Sodium in PDB 4j6w: Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp

The structure of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp, PDB code: 4j6w was solved by A.D.Nikulin, V.Murina, N.Lekontseva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.280, 74.550, 109.610, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.1

The structure of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp (pdb code 4j6w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp, PDB code: 4j6w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


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 Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:41.7 occ:1.00 O1 D:P6G103 2.5 41.6 1.0 C6 D:P6G103 2.7 36.2 1.0 C8 D:P6G103 2.7 37.9 1.0 O4 D:P6G103 2.8 38.4 1.0 O D:HOH227 2.8 42.4 1.0 C12 D:P6G103 2.8 24.7 1.0 C2 D:P6G103 2.9 36.2 1.0 O10 D:P6G103 3.0 44.1 1.0 C3 D:P6G103 3.0 38.8 1.0 C11 D:P6G103 3.0 32.4 1.0 C9 D:P6G103 3.0 26.8 1.0 C14 D:P6G103 3.0 34.1 1.0 C5 D:P6G103 3.1 35.9 1.0 O13 D:P6G103 3.2 37.4 1.0 O7 D:P6G103 3.2 45.3 1.0 O19 D:P6G103 3.5 50.7 1.0 O16 D:P6G103 3.5 46.9 1.0 C15 D:P6G103 3.7 35.4 1.0 C18 D:P6G103 4.1 41.2 1.0 C17 D:P6G103 4.3 45.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na104 b:37.9 occ:1.00 N F:ARG69 2.8 21.2 1.0 OE1 F:GLU18 3.0 40.7 1.0 OE2 F:GLU18 3.1 35.9 1.0 CD F:GLU18 3.3 38.8 1.0 CA F:VAL68 3.5 26.1 1.0 CB F:ARG69 3.5 31.6 1.0 CB F:VAL68 3.5 29.4 1.0 C F:VAL68 3.6 28.2 1.0 CG2 F:THR14 3.7 23.7 1.0 NH2 F:ARG69 3.7 40.8 0.5 CA F:ARG69 3.7 24.5 1.0 NH1 F:ARG66 3.8 26.2 1.0 CZ F:ARG69 3.9 40.2 0.4 NH1 F:ARG69 4.2 47.9 0.7 NE F:ARG69 4.4 41.1 0.3 CG1 F:VAL68 4.5 17.9 1.0 CG2 F:VAL68 4.6 23.0 1.0 NH2 F:ARG66 4.6 38.1 1.0 CZ F:ARG66 4.6 29.6 1.0 O F:ARG69 4.7 30.4 1.0 CG F:GLU18 4.7 27.1 1.0 C F:ARG69 4.8 34.8 1.0 O F:VAL68 4.8 25.3 1.0 N F:VAL68 4.9 20.9 1.0 CG F:ARG69 4.9 35.8 0.7 O F:PRO67 5.0 25.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hfq From Pseudomonas Aeruginosa in Complex with Ctp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na105 b:55.6 occ:1.00 O C:HOH224 2.5 44.9 1.0 O1A F:CDP101 2.7 28.9 0.8 OP2 D:C101 2.7 41.5 0.6 OP3 D:C101 2.9 34.8 0.6 O B:HOH237 3.0 48.4 1.0 OP1 C:C102 3.2 47.9 0.7 O3A F:CDP101 3.3 31.0 0.8 MG C:MG104 3.4 49.7 1.0 P D:C101 3.4 46.7 0.6 C5' F:CDP101 3.5 24.8 0.8 PA F:CDP101 3.5 28.6 0.8 O2B F:CDP101 3.6 43.8 0.8 O5' F:CDP101 3.9 29.2 0.8 P C:C102 4.0 51.5 0.7 PB F:CDP101 4.2 36.0 0.8 O1G B:CTP101 4.2 34.4 0.8 MG D:MG105 4.3 43.3 1.0 OP1 D:C101 4.3 40.2 0.6 C5' C:C102 4.6 32.9 0.7 O2G B:CTP101 4.6 41.9 0.8 CE1 F:PHE42 4.6 27.6 1.0 O5' D:C101 4.7 37.2 0.6 OP2 C:C102 4.9 46.1 0.7 O5' C:C102 4.9 33.4 0.7 C4' F:CDP101 4.9 26.5 0.8 O2A F:CDP101 4.9 20.7 0.8

V.Murina, N.Lekontseva, A.Nikulin. Hfq Binds Ribonucleotides in Three Different Rna-Binding Sites. Acta Crystallogr.,Sect.D V. 69 1504 2013.
ISSN: ISSN 0907-4449
PubMed: 23897473
DOI: 10.1107/S090744491301010X