Magnesium in PDB 6rr1: Structure of 10% Reduced Kpdyp

The structure of Structure of 10% Reduced Kpdyp, PDB code: 6rr1 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 / 19.1

The structure of Structure of 10% Reduced Kpdyp also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Structure of 10% Reduced Kpdyp (pdb code 6rr1). 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 10% Reduced Kpdyp, PDB code: 6rr1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 10% 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 10% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:20.9 occ:1.00 O A:HOH521 2.0 14.6 1.0 O A:HOH626 2.0 27.7 1.0 O A:HOH719 2.1 21.6 1.0 O A:HOH796 2.1 23.3 1.0 O A:HOH525 2.1 10.9 1.0 OD2 A:ASP220 2.3 12.2 1.0 CG A:ASP220 3.2 10.5 1.0 OD1 A:ASP220 3.6 10.4 1.0 O A:HOH507 3.9 23.5 1.0 O2D A:HEM401 4.0 5.7 0.1 O1D A:HEM401 4.0 5.4 0.1 O1D A:HEM401 4.1 6.8 0.9 O2D A:HEM401 4.1 6.7 0.9 OE1 A:GLU204 4.2 21.4 1.0 HG3 A:GLU146 4.4 3.1 1.0 HZ3 A:LYS229 4.4 11.6 1.0 CGD A:HEM401 4.5 5.8 0.9 CGD A:HEM401 4.5 4.7 0.1 OE2 A:GLU204 4.5 19.1 1.0 CB A:ASP220 4.6 3.3 1.0 HB2 A:ASP220 4.6 3.2 1.0 O A:HOH768 4.6 54.0 1.0 HE3 A:LYS222 4.6 34.2 1.0 CD A:GLU204 4.8 25.6 1.0 HZ1 A:LYS229 4.8 3.3 1.0 OE1 A:GLU146 4.8 24.8 1.0 HZ2 A:LYS229 4.9 6.3 1.0 NZ A:LYS229 4.9 7.2 1.0 HB3 A:ASP220 4.9 3.4 1.0 HZ1 A:LYS222 5.0 36.6 1.0

Magnesium binding site 2 out of 2 in the Structure of 10% 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 10% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:14.8 occ:1.00 O B:HOH593 1.9 18.2 1.0 O B:HOH771 2.0 23.9 1.0 O B:HOH522 2.1 12.2 1.0 O B:HOH588 2.1 10.9 1.0 O B:HOH709 2.2 23.9 1.0 OD2 B:ASP220 2.2 12.2 1.0 CG B:ASP220 3.1 12.5 1.0 OD1 B:ASP220 3.5 9.2 1.0 HZ2 B:LYS222 3.7 36.0 1.0 O B:HOH504 3.8 26.6 1.0 O1D B:HEM401 3.9 4.7 0.1 O2D B:HEM401 3.9 5.0 0.1 O2D B:HEM401 3.9 5.8 0.9 O1D B:HEM401 4.0 5.6 0.9 HG3 B:GLU146 4.2 9.6 1.0 CGD B:HEM401 4.3 5.0 0.9 CGD B:HEM401 4.4 4.2 0.1 OE1 B:GLU204 4.4 21.4 1.0 CB B:ASP220 4.5 5.5 1.0 HB2 B:ASP220 4.5 3.6 1.0 NZ B:LYS222 4.5 36.1 1.0 HZ1 B:LYS222 4.6 36.6 1.0 OE2 B:GLU204 4.6 12.0 1.0 O B:HOH779 4.6 43.5 1.0 OE1 B:GLU146 4.6 23.9 1.0 HB3 B:ASP220 4.8 7.5 1.0 CD B:GLU204 4.9 23.3 1.0 O B:HOH778 4.9 38.1 1.0 O B:HOH603 4.9 22.2 1.0 CD B:GLU146 4.9 27.6 1.0 HZ3 B:LYS222 4.9 35.9 1.0 O B:HOH760 5.0 37.3 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