 25.5 1.0 O A:HOH762 4.4 35.8 1.0 HZ3 A:LYS229 4.4 11.5 1.0 CGD A:HEM401 4.5 5.5 0.9 CGD A:HEM401 4.5 4.6 0.1 HG3 A:GLU146 4.5 3.3 1.0 CB A:ASP220 4.6 3.6 1.0 OE2 A:GLU204 4.6 17.0 1.0 HB2 A:ASP220 4.6 3.4 1.0 HE3 A:LYS222 4.6 34.1 1.0 HZ1 A:LYS229 4.7 3.6 1.0 CD A:GLU204 4.9 25.4 1.0 NZ A:LYS229 4.9 7.3 1.0 HB3 A:ASP220 4.9 3.8 1.0

Magnesium binding site 2 out of 2 in the Structure of % Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of % Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:18.1 occ:1.00 O B:HOH668 1.9 22.7 1.0 O B:HOH771 2.0 23.0 1.0 O B:HOH675 2.1 12.1 1.0 O B:HOH537 2.1 12.3 1.0 O B:HOH736 2.2 30.2 1.0 OD2 B:ASP220 2.3 17.2 1.0 CG B:ASP220 3.2 13.0 1.0 OD1 B:ASP220 3.5 10.9 1.0 O B:HOH503 3.8 20.1 1.0 O2D B:HEM401 4.0 5.6 0.1 O2D B:HEM401 4.0 6.3 0.9 O1D B:HEM401 4.0 5.8 0.9 O1D B:HEM401 4.0 5.3 0.1 HG3 B:GLU146 4.2 9.4 1.0 OE1 B:GLU204 4.4 22.7 1.0 CGD B:HEM401 4.4 5.2 0.9 CGD B:HEM401 4.4 4.7 0.1 CB B:ASP220 4.5 6.1 1.0 HB2 B:ASP220 4.5 4.4 1.0 OE2 B:GLU204 4.6 13.0 1.0 OE1 B:GLU146 4.6 22.5 1.0 O B:HOH777 4.8 50.6 1.0 HB3 B:ASP220 4.9 7.8 1.0 CD B:GLU204 4.9 22.3 1.0 O B:HOH806 4.9 28.7 1.0 CD B:GLU146 5.0 24.5 1.0 HE3 B:LYS222 5.0 34.1 1.0

V.Pfanzagl, J.H.Beale, H.Michlits, D.Schmidt, T.Gabler, C.Obinger, K.Djinovic-Carugo, S.Hofbauer. X-Ray-Induced Photoreduction of Heme Metal Centers Rapidly Induces Active-Site Perturbations in A Protein-Independent Manner. J.Biol.Chem. V. 295 13488 2020.
ISSN: ESSN 1083-351X
PubMed: 32723869
DOI: 10.1074/JBC.RA120.014087