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Sodium in PDB 4mmk: Q8A Hfq From Pseudomonas Aeruginosa

Protein crystallography data

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

Other elements in 4mmk:

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

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

Sodium Binding Sites:

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 4mmk

Go back to Sodium Binding Sites List in 4mmk
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 4mmk

Go back to Sodium Binding Sites List in 4mmk
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 4mmk

Go back to Sodium Binding Sites List in 4mmk
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

Reference:

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
Page generated: Tue Dec 15 06:54:29 2020

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