Magnesium in PDB 4nic: Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain

The structure of Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain, PDB code: 4nic was solved by Y.C.Li, C.D.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.60 / 3.18
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.475, 113.475, 243.685, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.3

The structure of Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain (pdb code 4nic). 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 Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain, PDB code: 4nic:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain


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 Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:52.4 occ:1.00 F1 A:BEF202 1.9 62.0 1.0 OD1 A:ASP9 2.4 61.2 1.0 OD2 A:ASP52 2.4 46.7 1.0 OD2 A:ASP9 2.5 57.2 1.0 O A:MET54 2.5 51.9 1.0 CG A:ASP9 2.7 59.8 1.0 BE A:BEF202 3.2 55.4 1.0 NH2 C:ARG65 3.3 63.4 1.0 CG A:ASP52 3.6 49.5 1.0 C A:MET54 3.6 53.7 1.0 OE1 A:GLU8 3.6 68.3 1.0 F3 A:BEF202 4.0 59.1 1.0 OD1 A:ASP52 4.0 51.9 1.0 CB A:MET54 4.1 55.7 1.0 F2 A:BEF202 4.1 48.0 1.0 CB A:ASP9 4.2 50.8 1.0 O A:HOH302 4.2 59.0 1.0 CA A:MET54 4.3 52.0 1.0 NZ A:LYS101 4.4 57.0 1.0 CZ C:ARG65 4.5 61.2 1.0 N A:ASP10 4.6 61.0 1.0 N A:ASP9 4.6 50.1 1.0 N A:MET54 4.7 51.4 1.0 N A:LEU55 4.7 52.7 1.0 CD A:GLU8 4.8 65.6 1.0 CG2 C:THR62 4.8 58.1 1.0 CB A:ASP52 4.8 42.9 1.0 OG1 C:THR62 4.9 61.5 1.0 CA A:ASP9 4.9 51.5 1.0 NE C:ARG65 4.9 62.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain


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 Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:58.1 occ:1.00 F1 B:BEF202 1.9 74.1 1.0 OD2 B:ASP9 2.3 84.8 1.0 O B:MET54 2.4 72.1 1.0 OD2 B:ASP52 2.4 62.5 1.0 OD1 B:ASP9 2.6 78.5 1.0 CG B:ASP9 2.8 80.9 1.0 BE B:BEF202 3.2 69.0 1.0 C B:MET54 3.4 74.3 1.0 CG B:ASP52 3.5 62.4 1.0 CB B:MET54 3.6 73.5 1.0 OD1 B:ASP52 3.9 60.9 1.0 F2 B:BEF202 3.9 59.0 1.0 CA B:MET54 4.0 67.7 1.0 F3 B:BEF202 4.0 73.4 1.0 OE2 B:GLU8 4.0 87.6 1.0 CB B:ASP9 4.3 74.6 1.0 N B:MET54 4.4 67.8 1.0 N B:LEU55 4.5 74.3 1.0 CD B:GLU8 4.6 83.8 1.0 N B:ASP9 4.8 72.2 1.0 CG B:MET54 4.8 79.7 1.0 CB B:ASP52 4.8 55.7 1.0 OE1 B:GLU8 4.8 84.7 1.0 N B:ASP10 4.9 74.4 1.0 CA B:LEU55 4.9 73.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain


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 Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:44.0 occ:1.00 F1 C:BEF202 1.8 50.9 1.0 OD1 C:ASP9 2.2 63.3 1.0 O C:MET54 2.5 50.9 1.0 OD2 C:ASP52 2.7 48.5 1.0 CG C:ASP9 2.9 57.4 1.0 OD2 C:ASP9 2.9 57.0 1.0 BE C:BEF202 3.1 50.0 1.0 C C:MET54 3.7 53.1 1.0 F3 C:BEF202 3.8 50.4 1.0 CG C:ASP52 3.8 50.8 1.0 CB C:MET54 3.9 52.2 1.0 F2 C:BEF202 4.0 46.4 1.0 OD1 C:ASP52 4.2 55.2 1.0 CA C:MET54 4.3 47.8 1.0 CB C:ASP9 4.3 54.7 1.0 OE2 C:GLU8 4.5 68.1 1.0 N C:ASP10 4.7 59.8 1.0 N C:ASP9 4.7 52.7 1.0 OE1 C:GLU8 4.8 66.2 1.0 N C:LEU55 4.8 56.0 1.0 N C:MET54 4.8 44.3 1.0 CD C:GLU8 4.9 64.0 1.0 CA C:ASP9 5.0 55.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain


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 Klebsiella Pneumoniae Rsta BEF3-Activated N- Terminal Receiver Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:39.4 occ:1.00 F1 D:BEF202 1.8 49.4 1.0 OD1 D:ASP9 2.0 51.9 1.0 O D:MET54 2.4 51.8 1.0 OD2 D:ASP52 2.5 48.2 1.0 CG D:ASP9 2.7 52.3 1.0 OD2 D:ASP9 2.8 54.1 1.0 BE D:BEF202 3.1 48.3 1.0 CG D:ASP52 3.6 50.1 1.0 C D:MET54 3.6 50.7 1.0 F3 D:BEF202 3.9 55.1 1.0 OD1 D:ASP52 3.9 50.9 1.0 CB D:MET54 4.0 48.1 1.0 F2 D:BEF202 4.1 41.1 1.0 CA D:MET54 4.2 46.2 1.0 CB D:ASP9 4.2 47.9 1.0 N D:MET54 4.5 50.0 1.0 OE2 D:GLU8 4.7 66.2 1.0 N D:LEU55 4.7 49.7 1.0 OE1 D:GLU8 4.7 64.0 1.0 N D:ASP9 4.7 51.0 1.0 NZ D:LYS101 4.8 52.3 1.0 CA D:ASP9 4.9 44.5 1.0 CB D:ASP52 4.9 43.9 1.0 N D:ASP10 4.9 49.9 1.0 CG D:MET54 5.0 51.0 1.0 CD D:GLU8 5.0 62.0 1.0

Y.C.Li, C.K.Chang, C.F.Chang, Y.H.Cheng, P.J.Fang, T.Yu, S.C.Chen, Y.C.Li, C.D.Hsiao, T.H.Huang. Structural Dynamics of the Two-Component Response Regulator Rsta in Recognition of Promoter Dna Element. Nucleic Acids Res. V. 42 8777 2014.
ISSN: ISSN 0305-1048
PubMed: 24990372
DOI: 10.1093/NAR/GKU572