Magnesium in PDB 4lrz: Crystal Structure of the E.Coli Dhar(N)-Dhal Complex

The structure of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex, PDB code: 4lrz was solved by R.Shi, L.Mcdonald, M.Cygler, I.Ekiel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.91 / 2.32
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	89.766, 91.500, 93.808, 84.15, 72.42, 90.01
R / Rfree (%)	20 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex (pdb code 4lrz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex, PDB code: 4lrz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:35.5 occ:1.00 O A:HOH456 2.0 25.0 1.0 O1A A:ADP300 2.0 32.2 1.0 OD2 A:ASP35 2.1 41.3 1.0 OD2 A:ASP30 2.2 45.1 1.0 OD1 A:ASP37 2.2 38.4 1.0 O1B A:ADP300 2.2 37.9 1.0 CG A:ASP30 3.0 43.8 1.0 CG A:ASP37 3.1 38.9 1.0 PB A:ADP300 3.1 32.2 1.0 OD1 A:ASP30 3.1 41.0 1.0 CG A:ASP35 3.1 41.0 1.0 PA A:ADP300 3.3 32.0 1.0 O3B A:ADP300 3.3 36.3 1.0 OD2 A:ASP37 3.4 40.4 1.0 O3A A:ADP300 3.6 29.9 1.0 OD1 A:ASP35 3.6 33.5 1.0 MG A:MG302 3.9 36.9 1.0 N A:HIS38 4.0 36.8 1.0 N A:ASP37 4.0 40.0 1.0 N A:ASP35 4.1 44.5 1.0 O2A A:ADP300 4.3 33.2 1.0 CB A:ASP37 4.3 38.9 1.0 O5' A:ADP300 4.4 31.8 1.0 CB A:ASP35 4.4 42.7 1.0 O A:HOH457 4.5 26.3 1.0 CA A:ASP37 4.5 39.0 1.0 O2B A:ADP300 4.5 35.0 1.0 CB A:ASP30 4.5 43.0 1.0 C A:ASP37 4.5 37.5 1.0 C5' A:ADP300 4.6 35.6 1.0 CA A:ASP35 4.6 43.0 1.0 CB A:HIS38 4.6 35.6 1.0 N A:ALA36 4.6 41.4 1.0 CA A:HIS38 4.6 35.7 1.0 C A:ASP35 4.6 42.5 1.0 O A:HOH458 4.8 24.7 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:36.9 occ:1.00 O A:HOH457 1.9 26.3 1.0 O A:HOH458 2.0 24.7 1.0 OD2 A:ASP37 2.1 40.4 1.0 OD1 A:ASP35 2.2 33.5 1.0 O1B A:ADP300 2.3 37.9 1.0 CG A:ASP37 3.2 38.9 1.0 CG A:ASP35 3.2 41.0 1.0 PB A:ADP300 3.5 32.2 1.0 OD2 A:ASP35 3.5 41.3 1.0 O2B A:ADP300 3.6 35.0 1.0 OD1 A:ASP37 3.6 38.4 1.0 MG A:MG301 3.9 35.5 1.0 O3A A:ADP300 4.3 29.9 1.0 O A:HOH408 4.3 22.8 1.0 NH2 A:ARG178 4.4 54.5 1.0 OD1 A:ASN41 4.4 43.0 1.0 CB A:ASP37 4.5 38.9 1.0 CB A:ASP35 4.6 42.7 1.0 O3B A:ADP300 4.7 36.3 1.0 CA A:GLY78 4.8 34.2 1.0 NE A:ARG178 4.8 53.5 1.0 O1A A:ADP300 4.9 32.2 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:34.4 occ:1.00 O1A B:ADP300 1.9 34.9 1.0 O B:HOH441 2.0 25.0 1.0 OD2 B:ASP35 2.2 39.0 1.0 OD1 B:ASP37 2.3 37.4 1.0 O1B B:ADP300 2.3 37.7 1.0 OD2 B:ASP30 2.3 39.9 1.0 OD1 B:ASP30 3.0 36.1 1.0 CG B:ASP30 3.0 41.0 1.0 CG B:ASP37 3.1 39.9 1.0 PB B:ADP300 3.2 35.5 1.0 CG B:ASP35 3.2 39.9 1.0 O3B B:ADP300 3.3 38.6 1.0 PA