Magnesium in PDB 6ob8: Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State

The structure of Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State, PDB code: 6ob8 was solved by S.Heewhan, R.Zhong, Z.Xiaoli, B.Sepalika, Y.Xiaojing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.50 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.059, 72.059, 253.804, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State (pdb code 6ob8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State, PDB code: 6ob8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State


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 A Dual Sensor Histidine Kinase in Green Light Illuminated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:0.8 occ:1.00 O A:HOH550 1.9 78.8 1.0 O A:HOH510 1.9 55.2 1.0 OD1 A:ASP13 2.0 59.3 0.4 O A:HOH546 2.0 0.9 1.0 OD2 A:ASP59 2.0 63.5 0.6 OD2 A:ASP59 2.0 64.0 0.4 OD1 A:ASP13 2.8 59.8 0.6 OD2 A:ASP13 3.0 62.2 0.6 OD1 A:ASP12 3.0 67.9 0.6 CG A:ASP13 3.1 58.8 0.4 CG A:ASP13 3.1 57.5 0.6 OD1 A:ASP12 3.2 68.5 0.4 CG A:ASP59 3.2 57.7 0.6 CG A:ASP59 3.2 59.2 0.4 OD2 A:ASP13 3.6 61.3 0.4 OD1 A:ASP59 3.8 64.6 0.4 OD1 A:ASP59 3.8 61.2 0.6 CG A:ASP12 3.9 65.3 0.6 O A:ARG61 4.0 56.5 0.6 N A:ASP13 4.0 42.1 0.4 CG A:ASP12 4.0 67.0 0.4 O A:ARG61 4.0 58.7 0.4 N A:ASP13 4.1 44.6 0.6 NZ A:LYS111 4.2 74.3 0.4 OD2 A:ASP12 4.2 71.6 0.6 N A:SER14 4.3 48.2 0.4 NZ A:LYS111 4.3 74.0 0.6 CB A:ASP59 4.3 51.9 0.6 CB A:ASP13 4.4 53.7 0.4 CB A:ASP59 4.4 48.5 0.4 N A:SER14 4.4 47.6 0.6 OD2 A:ASP12 4.4 70.0 0.4 CB A:ASP13 4.4 49.7 0.6 CB A:SER14 4.5 49.6 0.4 CA A:ASP13 4.5 48.8 0.4 C A:ASP13 4.6 50.0 0.4 CA A:ASP13 4.7 48.1 0.6 CB A:SER14 4.8 49.9 0.6 C A:ASP13 4.8 48.6 0.6 C A:ASP12 4.9 42.9 0.4 CE A:LYS111 4.9 73.9 0.4 CE A:LYS111 4.9 74.8 0.6 C A:ASP12 5.0 43.3 0.6

Magnesium binding site 2 out of 4 in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State


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 A Dual Sensor Histidine Kinase in Green Light Illuminated State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:70.2 occ:1.00 O B:HOH553 2.0 54.1 1.0 O A:HOH568 2.3 58.5 1.0 O A:HOH575 2.4 50.9 1.0 O B:HOH507 2.5 57.9 1.0 O B:HOH552 2.5 42.5 1.0 O A:HOH560 2.6 47.2 1.0 O B:HOH527 3.9 39.9 1.0 O B:HOH546 4.1 69.9 1.0 O A:HOH516 4.1 34.1 1.0 O B:HOH533 4.1 62.1 1.0 O B:HOH524 4.2 53.6 1.0 OG1 B:THR129 4.4 44.6 0.6 OD2 A:ASP107 4.4 37.9 0.4 OG1 B:THR129 4.4 38.7 0.4 O A:GLN106 4.5 37.4 0.4 CA B:GLY125 4.6 36.3 0.6 OG1 A:THR129 4.6 34.0 0.4 OD2 A:ASP107 4.7 37.3 0.6 O A:GLN106 4.8 36.7 0.6 OG1 A:THR129 4.8 35.6 0.6 CG A:ASP107 4.8 43.6 0.6 CA B:GLY125 4.9 36.1 0.4 C B:GLY125 4.9 36.7 0.6 CG A:ASP107 4.9 42.2 0.4 O B:GLY125 4.9 38.4 0.6 OD2 B:ASP107 4.9 39.0 0.4

Magnesium binding site 3 out of 4 in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State


