Sodium in PDB 8ff9: Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)

The structure of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form), PDB code: 8ff9 was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	129.541, 129.82, 156.598, 90, 90, 90
R / Rfree (%)	14.6 / 17

The structure of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) also contains other interesting chemical elements:

Chlorine

(Cl)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) (pdb code 8ff9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form), PDB code: 8ff9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:34.9 occ:1.00 O B:HOH344 2.2 39.6 1.0 OD2 B:ASP64 2.2 20.5 0.5 O B:HOH302 2.2 31.0 1.0 NE2 L:HIS37 2.3 20.8 1.0 OD1 B:ASP64 2.5 19.4 0.5 CG B:ASP64 2.6 21.3 0.5 OE2 B:GLU68 2.9 33.2 1.0 CD2 L:HIS37 3.2 19.2 1.0 CE1 L:HIS37 3.3 20.3 1.0 CD B:GLU68 3.8 30.3 1.0 OH L:TYR56 3.8 29.3 1.0 O B:HOH326 3.8 36.5 1.0 OD1 B:ASP64 3.9 26.9 0.5 CG B:ASP64 3.9 23.3 0.5 CB B:ASP64 4.1 22.0 0.5 CE1 L:HIS49 4.2 21.1 1.0 CB B:ASP64 4.2 22.1 0.5 OD2 B:ASP64 4.2 29.8 0.5 CG B:GLU68 4.2 31.6 1.0 NE2 L:HIS49 4.3 23.1 1.0 CG L:HIS37 4.4 16.3 1.0 ND1 L:HIS37 4.4 19.1 1.0 CD1 L:TRP38 4.5 15.4 1.0 NE1 L:TRP38 4.5 18.5 1.0 OE2 L:GLU53 4.6 46.2 1.0 OE1 B:GLU68 4.8 35.3 1.0 O L:HOH302 4.8 44.4 1.0 O L:HOH342 5.0 43.4 1.0 CZ L:TYR56 5.0 24.0 1.0

Sodium binding site 2 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:37.2 occ:1.00 O L:HOH313 2.1 26.2 1.0 O B:HOH394 2.1 28.9 1.0 NE2 B:HIS37 2.3 17.7 1.0 OE2 L:GLU68 2.9 26.9 1.0 O L:HOH368 3.0 38.8 1.0 CD2 B:HIS37 3.2 19.3 1.0 CE1 B:HIS37 3.3 18.2 1.0 O B:HOH453 3.6 42.3 1.0 CG L:ASP64 3.7 32.1 1.0 OD1 L:ASP64 3.7 28.9 1.0 O B:HOH362 3.8 34.9 1.0 OD2 L:ASP64 3.9 32.4 1.0 CD L:GLU68 3.9 30.0 1.0 OH B:TYR56 4.0 28.9 1.0 CB L:ASP64 4.0 25.1 1.0 CE1 B:HIS49 4.2 17.4 1.0 NE2 B:HIS49 4.2 20.9 1.0 CD1 B:TRP38 4.3 15.5 1.0 CG L:GLU68 4.3 25.6 1.0 ND1 B:HIS37 4.4 17.0 1.0 CG B:HIS37 4.4 16.2 1.0 NE1 B:TRP38 4.4 16.7 1.0 CA L:ASP64 4.9 21.1 1.0 OE1 L:GLU68 5.0 26.7 1.0

Sodium binding site 3 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


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 Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:33.3 occ:1.00 OD2 C:ASP64 2.0 32.4 0.5 O C:HOH311 2.1 33.6 1.0 NE2 J:HIS37 2.2 19.6 1.0 O C:HOH305 2.3 27.3 1.0 CG C:ASP64 2.7 26.1 0.5 OD1 C:ASP64 2.8 23.6 0.5 OE2 C:GLU68 3.0 30.8 1.0 CD2 J:HIS37 3.2 18.6 1.0 CE1 J:HIS37 3.2 23.5 1.0 O J:HOH319 3.8 32.2 1.0 CG C:ASP64 3.9 22.0 0.5 OH J:TYR56 3.9 30.4 1.0 OD2 C:ASP64 4.0 24.1 0.5 CD C:GLU68 4.1 35.6 1.0 CB C:ASP64 4.1 25.2 0.5 OD1 C:ASP64 4.1 19.9 0.5 CE1 J:HIS49 4.1 21.2 1.0 CB C:ASP64 4.1 25.2 0.5 NE2 J:HIS49 4.2 23.3 1.0 ND1 J:HIS37 4.3 18.0 1.0 CG J:HIS37 4.3 18.1 1.0 CD1 J:TRP38 4.5 18.2 1.0 CG C:GLU68 4.6 33.0 1.0 NE1 J:TRP38 4.6 20.0 1.0 O C:HOH303 4.7 40.2 1.0 O C:HOH421 4.8 39.8 1.0 OE2 J:GLU53 4.9 42.3 1.0 CA C:ASP64 5.0 21.0 0.5 CA C:ASP64 5.0 21.0 0.5