B:ADP300 3.3 35.2 1.0 OD2 B:ASP37 3.5 41.1 1.0 O3A B:ADP300 3.6 33.8 1.0 OD1 B:ASP35 3.7 34.6 1.0 MG B:MG302 3.8 36.9 1.0 N B:ASP35 4.0 43.3 1.0 N B:ASP37 4.1 40.9 1.0 N B:HIS38 4.2 38.5 1.0 O2A B:ADP300 4.3 34.2 1.0 CB B:ASP37 4.4 39.9 1.0 CB B:HIS38 4.4 36.7 1.0 CB B:ASP35 4.4 40.7 1.0 O5' B:ADP300 4.4 33.5 1.0 N B:ALA36 4.5 40.7 1.0 CA B:ASP35 4.5 41.6 1.0 C B:ASP35 4.5 41.7 1.0 CB B:ASP30 4.5 41.0 1.0 O2B B:ADP300 4.6 38.2 1.0 CA B:ASP37 4.6 39.8 1.0 CA B:HIS38 4.6 37.2 1.0 C5' B:ADP300 4.6 38.0 1.0 C B:ASP37 4.7 39.3 1.0 CD B:ARG178 4.7 51.3 1.0 O B:HOH429 4.7 18.9 1.0 O B:HOH444 4.7 24.7 1.0 CA B:GLY34 4.9 45.2 1.0 C B:GLY34 5.0 44.8 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:36.9 occ:1.00 OD2 B:ASP37 2.0 41.1 1.0 O B:HOH429 2.1 18.9 1.0 O B:HOH444 2.1 24.7 1.0 O1B B:ADP300 2.2 37.7 1.0 OD1 B:ASP35 2.3 34.6 1.0 CG B:ASP37 3.1 39.9 1.0 CG B:ASP35 3.2 39.9 1.0 OD2 B:ASP35 3.3 39.0 1.0 PB B:ADP300 3.4 35.5 1.0 OD1 B:ASP37 3.5 37.4 1.0 O2B B:ADP300 3.7 38.2 1.0 MG B:MG301 3.8 34.4 1.0 O3A B:ADP300 4.2 33.8 1.0 O H:HOH454 4.2 25.2 1.0 O B:HOH426 4.3 21.9 1.0 CB B:ASP37 4.4 39.9 1.0 NE B:ARG178 4.4 56.6 1.0 OD1 B:ASN41 4.6 37.6 1.0 O3B B:ADP300 4.6 38.6 1.0 CB B:ASP35 4.6 40.7 1.0 O1A B:ADP300 4.6 34.9 1.0 CA B:GLY78 4.8 34.0 1.0 CD B:ARG178 4.9 51.3 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:34.4 occ:1.00 O1A C:ADP300 1.9 35.6 1.0 O C:HOH457 2.0 27.8 1.0 OD2 C:ASP35 2.0 37.9 1.0 OD1 C:ASP37 2.3 40.0 1.0 O1B C:ADP300 2.3 36.5 1.0 OD2 C:ASP30 2.3 44.7 1.0 CG C:ASP30 3.1 43.1 1.0 OD1 C:ASP30 3.1 38.0 1.0 CG C:ASP35 3.1 40.7 1.0 PB C:ADP300 3.1 34.1 1.0 CG C:ASP37 3.1 39.2 1.0 O3B C:ADP300 3.2 36.7 1.0 PA C:ADP300 3.3 33.8 1.0 OD2 C:ASP37 3.5 39.2 1.0 O3A C:ADP300 3.6 32.9 1.0 OD1 C:ASP35 3.6 37.3 1.0 MG C:MG302 3.7 40.3 1.0 N C:ASP35 4.0 44.6 1.0 N C:ASP37 4.0 40.2 1.0 N C:HIS38 4.1 38.2 1.0 O2A C:ADP300 4.3 37.7 1.0 O5' C:ADP300 4.4 33.8 1.0 CB C:ASP37 4.4 39.8 1.0 CB C:ASP35 4.4 42.2 1.0 N C:ALA36 4.4 40.6 1.0 O C:HOH456 4.5 21.1 1.0 O2B C:ADP300 4.5 33.4 1.0 CA C:ASP37 4.5 39.5 1.0 CB C:ASP30 4.5 42.0 1.0 C C:ASP35 4.6 41.9 1.0 CA C:ASP35 4.6 42.7 1.0 C5' C:ADP300 4.6 35.4 1.0 CB C:HIS38 4.6 37.4 1.0 C C:ASP37 4.6 38.3 1.0 CA C:HIS38 4.6 36.8 1.0 O C:HOH449 4.8 23.8 1.0 CD C:ARG178 4.8 48.4 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:40.3 occ:1.00 O C:HOH456 1.9 21.1 1.0 OD2 C:ASP37 1.9 39.2 1.0 O C:HOH449 2.1 23.8 1.0 O1B C:ADP300 2.1 36.5 1.0 OD1 C:ASP35 2.3 37.3 1.0 CG C:ASP37 3.0 39.2 1.0 