Magnesium in PDB 6yrc: Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State

The structure of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State, PDB code: 6yrc was solved by M.Lucic, F.S.N.Dworkowski, J.A.R.Worrall, M.A.Hough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.05 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.79, 120.27, 196.01, 90, 90, 90
R / Rfree (%)	17.6 / 21.8

The structure of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State (pdb code 6yrc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State, PDB code: 6yrc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:27.8 occ:1.00 OD2 A:ASP191 2.0 23.7 1.0 O A:HOH616 2.2 24.4 1.0 O A:HOH502 2.2 25.1 1.0 CG A:ASP191 3.1 25.6 1.0 CB A:ASP191 3.6 23.3 1.0 NH2 C:ARG127 3.8 36.5 1.0 OE1 A:GLU254 4.0 36.6 1.0 O A:HOH662 4.0 24.2 1.0 OD1 A:ASP189 4.1 25.6 1.0 OD1 A:ASP191 4.2 27.5 1.0 O A:HOH685 4.2 36.6 1.0 O A:HOH599 4.3 28.7 1.0 N A:ASP191 4.4 21.0 1.0 CA A:ASP191 4.6 24.3 1.0

Magnesium binding site 2 out of 5 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:41.8 occ:1.00 O A:HOH693 1.6 38.8 1.0 O A:HOH714 1.9 46.5 1.0 O A:HOH622 2.1 32.1 1.0 O A:HOH563 2.1 40.4 1.0 O A:HOH557 2.2 37.8 1.0 O A:HOH627 2.2 38.9 1.0 O1D A:HEM401 4.2 26.9 1.0 O2D A:HEM401 4.2 25.6 1.0 OE1 A:GLU214 4.2 42.7 1.0 OG A:SER230 4.4 29.0 1.0 O13 A:7PE402 4.4 55.1 1.0 OE2 A:GLU214 4.5 38.2 1.0 O A:HOH589 4.5 34.1 1.0 OE1 A:GLU155 4.6 30.5 1.0 CGD A:HEM401 4.6 28.9 1.0 CD A:GLU214 4.8 36.7 1.0 O A:HOH516 4.9 40.4 1.0

Magnesium binding site 3 out of 5 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:57.0 occ:1.00 O A:HOH649 1.9 45.1 1.0 O A:HOH508 2.2 30.9 1.0 O A:HOH688 2.2 39.6 1.0 O A:HOH565 2.3 43.1 1.0 OE1 A:GLU144 2.4 35.9 1.0 O A:HOH630 3.2 40.2 1.0 CD A:GLU144 3.5 33.4 1.0 O A:ASP152 4.0 23.7 1.0 OD1 A:ASP244 4.0 35.5 1.0 O A:HOH638 4.0 53.7 1.0 O A:ASN245 4.1 28.8 1.0 OE2 A:GLU144 4.1 49.4 1.0 O A:HOH689 4.4 40.8 1.0 O A:HOH541 4.5 26.9 1.0 CG A:GLU144 4.7 30.5 1.0 SD A:MET246 4.7 31.1 1.0 CB A:GLU144 4.7 27.9 1.0 CA A:GLU144 5.0 27.6 1.0

Magnesium binding site 4 out of 5 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:30.5 occ:1.00 O C:HOH564 2.0 26.8 1.0 O C:HOH679 2.1 31.9 1.0 O C:HOH569 2.1 36.3 1.0 O C:HOH520 4.1 41.4 1.0 O C:ARG127 4.2 41.9 1.0 OD2 C:ASP29 4.2 29.2 1.0 O C:HOH676 4.2 39.5 1.0 O C:VAL130 4.3 22.9 1.0 OG1 C:THR131 4.4 26.8 1.0 O A:HOH577 4.4 33.7 1.0 O C:HOH703 4.4 40.9 1.0

Magnesium binding site 5 out of 5 in the Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Spectroscopically-Validated Structure of Dtpb From Streptomyces Lividans in the Ferric State within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:54.8 occ:1.00 O E:HOH674 1.8 44.3 1.0 O E:HOH637 1.9 50.5 1.0 O F:HOH545 2.1 42.7 1.0 O E:HOH670 2.1 50.0 1.0 O F:HOH541 2.5 37.7 1.0 OE2 E:GLU310 3.6 49.3 1.0 OE1 E:GLU310 3.6 44.5 1.0 CD E:GLU310 4.0 46.7 1.0 OE1 E:GLU9 4.1 53.3 1.0 OE2 E:GLU9 4.2 58.4 1.0 O F:HOH633 4.2 36.9 1.0 O E:HOH510 4.4 38.5 1.0 C6 F:7PE410 4.4 50.5 1.0 OE2 F:GLU240 4.5 33.4 1.0 OE1 F:GLU240 4.5 33.2 1.0 CD E:GLU9 4.6 55.8 1.0 O4 F:7PE410 4.8 49.7 1.0 CD F:GLU240 4.8 31.0 1.0 O7 F:7PE410 4.9 46.9 1.0 C5 F:7PE410 4.9 47.7 1.0 CB F:ALA161 4.9 31.9 1.0

M.Lucic, D.A.Svistunenko, M.T.Wilson, A.K.Chaplin, B.Davy, A.Ebrahim, D.Axford, T.Tosha, H.Sugimoto, S.Owada, F.S.N.Dworkowski, I.Tews, R.L.Owen, M.A.Hough, J.A.R.Worrall. Serial Femtosecond Zero Dose Crystallography Captures A Water-Free Distal Heme Site in A Dye-Decolorising Peroxidase to Reveal A Catalytic Role For An Arginine in Fe IV =O Formation. Angew.Chem.Int.Ed.Engl. V. 59 21656 2020.
ISSN: ESSN 1521-3773
PubMed: 32780931
DOI: 10.1002/ANIE.202008622