Magnesium in PDB 1rlt: Transition State Analogue of Ybiv From E. Coli K12

The structure of Transition State Analogue of Ybiv From E. Coli K12, PDB code: 1rlt was solved by A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.761, 91.166, 183.850, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.4

The structure of Transition State Analogue of Ybiv From E. Coli K12 also contains other interesting chemical elements:

Fluorine	(F)	12 atoms
Aluminium	(Al)	4 atoms

The binding sites of Magnesium atom in the Transition State Analogue of Ybiv From E. Coli K12 (pdb code 1rlt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Transition State Analogue of Ybiv From E. Coli K12, PDB code: 1rlt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:26.0 occ:1.00 O A:ASP11 1.9 23.9 1.0 OD2 A:ASP9 2.0 19.8 1.0 F3 A:AF3801 2.0 47.0 1.0 O A:HOH892 2.1 26.5 1.0 OD1 A:ASP215 2.2 19.0 1.0 O A:HOH807 2.3 22.5 1.0 C A:ASP11 3.1 23.5 1.0 CG A:ASP9 3.1 24.3 1.0 CG A:ASP215 3.2 22.7 1.0 AL A:AF3801 3.5 44.1 1.0 OD1 A:ASP9 3.5 22.4 1.0 OD2 A:ASP215 3.5 21.5 1.0 CA A:ASP11 3.8 22.6 1.0 N A:ASP11 3.9 20.9 1.0 CB A:ASP11 3.9 21.8 1.0 OG1 A:THR13 3.9 31.1 1.0 O A:GLY179 4.0 26.9 1.0 N A:GLY12 4.1 24.2 1.0 OG A:SER216 4.2 32.5 1.0 OD2 A:ASP219 4.3 28.5 1.0 F2 A:AF3801 4.3 41.0 1.0 CA A:GLY179 4.4 24.4 1.0 CB A:ASP9 4.4 23.9 1.0 CA A:GLY12 4.4 24.9 1.0 C A:MET10 4.5 21.6 1.0 CB A:ASP215 4.6 20.9 1.0 C A:GLY12 4.6 26.4 1.0 CB A:SER216 4.6 26.1 1.0 C A:GLY179 4.6 28.0 1.0 N A:THR13 4.7 25.0 1.0 N A:SER216 4.7 25.2 1.0 N A:MET10 4.7 21.4 1.0 F1 A:AF3801 4.8 43.7 1.0 N A:ASP215 4.9 22.5 1.0 CB A:THR13 4.9 28.9 1.0

Magnesium binding site 2 out of 4 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg806 b:37.3 occ:1.00 F3 B:AF3802 1.9 52.4 1.0 O B:ASP11 2.1 27.9 1.0 O B:HOH889 2.1 34.5 1.0 OD2 B:ASP9 2.1 26.6 1.0 O B:HOH816 2.2 29.9 1.0 OD1 B:ASP215 2.2 25.4 1.0 CG B:ASP215 3.2 27.1 1.0 C B:ASP11 3.2 25.9 1.0 CG B:ASP9 3.2 28.5 1.0 AL B:AF3802 3.3 51.8 1.0 OD2 B:ASP215 3.5 22.4 1.0 OD1 B:ASP9 3.6 27.5 1.0 CA B:ASP11 3.9 26.2 1.0 OG1 B:THR13 4.0 19.6 1.0 N B:ASP11 4.0 24.1 1.0 CB B:ASP11 4.0 25.6 1.0 OG B:SER216 4.0 38.5 1.0 OD2 B:ASP219 4.0 29.8 1.0 N B:GLY12 4.3 26.8 1.0 F2 B:AF3802 4.3 52.1 1.0 F1 B:AF3802 4.4 52.3 1.0 O B:GLY179 4.5 65.1 1.0 CB B:ASP9 4.5 25.1 1.0 N B:SER216 4.5 30.9 1.0 CB B:ASP215 4.5 24.2 1.0 CA B:GLY12 4.5 25.7 1.0 CB B:SER216 4.6 34.8 1.0 CA B:GLY179 4.6 61.4 1.0 C B:MET10 4.7 23.5 1.0 N B:ASP215 4.7 26.8 1.0 N B:THR13 4.7 23.1 1.0 C B:GLY12 4.7 24.9 1.0 N B:MET10 4.8 20.3 1.0 CB B:THR13 4.9 22.0 1.0

