Sodium in PDB 1u8r: Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions

The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r was solved by G.Wisedchaisri, R.K.Holmes, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.75
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	107.959, 107.959, 215.124, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.5

The structure of Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions also contains other interesting chemical elements:

Cobalt

(Co)

24 atoms

The binding sites of Sodium atom in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions (pdb code 1u8r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions, PDB code: 1u8r:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:65.0 occ:1.00 OP1 F:DC19 2.2 47.7 1.0 O A:ASP35 2.3 55.8 1.0 O A:HOH1103 2.5 39.2 1.0 O F:HOH37 2.6 45.3 1.0 OD1 A:ASP35 2.9 0.6 1.0 C A:ASP35 3.5 56.8 1.0 P F:DC19 3.7 42.0 1.0 CG A:ASP35 4.0 0.3 1.0 CA A:GLN36 4.1 62.2 1.0 N A:GLN36 4.3 63.7 1.0 O5' F:DC19 4.3 41.4 1.0 O3' F:DC18 4.4 41.9 1.0 CB A:ASP35 4.5 0.5 1.0 CA A:ASP35 4.6 57.6 1.0 OP2 F:DC19 4.7 44.4 1.0 C A:GLN36 5.0 62.4 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2102 b:41.1 occ:1.00 OP1 E:DC21 2.4 62.8 1.0 O B:ASP35 2.6 66.0 1.0 OD1 B:ASP35 3.1 0.7 1.0 P E:DC21 3.8 59.0 1.0 C B:ASP35 3.8 64.9 1.0 O3' E:DC20 4.1 60.4 1.0 CG B:ASP35 4.2 0.5 1.0 CA B:GLN36 4.3 67.4 1.0 N B:GLN36 4.5 67.2 1.0 CB B:ASP35 4.6 0.1 1.0 OP2 E:DC21 4.7 61.0 1.0 O5' E:DC21 4.8 58.9 1.0 CA B:ASP35 4.9 67.1 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ C:Na3103 b:58.8 occ:1.00 OP1 E:DC16 2.6 58.7 1.0 O C:ASP35 2.7 57.1 1.0 OD1 C:ASP35 3.4 0.3 1.0 C C:ASP35 3.9 59.4 1.0 P E:DC16 3.9 49.5 1.0 O3' E:DG15 4.2 56.2 1.0 CG C:ASP35 4.4 0.5 1.0 CA C:GLN36 4.5 57.5 1.0 N C:GLN36 4.6 59.6 1.0 CB C:ASP35 4.7 0.5 1.0 OP2 E:DC16 4.7 56.0 1.0 CA C:ASP35 5.0 61.4 1.0 O5' E:DC16 5.0 47.7 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ D:Na4104 b:50.9 occ:1.00 O D:HOH4111 2.3 46.1 1.0 OP1 F:DC24 2.5 51.0 1.0 O D:ASP35 2.6 70.0 1.0 OD1 D:ASP35 3.0 0.8 1.0 C D:ASP35 3.7 69.6 1.0 P F:DC24 3.9 51.9 1.0 CG D:ASP35 4.1 99.0 1.0 CA D:GLN36 4.3 48.3 1.0 O3' F:DG23 4.3 53.1 1.0 N D:GLN36 4.4 50.6 1.0 CB D:ASP35 4.5 92.1 1.0 CA D:ASP35 4.7 70.4 1.0 O5' F:DC24 4.8 52.4 1.0 OP2 F:DC24 4.9 55.0 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ G:Na5105 b:51.5 occ:1.00 OP1 L:DC19 2.3 51.0 1.0 O L:HOH42 2.3 44.1 1.0 O L:HOH35 2.5 33.2 1.0 O G:ASP35 2.9 76.7 1.0 OD1 G:ASP35 3.2 0.3 1.0 P L:DC19 3.7 48.3 1.0 C G:ASP35 4.0 77.2 1.0 O5' L:DC19 4.2 48.2 1.0 O3' L:DC18 4.3 48.2 1.0 CG G:ASP35 4.3 1.0 1.0 CA G:GLN36 4.6 55.0 1.0 O L:HOH38 4.7 45.8 1.0 N G:GLN36 4.8 56.5 1.0 CB G:ASP35 4.8 0.4 1.0 OP2 L:DC19 4.9 48.6 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6106 b:59.2 occ:1.00 OP1 K:DC21 2.7 57.5 1.0 O H:ASP35 2.9 67.9 1.0 O H:HOH6109 3.0 43.5 1.0 OD1 H:ASP35 3.4 0.7 1.0 P K:DC21 4.0 58.6 1.0 C H:ASP35 4.1 68.0 1.0 O3' K:DC20 4.4 64.6 1.0 CG H:ASP35 4.5 0.9 1.0 CA H:GLN36 4.6 49.4 1.0 N H:GLN36 4.8 52.2 1.0 CB H:ASP35 4.9 0.9 1.0 OP2 K:DC21 5.0 55.8 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ I:Na7107 b:50.3 occ:1.00 O I:ASP35 2.4 78.6 1.0 OP1 K:DC16 2.5 50.3 1.0 OD1 I:ASP35 3.0 0.6 1.0 O I:HOH7109 3.1 33.8 1.0 C I:ASP35 3.6 77.4 1.0 P K:DC16 3.9 51.7 1.0 CG I:ASP35 4.1 0.9 1.0 CA I:GLN36 4.3 64.2 1.0 N I:GLN36 4.4 65.3 1.0 CB I:ASP35 4.4 0.1 1.0 O3' K:DG15 4.4 48.0 1.0 CA I:ASP35 4.7 78.2 1.0 OP2 K:DC16 4.8 51.5 1.0 O5' K:DC16 4.9 48.4 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions


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 An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Na8108 b:50.8 occ:1.00 O L:HOH36 2.5 34.4 1.0 OP1 L:DC24 2.7 64.1 1.0 O J:ASP35 2.7 73.2 1.0 OD1 J:ASP35 3.6 0.1 1.0 P L:DC24 3.9 63.1 1.0 C J:ASP35 4.0 71.9 1.0 O3' L:DG23 4.1 55.0 1.0 CA J:GLN36 4.4 53.8 1.0 CG J:ASP35 4.6 0.8 1.0 N J:GLN36 4.7 55.0 1.0 CB J:ASP35 4.8 0.3 1.0 OP2 L:DC24 4.8 62.3 1.0

G.Wisedchaisri, R.K.Holmes, W.G.J.Hol. Crystal Structure of An Ider-Dna Complex Reveals A Conformational Change in Activated Ider For Base-Specific Interactions. J.Mol.Biol. V. 342 1155 2004.
ISSN: ISSN 0022-2836
PubMed: 15351642
DOI: 10.1016/J.JMB.2004.07.083