Magnesium in PDB 4yn8: Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System

The structure of Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System, PDB code: 4yn8 was solved by A.Doi, H.Nakamura, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 1.80
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.880, 84.880, 169.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System (pdb code 4yn8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System, PDB code: 4yn8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:19.0 occ:1.00 O A:HOH397 2.0 17.5 1.0 O A:HOH308 2.1 18.4 1.0 OD1 A:ASP8 2.1 13.1 1.0 OD2 A:ASP50 2.1 14.7 0.5 O A:HOH387 2.2 5.3 0.5 OD1 A:ASP50 2.3 19.9 0.5 ND1 A:HIS10 2.4 20.0 1.0 CG A:ASP50 2.8 15.2 0.5 OD2 A:ASP50 2.8 15.6 0.5 CG A:ASP50 2.8 15.4 0.5 CG A:ASP8 2.9 13.9 1.0 OD1 A:ASP9 3.1 11.9 0.5 CE1 A:HIS10 3.2 19.0 1.0 OD2 A:ASP8 3.3 19.8 1.0 OD1 A:ASP50 3.4 14.7 0.5 CG A:HIS10 3.5 15.9 1.0 NZ A:LYS99 3.7 16.4 1.0 CB A:ASP50 3.8 12.2 0.5 CB A:HIS10 3.9 14.5 1.0 CB A:ASP50 4.0 12.4 0.5 N A:ASP9 4.0 10.2 1.0 O3 A:SO4200 4.1 28.0 0.9 N A:HIS10 4.1 12.4 1.0 O A:HOH324 4.1 14.3 1.0 CB A:ASP8 4.2 11.7 1.0 CG A:ASP9 4.2 12.8 0.5 O A:HOH366 4.3 25.9 1.0 O A:GLN52 4.4 14.7 1.0 NE2 A:HIS10 4.4 18.0 1.0 CA A:ASP8 4.5 10.3 1.0 CD2 A:HIS10 4.6 16.7 1.0 C A:ASP8 4.6 9.6 1.0 CA A:HIS10 4.7 12.9 1.0 CA A:ASP9 4.8 11.0 0.5 CA A:ASP9 4.8 11.1 0.5 C A:ASP9 4.9 11.9 1.0 CE A:LYS99 4.9 15.1 1.0 CB A:ASP9 5.0 11.4 0.5 OD2 A:ASP9 5.0 15.0 0.5

