Magnesium in PDB 6rr6: Structure of 100% Reduced Kpdyp

Protein crystallography data

The structure of Structure of 100% Reduced Kpdyp, PDB code: 6rr6 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 (%) 18.1 / 19.9

Other elements in 6rr6:

The structure of Structure of 100% Reduced Kpdyp also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of 100% Reduced Kpdyp (pdb code 6rr6). 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, PDB code: 6rr6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6rr6

Go back to Magnesium Binding Sites List in 6rr6
Magnesium binding site 1 out of 2 in the Structure of 100% 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 100% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:19.6
occ:1.00
O A:HOH711 1.9 21.0 1.0
O A:HOH536 2.0 21.1 1.0
O A:HOH661 2.0 17.3 1.0
O A:HOH526 2.1 11.0 1.0
O A:HOH791 2.1 20.1 1.0
OD2 A:ASP220 2.2 14.4 1.0
CG A:ASP220 3.2 10.1 1.0
OD1 A:ASP220 3.6 10.0 1.0
O A:HOH510 3.8 25.4 1.0
O1D A:HEM401 4.0 5.7 1.0
O2D A:HEM401 4.0 6.1 1.0
OE1 A:GLU204 4.2 18.6 1.0
HG3 A:GLU146 4.3 3.0 1.0
CGD A:HEM401 4.4 5.0 1.0
HZ3 A:LYS229 4.5 10.6 1.0
OE2 A:GLU204 4.5 18.5 1.0
CB A:ASP220 4.5 3.0 1.0
O A:HOH747 4.5 44.5 1.0
HB2 A:ASP220 4.6 3.0 1.0
OE1 A:GLU146 4.6 32.2 1.0
HE3 A:LYS222 4.7 33.4 1.0
CD A:GLU204 4.7 26.5 1.0
HZ1 A:LYS229 4.9 3.1 1.0
HB3 A:ASP220 4.9 3.0 1.0
HZ1 A:LYS222 5.0 35.9 1.0

Magnesium binding site 2 out of 2 in 6rr6

Go back to Magnesium Binding Sites List in 6rr6
Magnesium binding site 2 out of 2 in the Structure of 100% 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 100% Reduced Kpdyp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:18.5
occ:1.00
O B:HOH759 2.0 26.8 1.0
O B:HOH571 2.0 13.1 1.0
O B:HOH624 2.1 23.1 1.0
O B:HOH596 2.1 11.1 1.0
OD2 B:ASP220 2.2 17.1 1.0
O B:HOH739 2.2 19.6 1.0
CG B:ASP220 3.2 12.1 1.0
OD1 B:ASP220 3.6 12.1 1.0
O B:HOH508 3.8 25.3 1.0
O2D B:HEM401 3.9 5.6 1.0
O1D B:HEM401 4.0 5.3 1.0
HG3 B:GLU146 4.2 8.5 1.0
OE1 B:GLU204 4.3 17.6 1.0
CGD B:HEM401 4.3 4.7 1.0
CB B:ASP220 4.5 5.0 1.0
HB2 B:ASP220 4.5 3.4 1.0
OE1 B:GLU146 4.6 23.2 1.0
OE2 B:GLU204 4.6 12.6 1.0
HE3 B:LYS222 4.8 33.4 1.0
CD B:GLU204 4.8 25.5 1.0
CD B:GLU146 4.9 30.1 1.0
HB3 B:ASP220 4.9 6.4 1.0
CG B:GLU146 4.9 8.3 1.0
O B:HOH582 4.9 25.4 1.0
O B:HOH769 5.0 33.1 1.0

Reference:

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
Page generated: Mon Jan 25 15:11:49 2021

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