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 A Dual Sensor Histidine Kinase in Green Light Illuminated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:39.5 occ:1.00 O B:HOH526 1.9 63.1 1.0 OD2 B:ASP59 2.0 40.0 0.4 O B:HOH530 2.0 63.9 1.0 O B:HOH506 2.1 43.3 1.0 OD2 B:ASP59 2.2 41.2 0.6 O B:ARG61 2.2 38.1 0.6 OD1 B:ASP13 2.3 37.3 0.4 OD1 B:ASP13 2.3 49.9 0.6 O B:ARG61 2.8 37.4 0.4 CG B:ASP59 3.0 40.0 0.4 CG B:ASP13 3.1 37.9 0.6 CG B:ASP59 3.1 39.1 0.6 OD2 B:ASP13 3.2 34.8 0.6 CG B:ASP13 3.3 35.2 0.4 C B:ARG61 3.4 36.8 0.6 OD1 B:ASP59 3.4 39.6 0.4 OD1 B:ASP59 3.4 39.4 0.6 OD2 B:ASP13 3.6 35.8 0.4 OD1 B:ASP12 3.8 57.6 0.4 C B:ARG61 4.0 35.3 0.4 CB B:ARG61 4.2 37.9 0.6 OD1 B:ASP12 4.2 52.7 0.6 N B:ASP13 4.2 27.1 0.4 CA B:ARG61 4.2 36.5 0.6 CB B:ASP59 4.4 36.6 0.4 N B:LEU62 4.4 32.2 0.6 CB B:ASP59 4.4 35.6 0.6 CG B:ARG61 4.5 43.9 0.6 CB B:ASP13 4.5 28.6 0.6 CG B:ASP12 4.5 52.4 0.4 N B:ASP13 4.5 28.6 0.6 CB B:ASP13 4.6 29.6 0.4 CA B:LEU62 4.6 31.3 0.6 N B:ARG61 4.6 37.3 0.6 CA B:ASP13 4.8 29.1 0.4 OD2 B:ASP12 4.8 55.1 0.4 N B:SER14 4.8 31.2 0.4 CA B:ARG61 4.9 36.8 0.4 CB B:ARG61 4.9 38.3 0.4 N B:LEU62 4.9 30.5 0.4 C B:ASP13 5.0 29.3 0.4 CA B:LEU62 5.0 31.0 0.4 CD2 B:LEU62 5.0 23.2 0.6 CG B:ASP12 5.0 48.4 0.6

Magnesium binding site 4 out of 4 in the Crystal Structure of A Dual Sensor Histidine Kinase in Green Light Illuminated State


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 A Dual Sensor Histidine Kinase in Green Light Illuminated State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:0.4 occ:1.00 O B:HOH540 2.0 0.5 1.0 O A:HOH523 2.0 0.3 1.0 O A:HOH562 2.0 69.4 1.0 O B:HOH503 2.2 44.6 1.0 O A:HOH507 2.4 58.1 1.0 OD2 B:ASP107 3.3 37.4 0.6 OD1 B:ASP107 3.3 38.3 0.6 O B:HOH548 3.4 40.5 1.0 O B:HOH546 3.6 69.9 1.0 OD2 B:ASP107 3.6 39.0 0.4 OD1 B:ASP107 3.7 37.1 0.4 CG B:ASP107 3.7 38.1 0.6 CD2 A:LEU121 4.0 49.1 0.4 CG B:ASP107 4.1 36.9 0.4 O A:HOH547 4.2 57.2 1.0 OD2 A:ASP107 4.3 37.3 0.6 OD2 A:ASP107 4.3 37.9 0.4 OE2 A:GLU118 4.5 87.7 0.6 OD1 A:ASP107 4.5 43.7 0.4 O B:HOH553 4.6 54.1 1.0 O B:TYR108 4.7 37.3 0.6 OD1 A:ASP107 4.8 43.0 0.6 OE2 A:GLU118 4.8 89.5 0.4 CG A:LEU121 4.8 41.8 0.4 CG A:ASP107 4.9 42.2 0.4 CD2 B:LEU121 4.9 54.8 0.4 CD2 A:LEU109 5.0 37.1 0.4

H.Shin, Z.Ren, X.Zeng, S.Bandara, X.Yang. Structural Basis of Molecular Logic or in A Dual-Sensor Histidine Kinase. Proc.Natl.Acad.Sci.Usa V. 116 19973 2019.
ISSN: ESSN 1091-6490
PubMed: 31527275
DOI: 10.1073/PNAS.1910855116