Magnesium in PDB 3jv2: Crystal Structure of B. Subtilis Seca with Bound Peptide

The structure of Crystal Structure of B. Subtilis Seca with Bound Peptide, PDB code: 3jv2 was solved by J.Zimmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	106.724, 106.724, 175.605, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.8

The binding sites of Magnesium atom in the Crystal Structure of B. Subtilis Seca with Bound Peptide (pdb code 3jv2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of B. Subtilis Seca with Bound Peptide, PDB code: 3jv2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of B. Subtilis Seca with Bound Peptide


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 B. Subtilis Seca with Bound Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:60.6 occ:1.00 O A:HOH860 2.2 31.2 1.0 O1B A:ADP873 2.3 52.7 1.0 O A:HOH861 2.5 35.0 1.0 O A:HOH810 2.6 44.1 1.0 O A:HOH859 2.7 27.9 1.0 OD1 A:ASP207 3.2 41.6 1.0 OG1 A:THR107 3.2 44.3 1.0 OD2 A:ASP207 3.7 38.8 1.0 PB A:ADP873 3.8 50.5 1.0 CG A:ASP207 3.9 35.4 1.0 O A:HOH782 3.9 39.2 1.0 O2A A:ADP873 3.9 58.8 1.0 O1A A:ADP873 4.2 62.9 1.0 N A:THR107 4.2 36.9 1.0 CB A:LYS106 4.3 33.3 1.0 OE2 A:GLU208 4.3 65.3 1.0 PA A:ADP873 4.4 59.7 1.0 CB A:THR107 4.5 40.6 1.0 CE A:LYS106 4.5 32.5 1.0 NH2 A:ARG136 4.6 35.2 1.0 O2B A:ADP873 4.6 54.6 1.0 O3A A:ADP873 4.6 57.9 1.0 O3B A:ADP873 4.7 51.5 1.0 CA A:THR107 4.7 38.1 1.0 C A:LYS106 4.9 37.1 1.0 O A:GLY490 4.9 39.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of B. Subtilis Seca with Bound Peptide


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 B. Subtilis Seca with Bound Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg872 b:69.1 occ:1.00 O B:HOH794 2.2 40.0 1.0 O1B B:ADP873 2.3 57.5 1.0 O B:HOH800 2.4 37.7 1.0 O B:HOH850 2.4 45.9 1.0 O B:HOH851 2.6 26.9 1.0 OD2 B:ASP207 3.3 43.8 1.0 OG1 B:THR107 3.5 47.1 1.0 OD1 B:ASP207 3.6 38.1 1.0 PB B:ADP873 3.7 50.9 1.0 CG B:ASP207 3.8 38.0 1.0 OE1 B:GLU208 3.9 61.7 1.0 O B:HOH784 4.0 37.8 1.0 CE B:LYS106 4.3 36.4 1.0 CB B:LYS106 4.3 33.4 1.0 O2A B:ADP873 4.4 56.5 1.0 O1A B:ADP873 4.4 57.9 1.0 N B:THR107 4.4 37.8 1.0 O3B B:ADP873 4.4 49.6 1.0 O2B B:ADP873 4.5 55.3 1.0 NH2 B:ARG136 4.5 35.8 1.0 PA B:ADP873 4.6 58.0 1.0 O3A B:ADP873 4.7 57.2 1.0 CB B:THR107 4.8 41.2 1.0 CA B:GLY490 4.9 34.5 1.0 O B:GLY490 4.9 39.5 1.0 CA B:THR107 4.9 39.0 1.0

J.Zimmer, T.A.Rapoport. Conformational Flexibility and Peptide Interaction of the Translocation Atpase Seca. J.Mol.Biol. V. 394 606 2009.
ISSN: ISSN 0022-2836
PubMed: 19850053
DOI: 10.1016/J.JMB.2009.10.024