Magnesium in PDB 6rpd: Structure of Ferrous Kpdyp in Complex with Cyanide

The structure of Structure of Ferrous Kpdyp in Complex with Cyanide, PDB code: 6rpd 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)	40.62 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.570, 75.740, 75.710, 90.00, 107.85, 90.00
R / Rfree (%)	17.1 / 18.9

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

Iron

(Fe)

2 atoms

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

Magnesium binding site 1 out of 2 in the Structure of Ferrous 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 Ferrous Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:25.4 occ:1.00 O A:HOH504 2.0 25.7 1.0 O A:HOH517 2.0 23.2 1.0 O A:HOH689 2.0 27.5 1.0 O A:HOH610 2.0 34.0 1.0 O A:HOH764 2.0 33.6 1.0 OD2 A:ASP220 2.1 25.9 1.0 CG A:ASP220 3.1 23.2 1.0 OD1 A:ASP220 3.5 22.9 1.0 O A:HOH507 3.7 37.8 1.0 O2D A:HEM401 3.9 19.5 1.0 O1D A:HEM401 3.9 19.7 1.0 OE1 A:GLU204 4.1 32.9 1.0 HG3 A:GLU146 4.1 27.0 1.0 O A:HOH678 4.3 47.5 1.0 CGD A:HEM401 4.3 19.1 1.0 CB A:ASP220 4.4 20.9 1.0 HZ1 A:LYS229 4.4 43.8 1.0 HB2 A:ASP220 4.4 20.9 1.0 OE2 A:GLU204 4.4 31.9 1.0 OE1 A:GLU146 4.5 40.3 1.0 HE3 A:LYS222 4.6 64.1 1.0 CD A:GLU204 4.7 32.2 1.0 HZ1 A:LYS222 4.8 75.4 1.0 HB3 A:ASP220 4.8 21.1 1.0 CD A:GLU146 4.8 44.0 1.0 HZ2 A:LYS229 4.9 43.5 1.0 HZ3 A:LYS229 4.9 43.6 1.0 CG A:GLU146 4.9 27.0 1.0 NZ A:LYS229 5.0 43.6 1.0 HB3 A:GLU146 5.0 20.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Ferrous 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 Ferrous Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:25.9 occ:1.00 O B:HOH639 2.0 33.8 1.0 OD2 B:ASP220 2.0 27.6 1.0 O B:HOH656 2.0 31.8 1.0 O B:HOH545 2.1 26.3 1.0 O B:HOH704 2.1 32.2 1.0 O B:HOH504 2.1 25.2 1.0 CG B:ASP220 3.0 27.4 1.0 OD1 B:ASP220 3.4 26.8 1.0 O B:HOH505 3.7 40.2 1.0 O1D B:HEM401 3.9 21.9 1.0 O2D B:HEM401 4.0 22.3 1.0 OE1 B:GLU204 4.1 40.3 1.0 HG3 B:GLU146 4.1 28.4 1.0 CGD B:HEM401 4.3 21.4 1.0 CB B:ASP220 4.4 20.9 1.0 HZ1 B:LYS229 4.4 40.3 0.5 HB2 B:ASP220 4.4 20.8 1.0 OE2 B:GLU204 4.5 29.6 1.0 HE3 B:LYS222 4.5 63.2 1.0 O B:HOH727 4.5 66.5 1.0 OE1 B:GLU146 4.5 42.0 1.0 HZ1 B:LYS222 4.7 81.3 1.0 CD B:GLU204 4.7 39.2 1.0 HB3 B:ASP220 4.7 21.0 1.0 CD B:GLU146 4.8 48.2 1.0 HZ3 B:LYS229 4.9 40.0 0.5 CG B:GLU146 4.9 28.4 1.0 NZ B:LYS229 5.0 40.2 0.5 HZ2 B:LYS229 5.0 40.2 0.5 HB3 B:GLU146 5.0 23.8 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