Magnesium binding site 3 out of 4 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg807 b:39.2 occ:1.00 OD1 C:ASP215 1.8 36.8 1.0 F3 C:AF3803 1.9 58.6 1.0 O C:ASP11 2.0 37.4 1.0 OD2 C:ASP9 2.1 28.8 1.0 O C:HOH839 2.2 46.7 1.0 CG C:ASP215 2.7 39.3 1.0 OD2 C:ASP215 2.9 39.1 1.0 C C:ASP11 3.1 34.7 1.0 CG C:ASP9 3.2 31.4 1.0 AL C:AF3803 3.5 58.7 1.0 OD1 C:ASP9 3.7 33.3 1.0 CB C:ASP11 3.8 33.8 1.0 CA C:ASP11 3.8 33.9 1.0 N C:ASP11 4.0 33.4 1.0 CB C:ASP215 4.1 40.2 1.0 OG C:SER216 4.1 53.0 1.0 OG1 C:THR13 4.1 35.1 1.0 N C:GLY12 4.1 34.9 1.0 OD2 C:ASP219 4.1 38.5 1.0 CA C:GLY12 4.3 34.1 1.0 F1 C:AF3803 4.4 58.8 1.0 CB C:ASP9 4.5 32.3 1.0 N C:SER216 4.6 48.1 1.0 C C:GLY12 4.6 34.4 1.0 N C:THR13 4.7 34.0 1.0 N C:ASP215 4.7 41.8 1.0 F2 C:AF3803 4.7 58.4 1.0 O C:SER178 4.7 92.9 1.0 C C:MET10 4.8 34.1 1.0 CA C:ASP215 4.8 43.2 1.0 N C:MET10 5.0 33.4 1.0 OD1 C:ASN218 5.0 48.5 1.0

Magnesium binding site 4 out of 4 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg808 b:32.9 occ:1.00 F3 D:AF3804 1.9 56.8 1.0 O D:ASP11 1.9 28.1 1.0 O D:HOH899 2.0 40.9 1.0 O D:HOH897 2.1 44.2 1.0 OD1 D:ASP215 2.1 29.9 1.0 OD2 D:ASP9 2.2 28.7 1.0 C D:ASP11 3.1 29.4 1.0 CG D:ASP215 3.1 34.4 1.0 CG D:ASP9 3.3 31.6 1.0 OD2 D:ASP215 3.4 33.6 1.0 AL D:AF3804 3.5 55.4 1.0 OD1 D:ASP9 3.7 33.8 1.0 CB D:ASP11 3.8 28.6 1.0 CA D:ASP11 3.8 29.4 1.0 OG D:SER216 3.9 44.2 1.0 CG2 D:THR13 4.0 31.1 1.0 OD2 D:ASP219 4.0 29.9 1.0 N D:GLY12 4.1 29.3 1.0 N D:ASP11 4.1 29.0 1.0 CA D:GLY12 4.2 30.1 1.0 CB D:ASP215 4.5 33.6 1.0 F1 D:AF3804 4.5 55.5 1.0 OD1 D:ASN218 4.5 74.8 1.0 N D:SER216 4.6 39.9 1.0 CB D:ASP9 4.6 28.4 1.0 CB D:SER216 4.6 42.1 1.0 F2 D:AF3804 4.6 54.8 1.0 C D:GLY12 4.6 28.9 1.0 N D:THR13 4.7 29.3 1.0 C D:MET10 4.8 29.8 1.0 N D:ASP215 4.8 34.0 1.0

A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer. Ybiv From Escherichia Coli K12 Is A Had Phosphatase. Proteins V. 58 790 2005.
ISSN: ISSN 0887-3585
PubMed: 15657928
DOI: 10.1002/PROT.20267