CG C:ASP35 3.2 40.7 1.0 OD1 C:ASP37 3.3 40.0 1.0 PB C:ADP300 3.4 34.1 1.0 OD2 C:ASP35 3.4 37.9 1.0 O2B C:ADP300 3.6 33.4 1.0 MG C:MG301 3.7 34.4 1.0 O G:HOH456 3.7 26.0 1.0 O3A C:ADP300 4.1 32.9 1.0 O G:HOH421 4.2 26.9 1.0 O C:HOH403 4.3 18.4 1.0 CB C:ASP37 4.3 39.8 1.0 OD1 C:ASN41 4.3 41.7 1.0 O3B C:ADP300 4.6 36.7 1.0 CB C:ASP35 4.6 42.2 1.0 O1A C:ADP300 4.6 35.6 1.0 CA C:GLY78 4.8 32.6 1.0 CD C:ARG178 4.9 48.4 1.0 PA C:ADP300 5.0 33.8 1.0 O C:HOH457 5.0 27.8 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:35.2 occ:1.00 O1A D:ADP300 1.8 34.5 1.0 O D:HOH447 1.9 23.7 1.0 OD1 D:ASP37 2.0 37.3 1.0 OD2 D:ASP35 2.0 40.4 1.0 OD2 D:ASP30 2.1 47.5 1.0 O1B D:ADP300 2.2 37.9 1.0 CG D:ASP37 3.0 38.6 1.0 CG D:ASP30 3.1 44.3 1.0 CG D:ASP35 3.1 41.6 1.0 PB D:ADP300 3.1 33.7 1.0 PA D:ADP300 3.2 32.7 1.0 OD1 D:ASP30 3.3 42.7 1.0 O3B D:ADP300 3.4 37.7 1.0 OD2 D:ASP37 3.4 37.9 1.0 O3A D:ADP300 3.5 32.1 1.0 OD1 D:ASP35 3.5 36.5 1.0 MG D:MG302 3.8 39.5 1.0 N D:HIS38 4.0 38.3 1.0 N D:ASP37 4.1 41.7 1.0 O2A D:ADP300 4.1 33.0 1.0 N D:ASP35 4.2 46.1 1.0 CB D:ASP37 4.3 40.1 1.0 O5' D:ADP300 4.4 31.5 1.0 CB D:ASP35 4.4 44.1 1.0 CA D:ASP37 4.5 40.3 1.0 C D:ASP37 4.5 39.4 1.0 CB D:ASP30 4.5 43.6 1.0 O2B D:ADP300 4.5 35.0 1.0 CB D:HIS38 4.5 36.3 1.0 CA D:HIS38 4.5 37.0 1.0 N D:ALA36 4.6 43.0 1.0 C5' D:ADP300 4.6 36.0 1.0 C D:ASP35 4.6 44.4 1.0 CA D:ASP35 4.6 44.9 1.0 O D:HOH446 4.6 22.7 1.0 O D:HOH440 4.7 20.0 1.0 O D:HOH416 4.9 19.3 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of the E.Coli Dhar(N)-Dhal Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the E.Coli Dhar(N)-Dhal Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:39.5 occ:1.00 OD2 D:ASP37 2.0 37.9 1.0 O D:HOH446 2.1 22.7 1.0 O D:HOH440 2.1 20.0 1.0 OD1 D:ASP35 2.2 36.5 1.0 O1B D:ADP300 2.3 37.9 1.0 CG D:ASP37 3.1 38.6 1.0 CG D:ASP35 3.2 41.6 1.0 OD1 D:ASP37 3.5 37.3 1.0 PB D:ADP300 3.5 33.7 1.0 OD2 D:ASP35 3.5 40.4 1.0 O2B D:ADP300 3.6 35.0 1.0 MG D:MG301 3.8 35.2 1.0 O D:HOH416 4.2 19.3 1.0 O3A D:ADP300 4.2 32.1 1.0 OD1 D:ASN41 4.3 41.4 1.0 CB D:ASP37 4.4 40.1 1.0 CB D:ASP35 4.6 44.1 1.0 NH2 D:ARG178 4.6 49.3 1.0 CA D:GLY78 4.7 33.7 1.0 O1A D:ADP300 4.7 34.5 1.0 O3B D:ADP300 4.7 37.7 1.0 O D:HOH447 4.9 23.7 1.0 CD D:ARG178 5.0 45.5 1.0

R.Shi, L.Mcdonald, M.Cygler, I.Ekiel. Coiled-Coil Helix Rotation Selects Repressing or Activating State of Transcriptional Regulator Dhar. Structure V. 22 478 2014.
ISSN: ISSN 0969-2126
PubMed: 24440518
DOI: 10.1016/J.STR.2013.11.012