Magnesium binding site 2 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:16.1 occ:1.00 O A:HOH360 2.0 13.7 1.0 O A:HOH312 2.1 17.5 1.0 OXT A:ILE199 2.1 18.7 1.0 O A:HOH401 2.1 19.4 1.0 O A:HOH310 2.2 17.6 1.0 C A:ILE199 3.0 17.5 1.0 O A:ILE199 3.4 17.4 1.0 NE2 A:GLN148 4.2 15.1 1.0 OE1 A:GLU151 4.2 20.6 1.0 O A:HOH443 4.2 29.4 1.0 O A:HOH306 4.3 17.0 1.0 CA A:ILE199 4.3 15.2 1.0 O A:HOH370 4.4 36.1 1.0 CB A:ILE199 4.5 15.6 1.0 CG A:GLN148 4.7 13.4 1.0 CD A:GLN148 4.9 14.6 1.0 CG1 A:ILE199 5.0 17.9 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:26.9 occ:1.00 O A:HOH313 2.1 21.8 1.0 O A:HOH307 2.1 24.0 1.0 O A:HOH384 2.2 34.6 1.0 OD2 A:ASP108 4.1 15.6 1.0 O A:HOH378 4.2 33.7 1.0 OD1 A:ASP108 4.2 14.6 1.0 O A:HOH371 4.2 26.2 1.0 CG A:ASP108 4.6 14.8 1.0 CB A:SER104 4.9 14.4 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:20.4 occ:1.00 O A:HOH429 2.3 25.6 1.0 O A:ILE27 2.3 12.6 1.0 O A:PHE24 2.4 15.7 1.0 O A:HOH476 2.5 30.7 1.0 O A:ASP22 2.5 17.3 1.0 O A:HOH419 2.6 21.9 1.0 C A:ASP22 3.5 15.8 1.0 C A:ILE27 3.5 11.6 1.0 C A:PHE24 3.5 16.8 1.0 CA A:ASP22 3.8 14.3 1.0 O A:HOH485 4.1 37.4 1.0 OG1 A:THR28 4.1 23.2 1.0 CA A:ASP25 4.2 20.3 0.5 N A:ILE27 4.2 12.2 1.0 CA A:ASP25 4.3 20.6 0.5 N A:ASP25 4.3 19.3 1.0 C A:ASP25 4.3 20.3 1.0 N A:PHE24 4.3 14.0 1.0 N A:THR28 4.4 11.4 1.0 CA A:ILE27 4.4 11.8 1.0 O A:LEU21 4.4 11.2 1.0 CA A:THR28 4.4 13.2 1.0 OD1 A:ASP22 4.5 19.2 1.0 CA A:PHE24 4.5 14.8 1.0 O A:ASP25 4.5 23.0 1.0 N A:SER23 4.6 14.4 1.0 CB A:ASP22 4.6 15.7 1.0 C A:SER23 4.7 15.8 1.0 N A:ASP26 4.7 16.3 1.0 OG A:SER1 4.9 28.0 1.0 CB A:THR28 4.9 16.1 1.0 N A:ASP22 5.0 12.7 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:35.4 occ:1.00 O A:HOH450 2.0 27.2 1.0 O A:HOH495 2.1 41.8 1.0 O A:HOH395 2.2 12.5 1.0 O A:HOH487 2.2 32.4 1.0 O A:HOH424 2.2 34.4 1.0 O A:HOH471 2.3 31.9 1.0 O A:HOH411 4.1 22.5 1.0 O A:HOH410 4.2 21.9 1.0 O A:ILE44 4.3 11.4 1.0 OD1 A:ASP45 4.3 13.1 1.0 O A:ASP45 4.4 7.8 1.0 CA A:ASP45 4.4 9.8 1.0 C A:ASP45 4.9 8.9 1.0 CB A:PRO71 5.0 11.5 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:35.6 occ:1.00 O A:HOH447 2.1 28.8 1.0 O A:HOH489 2.1 34.9 1.0 O A:HOH448 2.2 27.8 1.0 O A:HOH488 2.2 34.9 1.0 O A:HOH494 2.3 40.8 1.0 O A:HOH435 3.9 26.6 1.0 O1 A:SO4203 4.0 21.3 1.0 O A:HOH375 4.0 35.7 1.0 O A:ASP100 4.3 21.9 1.0 CA A:PRO102 4.3 15.1 1.0 O A:ALA101 4.4 13.4 1.0 N A:PRO102 4.6 15.6 1.0 O A:HOH381 4.7 24.4 1.0 C A:ALA101 4.7 14.0 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Response Regulator Chra in Heme-Sensing Two Component System


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 Response Regulator Chra in Heme-Sensing Two Component System within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:36.9 occ:1.00 O A:HOH407 2.0 20.0 1.0 O A:HOH467 2.1 29.9 1.0 O A:HOH373 2.1 39.6 1.0 OE1 A:GLU103 4.1 19.7 1.0 OE2 A:GLU103 4.2 20.8 1.0 O A:HOH380 4.4 30.2 1.0 OG A:SER19 4.4 15.2 0.5 CB A:SER23 4.4 15.6 1.0 OG A:SER23 4.4 15.8 1.0 CD A:GLU103 4.5 17.3 1.0 O A:SER19 4.8 14.1 1.0 CA A:ILE20 4.9 12.7 1.0 CG1 A:ILE20 4.9 14.2 1.0

A.Doi, H.Nakamura, Y.Shiro, H.Sugimoto. Structure of the Response Regulator Chra in the Haem-Sensing Two-Component System of Corynebacterium Diphtheriae. Acta Crystallogr.,Sect.F V. 71 966 2015.
ISSN: ESSN 2053-230X
PubMed: 26249683
DOI: 10.1107/S2053230X15009838