Magnesium in PDB 6rpe: Structure of 5% Reduced Kpdyp in Complex with Cyanide

The structure of Structure of 5% Reduced Kpdyp in Complex with Cyanide, PDB code: 6rpe 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)	36.31 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.853, 76.592, 76.308, 90.00, 107.87, 90.00
R / Rfree (%)	17.2 / 19.7

The structure of Structure of 5% Reduced Kpdyp in Complex with Cyanide also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Structure of 5% Reduced Kpdyp in Complex with Cyanide (pdb code 6rpe). 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 5% Reduced Kpdyp in Complex with Cyanide, PDB code: 6rpe:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 5% Reduced Kpdyp in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:17.9 occ:1.00 O A:HOH615 2.1 21.9 1.0 O A:HOH738 2.1 22.3 1.0 OD2 A:ASP220 2.1 12.0 1.0 O A:HOH570 2.1 7.1 1.0 O A:HOH527 2.2 12.3 1.0 O A:HOH801 2.2 17.2 1.0 CG A:ASP220 3.1 8.6 1.0 OD1 A:ASP220 3.5 7.5 1.0 HZ1 A:LYS222 3.7 53.2 1.0 O A:HOH517 3.7 17.6 1.0 O1D A:HEM401 4.0 4.9 0.1 O1D A:HEM401 4.0 5.8 0.9 O2D A:HEM401 4.0 5.2 0.1 O2D A:HEM401 4.0 6.4 0.9 HG3 A:GLU146 4.1 10.6 1.0 OE1 A:GLU204 4.2 15.7 1.0 OE1 A:GLU146 4.3 23.2 1.0 HZ2 A:LYS222 4.3 53.0 1.0 O A:HOH797 4.3 25.1 1.0 HZ2 A:LYS229 4.3 37.9 1.0 CB A:ASP220 4.4 3.9 1.0 CGD A:HEM401 4.4 5.3 0.9 CGD A:HEM401 4.4 4.3 0.1 HB2 A:ASP220 4.4 3.5 1.0 NZ A:LYS222 4.5 53.3 1.0 HZ1 A:LYS229 4.6 37.5 1.0 OE2 A:GLU204 4.6 13.5 1.0 CD A:GLU146 4.7 26.2 1.0 HB3 A:ASP220 4.8 4.1 1.0 O A:HOH815 4.8 35.7 1.0 CD A:GLU204 4.8 19.6 1.0 CG A:GLU146 4.9 10.5 1.0 NZ A:LYS229 4.9 37.7 1.0 HD23 A:LEU216 5.0 4.0 1.0

Magnesium binding site 2 out of 2 in the Structure of 5% Reduced Kpdyp in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:13.7 occ:1.00 O B:HOH627 2.0 11.4 1.0 O B:HOH629 2.0 21.4 1.0 OD2 B:ASP220 2.1 14.2 1.0 O B:HOH777 2.1 19.9 1.0 O B:HOH526 2.1 11.1 1.0 O B:HOH739 2.2 19.5 1.0 CG B:ASP220 3.1 11.5 1.0 OD1 B:ASP220 3.5 10.4 1.0 O B:HOH516 3.7 17.3 1.0 HZ1 B:LYS222 3.8 42.7 1.0 O2D B:HEM401 3.9 5.7 0.1 O1D B:HEM401 3.9 5.8 0.9 O2D B:HEM401 3.9 6.1 0.9 O1D B:HEM401 3.9 5.4 0.1 HG3 B:GLU146 4.0 9.9 1.0 OE1 B:GLU204 4.1 23.4 1.0 OE1 B:GLU146 4.2 25.2 1.0 CGD B:HEM401 4.3 5.2 0.9 CGD B:HEM401 4.3 4.8 0.1 CB B:ASP220 4.4 4.0 1.0 HB2 B:ASP220 4.4 3.9 1.0 HZ2 B:LYS222 4.4 42.3 1.0 OE2 B:GLU204 4.6 11.9 1.0 NZ B:LYS222 4.6 42.6 1.0 CD B:GLU146 4.6 23.7 1.0 HB3 B:ASP220 4.8 4.1 1.0 CD B:GLU204 4.8 20.6 1.0 CG B:GLU146 4.8 10.0 1.0 O B:HOH522 4.8 16.3 1.0 HD23 B:LEU216 4.9 4.1 1.0 O B:HOH840 4.9 33.3 1.0 HB3 B:GLU146 4.9 3.9 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