Sodium in PDB 4mmk: Q8A Hfq From Pseudomonas Aeruginosa

The structure of Q8A Hfq From Pseudomonas Aeruginosa, PDB code: 4mmk was solved by V.N.Murina, V.V.Filimonov, B.S.Melnik, M.Uhlein, U.Mueller, M.Weiss, A.D.Nikulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.31 / 2.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.590, 116.540, 66.620, 90.00, 119.98, 90.00
R / Rfree (%)	21.6 / 25.6

The structure of Q8A Hfq From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Zinc	(Zn)	23 atoms

The binding sites of Sodium atom in the Q8A Hfq From Pseudomonas Aeruginosa (pdb code 4mmk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Q8A Hfq From Pseudomonas Aeruginosa, PDB code: 4mmk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ G:Na102 b:30.9 occ:1.00 OE2 G:GLU18 2.3 27.7 1.0 OE1 G:GLU18 2.8 24.6 1.0 CD G:GLU18 2.9 27.4 1.0 N G:ARG69 3.3 38.6 1.0 CB G:ARG69 3.6 39.6 1.0 NH1 G:ARG66 3.7 23.0 1.0 CA G:ARG69 3.9 36.8 1.0 NH2 G:ARG66 4.1 26.4 1.0 CA G:VAL68 4.2 29.7 1.0 C G:VAL68 4.3 34.9 1.0 CZ G:ARG66 4.4 21.8 1.0 CG G:GLU18 4.4 29.3 1.0 CG2 G:THR14 4.4 26.6 1.0 CG G:ARG69 4.4 42.2 1.0 C G:ARG69 4.5 40.0 1.0 CG1 G:VAL68 4.6 27.2 1.0 O G:PRO67 4.8 31.2 1.0 CB G:VAL68 4.8 31.6 1.0 CD G:ARG69 4.9 38.0 1.0 CG2 G:VAL68 5.0 28.7 1.0

Sodium binding site 2 out of 3 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ J:Na102 b:39.9 occ:1.00 CD2 J:HIS5 2.5 38.6 1.0 O K:HOH209 3.0 24.2 1.0 NE2 J:HIS5 3.3 38.9 1.0 CG J:HIS5 3.4 38.2 1.0 CB J:HIS5 3.9 38.7 1.0 O I:HOH210 4.2 16.2 1.0 CA J:HIS5 4.3 35.0 1.0 NZ J:LYS56 4.3 24.6 1.0 CE1 J:HIS5 4.4 32.3 1.0 ND1 J:HIS5 4.4 35.6 1.0 CA J:GLN41 4.5 23.4 1.0 CB J:GLN41 4.6 24.5 1.0 CB J:ASP9 4.8 31.4 1.0 O J:ASP40 4.9 25.1 1.0 O K:SER2 5.0 33.6 1.0

Sodium binding site 3 out of 3 in the Q8A Hfq From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Q8A Hfq From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ K:Na103 b:30.6 occ:1.00 O K:HOH234 2.3 23.7 1.0 OE2 K:GLU18 2.5 22.6 1.0 CD K:GLU18 2.7 24.1 1.0 OE1 K:GLU18 2.8 20.4 1.0 CG K:GLU18 3.9 24.9 1.0 CG2 K:THR14 4.1 23.6 1.0 O K:ARG69 4.4 38.9 1.0 CB K:ARG69 4.5 47.7 1.0 NH1 K:ARG66 4.8 21.3 1.0 N K:ARG69 4.8 39.5 1.0 C K:ARG69 4.9 43.5 1.0 CB K:GLU18 5.0 28.0 1.0

V.N.Murina, B.S.Melnik, V.V.Filimonov, M.Uhlein, M.S.Weiss, U.Muller, A.D.Nikulin. Effect of Conserved Intersubunit Amino Acid Substitutions on Hfq Protein Structure and Stability. Biochemistry Mosc. V. 79 469 2014.
ISSN: ISSN 0006-2979
PubMed: 24954598
DOI: 10.1134/S0006297914050113