Magnesium in PDB 6rr8: Structure of 100% Reduced Kpdyp (Final Wedges)

The structure of Structure of 100% Reduced Kpdyp (Final Wedges), PDB code: 6rr8 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)	47.67 / 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

The structure of Structure of 100% Reduced Kpdyp (Final Wedges) also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Structure of 100% Reduced Kpdyp (Final Wedges) (pdb code 6rr8). 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 100% Reduced Kpdyp (Final Wedges), PDB code: 6rr8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 100% Reduced Kpdyp (Final Wedges)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 100% Reduced Kpdyp (Final Wedges) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:17.9 occ:1.00 O A:HOH640 1.9 27.3 1.0 O A:HOH725 2.0 20.0 1.0 O A:HOH812 2.0 24.6 1.0 O A:HOH505 2.0 20.3 1.0 O A:HOH513 2.1 10.1 1.0 OD2 A:ASP220 2.4 14.4 1.0 CG A:ASP220 3.3 11.8 1.0 OD1 A:ASP220 3.7 10.7 1.0 O A:HOH509 3.9 26.3 1.0 O2D A:HEM401 4.0 6.4 1.0 O1D A:HEM401 4.0 6.5 1.0 OE1 A:GLU204 4.2 23.4 1.0 HG3 A:GLU146 4.5 3.9 1.0 CGD A:HEM401 4.5 5.6 1.0 OE2 A:GLU204 4.5 21.5 1.0 HZ3 A:LYS229 4.6 11.7 1.0 CB A:ASP220 4.6 4.6 1.0 HB2 A:ASP220 4.6 3.5 1.0 O A:HOH619 4.7 62.2 1.0 HE3 A:LYS222 4.7 34.4 1.0 CD A:GLU204 4.8 26.7 1.0 HZ1 A:LYS229 4.8 4.6 1.0 HZ1 A:LYS222 4.9 36.7 1.0 HB3 A:ASP220 4.9 5.5 1.0

Magnesium binding site 2 out of 2 in the Structure of 100% Reduced Kpdyp (Final Wedges)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 100% Reduced Kpdyp (Final Wedges) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:19.5 occ:1.00 O B:HOH688 2.0 22.5 1.0 O B:HOH780 2.0 19.8 1.0 O B:HOH540 2.1 9.8 1.0 O B:HOH731 2.2 20.7 1.0 OD2 B:ASP220 2.2 14.4 1.0 O B:HOH504 2.2 12.9 1.0 CG B:ASP220 3.2 13.0 1.0 OD1 B:ASP220 3.6 11.7 1.0 O B:HOH516 3.8 25.7 1.0 O1D B:HEM401 4.0 7.1 1.0 O2D B:HEM401 4.0 7.0 1.0 OE1 B:GLU204 4.2 22.6 1.0 HG3 B:GLU146 4.3 9.5 1.0 CGD B:HEM401 4.4 6.3 1.0 OE1 B:GLU146 4.5 24.3 1.0 CB B:ASP220 4.5 7.2 1.0 HB2 B:ASP220 4.6 6.2 1.0 OE2 B:GLU204 4.6 12.1 1.0 O B:HOH800 4.6 47.8 1.0 CD B:GLU204 4.8 25.2 1.0 HE3 B:LYS222 4.8 34.1 1.0 O B:HOH600 4.8 28.1 1.0 HB3 B:ASP220 4.9 8.0 1.0 CD B:GLU146 4.9 28.5 1.0 O B:HOH802 5.0 37.0 1.0 HZ1 B:LYS222 5.0 36.4 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