Sodium in PDB 2wp0: Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.

The structure of Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori., PDB code: 2wp0 was solved by G.Natrajan, M.-F.Noirot-Gros, A.Zawilak-Pawlik, U.Kapp, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.76 / 2.67
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.560, 55.500, 96.830, 90.00, 97.55, 90.00
R / Rfree (%)	22.6 / 26.6

The structure of Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. (pdb code 2wp0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori., PDB code: 2wp0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:43.0 occ:1.00 CG1 A:ILE83 3.5 23.0 1.0 OH A:TYR107 3.5 33.4 1.0 CG2 A:ILE83 3.6 23.1 1.0 CB A:ILE83 4.2 23.5 1.0 CZ A:TYR107 4.6 31.1 1.0 CE1 A:TYR107 4.7 29.6 1.0 CD1 A:ILE83 4.7 22.1 1.0 O A:HOH321 4.8 13.3 1.0

Sodium binding site 2 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:43.4 occ:1.00 OE1 A:GLU139 3.5 90.1 1.0 CB A:GLU139 4.0 88.3 1.0 O A:HOH323 4.2 28.2 1.0 CD1 A:ILE118 4.3 38.7 1.0 O A:GLU139 4.4 88.4 1.0 CB A:ILE118 4.4 39.0 1.0 CD A:GLU139 4.5 90.5 1.0 CG1 A:ILE118 4.5 38.0 1.0 CG A:GLU139 4.8 90.7 1.0 C A:GLU139 5.0 90.1 1.0 CA A:GLU139 5.0 89.3 1.0

Sodium binding site 3 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:42.2 occ:1.00 N A:LYS93 3.5 64.4 1.0 O A:TYR91 3.8 46.2 1.0 CB A:LYS93 4.0 72.3 1.0 O A:ASN94 4.1 0.8 1.0 OG A:SER99 4.2 32.2 1.0 N A:ASN94 4.2 0.4 1.0 CA A:LYS93 4.3 67.4 1.0 C A:PRO92 4.4 53.7 1.0 CA A:PRO92 4.4 51.1 1.0 O A:ASP95 4.6 65.5 1.0 C A:ASN94 4.7 0.2 1.0 C A:LYS93 4.7 68.8 1.0 C A:TYR91 4.7 42.8 1.0 O A:SER89 4.8 44.5 1.0

Sodium binding site 4 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:79.2 occ:1.00 CL B:CL201 3.5 0.1 1.0 O B:HOH332 3.7 30.8 1.0 ND2 B:ASN168 3.7 36.8 1.0 CZ A:PHE11 3.9 29.4 1.0 CB B:LYS164 3.9 28.6 1.0 NE2 A:GLN15 4.1 30.4 1.0 CD B:LYS164 4.2 25.1 1.0 CE2 A:PHE11 4.6 29.8 1.0 CG B:LYS164 4.6 25.7 1.0 CG B:ASN168 4.7 39.2 1.0 CE1 A:PHE11 4.8 30.6 1.0 O B:LYS164 4.9 17.6 1.0 CG A:GLN15 4.9 32.5 1.0 C B:LYS164 5.0 31.6 1.0 CA B:LYS164 5.0 28.2 1.0

Sodium binding site 5 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:36.5 occ:1.00 OG B:SER153 3.3 28.8 1.0 O B:HOH317 3.5 41.5 1.0 N B:SER153 3.6 26.5 1.0 OD1 B:ASP152 3.8 31.5 1.0 CZ B:PHE18 3.9 39.8 1.0 NZ B:LYS149 4.0 76.8 1.0 CB B:SER153 4.0 28.4 1.0 CA B:ASP152 4.4 28.5 1.0 CA B:SER153 4.4 26.3 1.0 CE2 B:PHE18 4.4 37.5 1.0 C B:ASP152 4.5 28.9 1.0 CG B:ASP152 4.7 29.7 1.0 O B:HIS151 5.0 72.9 1.0

