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Sodium in PDB 4mdx: Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna, PDB code: 4mdx was solved by D.K.Simanshu, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.55 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.793, 69.885, 79.209, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 17.8

Other elements in 4mdx:

The structure of Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna also contains other interesting chemical elements:

Iodine (I) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna (pdb code 4mdx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna, PDB code: 4mdx:

Sodium binding site 1 out of 1 in 4mdx

Go back to Sodium Binding Sites List in 4mdx
Sodium binding site 1 out of 1 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:15.8
occ:0.45
O A:LEU88 2.4 16.3 1.0
O A:HOH338 2.4 31.0 1.0
O A:HOH428 2.4 36.4 1.0
O A:HOH309 2.4 20.6 1.0
O A:HOH355 2.4 38.8 1.0
O A:GLN86 2.4 14.8 1.0
C A:GLN86 3.3 12.9 1.0
C A:LEU88 3.5 13.0 1.0
CA A:GLN86 3.8 10.9 0.5
CA A:GLN86 3.9 11.7 0.5
N A:LEU88 4.0 12.2 1.0
O A:HOH437 4.1 44.5 0.9
O A:LYS85 4.2 12.1 1.0
O A:HOH441 4.2 49.3 1.0
O A:HOH367 4.2 33.5 1.0
C A:ARG87 4.2 12.0 1.0
N A:ARG87 4.3 11.8 1.0
CA A:LEU88 4.3 11.0 1.0
O A:HOH358 4.4 30.0 1.0
N A:THR89 4.5 12.6 1.0
CB A:GLN86 4.6 13.9 0.5
CA A:ARG87 4.7 11.1 1.0
CA A:THR89 4.7 14.4 1.0
O A:ARG87 4.7 13.1 1.0
CG2 A:THR89 4.7 24.4 1.0
CB A:GLN86 4.9 11.9 0.5
N A:GLN86 4.9 11.4 1.0
C A:LYS85 5.0 11.2 1.0
CB A:LEU88 5.0 13.6 1.0

Reference:

D.K.Simanshu, Y.Yamaguchi, J.H.Park, M.Inouye, D.J.Patel. Structural Basis of Mrna Recognition and Cleavage By Toxin Mazf and Its Regulation By Antitoxin Maze in Bacillus Subtilis. Mol.Cell V. 52 447 2013.
ISSN: ISSN 1097-2765
PubMed: 24120662
DOI: 10.1016/J.MOLCEL.2013.09.006
Page generated: Tue Dec 15 06:54:06 2020

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