Sodium binding site 4 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:33.8 occ:1.00 O C:HOH332 2.1 33.4 1.0 O J:HOH304 2.2 28.9 1.0 NE2 C:HIS37 2.3 20.4 1.0 OE2 J:GLU68 2.9 33.1 1.0 O J:HOH424 3.1 42.8 1.0 CD2 C:HIS37 3.2 18.9 1.0 CE1 C:HIS37 3.3 17.6 1.0 OH C:TYR56 3.7 28.6 1.0 CG J:ASP64 3.8 27.8 1.0 O C:HOH422 3.8 40.9 1.0 OD1 J:ASP64 3.9 30.0 1.0 O J:HOH334 3.9 34.7 1.0 CD J:GLU68 3.9 35.9 1.0 OD2 J:ASP64 4.1 25.7 1.0 CB J:ASP64 4.1 21.9 1.0 CE1 C:HIS49 4.3 22.4 1.0 CG C:HIS37 4.4 15.0 1.0 CG J:GLU68 4.4 29.6 1.0 ND1 C:HIS37 4.4 16.4 1.0 NE2 C:HIS49 4.4 19.1 1.0 CD1 C:TRP38 4.4 18.8 1.0 NE1 C:TRP38 4.5 19.5 1.0 CZ C:TYR56 4.9 22.6 1.0 OE1 J:GLU68 4.9 31.5 1.0 OE2 C:GLU53 5.0 40.6 1.0 CA J:ASP64 5.0 19.8 1.0

Sodium binding site 5 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:34.1 occ:1.00 OD2 D:ASP64 2.1 30.1 0.5 O D:HOH367 2.2 34.6 1.0 NE2 F:HIS37 2.2 20.4 1.0 O D:HOH307 2.3 27.3 1.0 OD1 D:ASP64 2.5 23.9 0.5 CG D:ASP64 2.6 27.5 0.5 OE2 D:GLU68 3.0 31.6 1.0 CD2 F:HIS37 3.2 19.1 1.0 CE1 F:HIS37 3.2 21.1 1.0 O D:HOH312 3.7 34.0 1.0 CG D:ASP64 3.8 19.2 0.5 OH F:TYR56 3.8 32.7 1.0 OD1 D:ASP64 3.9 19.7 0.5 OD2 D:ASP64 3.9 20.2 0.5 CD D:GLU68 4.0 34.5 1.0 CB D:ASP64 4.1 20.0 0.5 CB D:ASP64 4.1 20.0 0.5 CE1 F:HIS49 4.2 20.2 1.0 CG F:HIS37 4.3 16.8 1.0 ND1 F:HIS37 4.3 18.0 1.0 NE2 F:HIS49 4.4 23.2 1.0 CD1 F:TRP38 4.4 20.3 1.0 CG D:GLU68 4.4 26.2 1.0 NE1 F:TRP38 4.4 21.0 1.0 OE2 F:GLU53 4.9 40.4 1.0 CA D:ASP64 4.9 19.1 0.5 CZ F:TYR56 4.9 24.0 1.0 CA D:ASP64 4.9 19.1 0.5 OE1 D:GLU68 5.0 31.2 1.0

Sodium binding site 6 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na202 b:36.7 occ:1.00 O D:HOH358 2.2 34.7 1.0 O F:HOH302 2.2 33.2 1.0 NE2 D:HIS37 2.3 18.6 1.0 O F:HOH380 2.9 42.4 1.0 OE2 F:GLU68 3.0 31.7 1.0 CD2 D:HIS37 3.2 17.6 1.0 CE1 D:HIS37 3.3 22.1 1.0 CG F:ASP64 3.7 33.8 1.0 OH D:TYR56 3.7 28.3 1.0 OD1 F:ASP64 3.7 30.1 1.0 OD2 F:ASP64 3.9 32.9 1.0 O D:HOH338 4.0 32.0 1.0 CD F:GLU68 4.0 30.2 1.0 CB F:ASP64 4.1 25.4 1.0 CE1 D:HIS49 4.3 22.4 1.0 CG D:HIS37 4.4 16.8 1.0 CD1 D:TRP38 4.4 18.3 1.0 ND1 D:HIS37 4.4 17.0 1.0 NE1 D:TRP38 4.4 19.4 1.0 CG F:GLU68 4.5 25.2 1.0 NE2 D:HIS49 4.5 19.7 1.0 OE2 D:GLU53 4.7 45.3 1.0 CZ D:TYR56 4.8 25.5 1.0 CA F:ASP64 4.9 24.4 1.0 OE1 F:GLU68 4.9 28.2 1.0