Sodium binding site 6 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:39.5 occ:1.00 OE1 B:GLU119 3.2 47.0 1.0 O B:ALA54 3.2 26.4 1.0 N B:SER56 3.5 47.6 1.0 CL B:CL205 3.9 68.1 1.0 C B:ASP55 3.9 28.2 1.0 CA B:SER56 3.9 48.1 1.0 CB B:SER56 4.0 50.7 1.0 CA B:ASP55 4.1 26.4 1.0 OG B:SER56 4.1 52.9 1.0 CE1 B:HIS59 4.1 50.8 1.0 C B:ALA54 4.3 25.1 1.0 CD B:GLU119 4.4 47.8 1.0 OH B:TYR91 4.4 38.3 1.0 O B:ASP55 4.6 26.9 1.0 OD1 B:ASN86 4.7 31.0 1.0 N B:ASP55 4.7 25.7 1.0 ND2 B:ASN86 4.8 31.0 1.0 NE2 B:HIS59 5.0 52.3 1.0

Sodium binding site 7 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:55.7 occ:1.00 OH B:TYR107 3.3 30.7 1.0 CG1 B:ILE83 3.4 22.7 1.0 CG2 B:ILE83 3.7 22.1 1.0 O B:HOH321 4.1 19.5 1.0 CB B:ILE83 4.2 22.1 1.0 CZ B:TYR107 4.3 30.1 1.0 CE1 B:TYR107 4.4 29.1 1.0 CD1 B:ILE83 4.6 22.0 1.0

Sodium binding site 8 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:34.0 occ:1.00 O B:HOH315 3.0 27.8 1.0 OD1 B:ASP156 3.1 25.9 1.0 OD2 B:ASP156 3.2 25.8 1.0 NE1 B:TRP60 3.5 37.9 1.0 CG B:ASP156 3.5 25.8 1.0 OD1 A:ASN68 3.8 39.2 1.0 O B:SER57 3.9 21.0 1.0 ND2 A:ASN68 4.0 37.0 1.0 CE1 A:TYR64 4.1 24.2 1.0 CE2 B:TRP60 4.3 37.1 1.0 NH1 B:ARG58 4.3 28.1 1.0 CG A:ASN68 4.4 37.0 1.0 CD B:ARG58 4.4 30.2 1.0 CD1 B:TRP60 4.4 37.4 1.0 CZ2 B:TRP60 4.5 36.2 1.0 CD1 A:TYR64 4.8 23.7 1.0 OH A:TYR64 4.8 25.8 1.0 CZ A:TYR64 4.8 24.0 1.0 C B:SER57 4.9 21.4 1.0

Sodium binding site 9 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:63.7 occ:1.00 OE1 B:GLU167 3.2 57.5 1.0 OD1 B:ASN68 3.3 45.4 1.0 NZ B:LYS164 3.7 24.7 1.0 OH B:TYR64 4.2 22.8 1.0 O B:HOH332 4.2 30.8 1.0 CG B:ASN68 4.2 42.8 1.0 CD B:GLU167 4.2 57.2 1.0 CG B:LYS164 4.5 25.7 1.0 CE2 B:PHE163 4.6 32.1 1.0 CB B:ASN68 4.6 41.7 1.0 OE2 B:GLU167 4.6 58.1 1.0 OD2 A:ASP156 4.8 35.3 1.0 CE B:LYS164 4.9 26.8 1.0 CD2 B:PHE163 5.0 32.2 1.0 CD B:LYS164 5.0 25.1 1.0

Sodium binding site 10 out of 11 in the Crystal Structure of A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori.


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 A Hoba-Dnaa (Domain I-II) Complex From Helicobacter Pylori. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na211 b:57.4 occ:1.00 NZ B:LYS177 3.9 37.6 1.0

G.Natrajan, M.F.Noirot-Gros, A.Zawilak-Pawlik, U.Kapp, L.Terradot. The Structure of A Dnaa/Hoba Complex From Helicobacter Pylori Provides Insight Into Regulation of Dna Replication in Bacteria. Proc.Natl.Acad.Sci.Usa V. 106 21115 2009.
ISSN: ISSN 0027-8424
PubMed: 19940251
DOI: 10.1073/PNAS.0908966106