Magnesium in PDB 6rr4: Structure of 25% Reduced Kpdyp

The structure of Structure of 25% Reduced Kpdyp, PDB code: 6rr4 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 (%)	16.9 / 18.1

The structure of Structure of 25% Reduced Kpdyp also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Structure of 25% Reduced Kpdyp (pdb code 6rr4). 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 25% Reduced Kpdyp, PDB code: 6rr4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 25% 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 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:20.2 occ:1.00 O A:HOH610 1.9 22.4 1.0 O A:HOH519 1.9 15.8 1.0 O A:HOH517 2.1 11.7 1.0 O A:HOH749 2.1 31.5 1.0 O A:HOH810 2.1 18.5 1.0 OD2 A:ASP220 2.3 13.7 1.0 CG A:ASP220 3.2 10.8 1.0 OD1 A:ASP220 3.5 9.9 1.0 O A:HOH504 3.8 25.2 1.0 O2D A:HEM401 3.9 5.5 0.2 O2D A:HEM401 4.0 6.1 0.8 O1D A:HEM401 4.0 6.1 0.8 O1D A:HEM401 4.0 5.4 0.2 OE1 A:GLU204 4.1 22.9 1.0 HG3 A:GLU146 4.2 3.0 1.0 CGD A:HEM401 4.4 5.3 0.8 CGD A:HEM401 4.4 4.7 0.2 O A:HOH721 4.5 37.6 1.0 CB A:ASP220 4.5 3.3 1.0 HB2 A:ASP220 4.5 3.0 1.0 HZ3 A:LYS229 4.5 11.1 1.0 OE2 A:GLU204 4.6 20.1 1.0 HE3 A:LYS222 4.7 33.8 1.0 HZ1 A:LYS229 4.8 3.3 1.0 CD A:GLU204 4.8 23.9 1.0 HB3 A:ASP220 4.9 3.5 1.0 O A:HOH791 4.9 40.4 1.0

Magnesium binding site 2 out of 2 in the Structure of 25% 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 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:19.6 occ:1.00 O B:HOH701 2.2 23.6 1.0 O B:HOH560 2.2 12.2 1.0 O B:HOH760 2.2 19.5 1.0 O B:HOH713 2.2 22.3 1.0 O B:HOH509 2.2 15.5 1.0 OD2 B:ASP220 2.2 14.0 1.0 CG B:ASP220 3.2 13.2 1.0 OD1 B:ASP220 3.5 11.5 1.0 O B:HOH517 3.8 23.1 1.0 O2D B:HEM401 4.0 5.7 0.2 O1D B:HEM401 4.0 5.4 0.2 O2D B:HEM401 4.0 6.0 0.8 O B:HOH716 4.1 40.2 1.0 O1D B:HEM401 4.1 5.9 0.8 HZ1 B:LYS229 4.2 23.3 0.5 HG3 B:GLU146 4.4 9.2 1.0 CGD B:HEM401 4.4 4.8 0.2 CGD B:HEM401 4.4 5.2 0.8 OE1 B:GLU204 4.5 23.0 1.0 CB B:ASP220 4.5 6.0 1.0 OE1 B:GLU146 4.5 22.1 1.0 HB2 B:ASP220 4.6 4.5 1.0 HZ3 B:LYS229 4.6 21.4 0.5 OE2 B:GLU204 4.7 13.8 1.0 HE3 B:LYS222 4.7 33.9 1.0 NZ B:LYS229 4.8 22.7 0.5 HB3 B:ASP220 4.9 7.6 1.0 CD B:GLU204 4.9 22.9 1.0 CD B:GLU146 5.0 26.2 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