Sodium binding site 7 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na201 b:26.9 occ:1.00 O E:HOH319 2.1 39.0 1.0 OD2 E:ASP64 2.2 24.6 0.5 NE2 A:HIS37 2.2 18.7 1.0 OE2 E:GLU68 2.3 34.7 1.0 OD1 E:ASP64 2.5 23.7 0.5 CG E:ASP64 2.7 25.4 0.5 CD E:GLU68 3.0 39.7 1.0 CD2 A:HIS37 3.2 18.9 1.0 CE1 A:HIS37 3.2 20.1 1.0 OE1 E:GLU68 3.4 29.9 1.0 O A:HOH378 3.8 38.2 1.0 OH A:TYR56 3.8 30.4 1.0 CG E:ASP64 3.9 24.2 0.5 OD1 E:ASP64 3.9 27.9 0.5 CE1 A:HIS49 4.1 19.3 1.0 CG E:GLU68 4.1 27.5 1.0 OD2 E:ASP64 4.1 28.1 0.5 CB E:ASP64 4.2 24.2 0.5 CB E:ASP64 4.2 24.5 0.5 NE2 A:HIS49 4.2 21.8 1.0 CG A:HIS37 4.3 16.5 1.0 ND1 A:HIS37 4.3 18.0 1.0 CD1 A:TRP38 4.4 20.8 1.0 NE1 A:TRP38 4.5 22.0 1.0 CZ A:TYR56 5.0 26.0 1.0 CA E:ASP64 5.0 19.7 0.5

Sodium binding site 8 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na202 b:43.1 occ:1.00 O E:HOH376 2.2 31.8 1.0 O A:HOH306 2.2 29.8 1.0 NE2 E:HIS37 2.2 17.3 1.0 OE2 A:GLU68 2.9 29.1 1.0 O A:HOH334 3.0 46.2 1.0 CD2 E:HIS37 3.1 18.2 1.0 CE1 E:HIS37 3.3 20.6 1.0 O E:HOH440 3.6 39.7 1.0 CG A:ASP64 3.7 30.4 1.0 O A:HOH320 3.8 33.0 1.0 OD1 A:ASP64 3.9 31.1 1.0 OH E:TYR56 3.9 29.7 1.0 CD A:GLU68 4.0 28.5 1.0 OD2 A:ASP64 4.0 32.6 1.0 CB A:ASP64 4.1 22.6 1.0 CE1 E:HIS49 4.1 20.4 1.0 CD1 E:TRP38 4.3 18.3 1.0 NE2 E:HIS49 4.3 21.4 1.0 CG E:HIS37 4.3 15.7 1.0 ND1 E:HIS37 4.4 17.1 1.0 NE1 E:TRP38 4.4 17.6 1.0 CG A:GLU68 4.4 23.7 1.0 OE1 A:GLU68 4.9 26.4 1.0 CA A:ASP64 4.9 21.1 1.0

Sodium binding site 9 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Na201 b:39.1 occ:1.00 O G:HOH398 2.1 34.9 1.0 O I:HOH310 2.2 28.1 1.0 NE2 G:HIS37 2.3 19.8 1.0 OE2 I:GLU68 3.0 28.9 1.0 O I:HOH357 3.1 41.6 1.0 CD2 G:HIS37 3.2 20.0 1.0 CE1 G:HIS37 3.3 20.2 1.0 CG I:ASP64 3.6 32.7 1.0 O G:HOH437 3.7 43.5 1.0 OD1 I:ASP64 3.7 30.1 1.0 OD2 I:ASP64 3.8 34.6 1.0 O I:HOH339 3.9 33.2 1.0 OH G:TYR56 3.9 29.6 1.0 CB I:ASP64 4.0 27.4 1.0 CD I:GLU68 4.0 30.6 1.0 CE1 G:HIS49 4.2 19.7 1.0 NE2 G:HIS49 4.3 22.3 1.0 CD1 G:TRP38 4.3 19.9 1.0 CG G:HIS37 4.4 17.2 1.0 NE1 G:TRP38 4.4 20.0 1.0 ND1 G:HIS37 4.4 16.9 1.0 CG I:GLU68 4.4 30.1 1.0 CA I:ASP64 4.8 21.8 1.0

Sodium binding site 10 out of 12 in the Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Apo Dps Protein (PA0962) From Pseudomonas Aeruginosa (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ I:Na201 b:34.3 occ:1.00 O I:HOH413 2.2 38.5 1.0 NE2 I:HIS37 2.2 20.9 1.0 O G:HOH304 2.3 28.9 1.0 OE2 G:GLU68 2.9 31.2 1.0 CD2 I:HIS37 3.2 20.4 1.0 CE1 I:HIS37 3.3 22.1 1.0 CG G:ASP64 3.8 32.4 1.0 OD1 G:ASP64 3.8 30.5 1.0 O I:HOH325 3.8 34.6 1.0 OH I:TYR56 3.9 34.6 1.0 CD G:GLU68 3.9 35.6 1.0 OD2 G:ASP64 4.0 32.5 1.0 CE1 I:HIS49 4.1 21.6 1.0 CB G:ASP64 4.2 23.6 1.0 NE2 I:HIS49 4.2 22.6 1.0 CG I:HIS37 4.3 18.6 1.0 ND1 I:HIS37 4.4 19.0 1.0 CD1 I:TRP38 4.4 17.3 1.0 CG G:GLU68 4.4 30.1 1.0 NE1 I:TRP38 4.4 19.7 1.0 OE1 G:GLU68 4.9 31.2 1.0 CZ I:TYR56 5.0 26.1 1.0

N.Rajapaksha, A.Soldano, H.Yao, F.Donnarumma, M.M.Kashipathy, S.Seibold, K.P.Battaile, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits in Vitro Dna Cleaving Activity Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24054669