Sodium in PDB 2isz: Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I

The structure of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I, PDB code: 2isz was solved by G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.832, 69.739, 76.461, 106.57, 104.85, 99.66
R / Rfree (%)	19.9 / 23.9

The structure of Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I also contains other interesting chemical elements:

Nickel

(Ni)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I (pdb code 2isz). 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 A Two-Domain Ider-Dna Complex Crystal Form I, PDB code: 2isz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


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 Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2001 b:50.1 occ:1.00 O F:HOH51 1.9 43.1 1.0 O A:HOH2029 2.0 31.0 1.0 O F:HOH50 2.1 43.5 1.0 O A:HOH2028 2.2 30.5 1.0 OP1 F:DC19 2.9 28.3 1.0 P F:DC19 4.0 28.0 1.0 N A:SER37 4.0 30.8 1.0 O A:ASP35 4.1 30.2 1.0 OP2 F:DT20 4.2 29.3 1.0 O5' F:DC19 4.3 27.9 1.0 C A:GLN36 4.3 30.1 1.0 CA A:GLN36 4.5 30.2 1.0 OP2 F:DC19 4.5 28.0 1.0 OD1 A:ASP35 4.6 37.5 1.0 CA A:SER37 4.6 29.9 1.0 C A:ASP35 4.6 31.3 1.0 CB A:SER37 4.6 30.0 1.0 C5' F:DC19 4.6 28.5 1.0 N A:GLN36 4.8 31.4 1.0 O A:GLN36 4.9 32.0 1.0 P F:DT20 4.9 28.5 1.0 O3' F:DC19 4.9 27.1 1.0 OP1 F:DT20 5.0 28.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


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 Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2001 b:48.0 occ:1.00 O E:HOH55 2.3 26.2 1.0 O E:HOH58 2.5 54.6 1.0 O C:HOH2018 2.5 37.9 1.0 OP1 E:DC16 3.2 30.0 1.0 O C:HOH2019 3.3 36.2 1.0 O C:ASP35 4.1 33.4 1.0 P E:DC16 4.3 30.8 1.0 OP2 E:DT17 4.3 27.7 1.0 O5' E:DC16 4.4 30.5 1.0 N C:SER37 4.4 29.6 1.0 C C:GLN36 4.6 30.8 1.0 C5' E:DC16 4.6 27.6 1.0 OD1 C:ASP35 4.6 42.7 1.0 CA C:GLN36 4.7 31.6 1.0 C C:ASP35 4.8 34.4 1.0 CA C:SER37 4.9 28.0 1.0 CB C:SER37 4.9 28.2 1.0 OP2 E:DC16 4.9 31.6 1.0 P E:DT17 5.0 28.1 1.0 OP1 E:DT17 5.0 27.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Two-Domain Ider-Dna Complex Crystal Form I


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 Two-Domain Ider-Dna Complex Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ D:Na2001 b:50.0 occ:1.00 O D:HOH2015 1.9 45.5 1.0 O D:HOH2014 2.1 41.6 1.0 O F:HOH49 2.3 32.4 1.0 OP1 F:DC24 3.2 32.0 1.0 O D:ASP35 4.2 39.9 1.0 P F:DC24 4.3 31.1 1.0 O5' F:DC24 4.4 32.6 1.0 C D:GLN36 4.5 37.8 1.0 N D:SER37 4.5 37.3 1.0 CA D:GLN36 4.5 37.7 1.0 OP2 F:DT25 4.6 39.4 1.0 OD2 D:ASP35 4.6 45.3 1.0 C5' F:DC24 4.7 34.5 1.0 C D:ASP35 4.7 39.7 1.0 O D:GLN36 4.9 37.4 1.0 N D:GLN36 4.9 38.2 1.0 CG D:ASP35 5.0 44.5 1.0 CB D:SER37 5.0 37.2 1.0 CA D:SER37 5.0 36.1 1.0

G.Wisedchaisri, C.J.Chou, M.Wu, C.Roach, A.E.Rice, R.K.Holmes, C.Beeson, W.G.Hol. Crystal Structures, Metal Activation, and Dna-Binding Properties of Two-Domain Ider From Mycobacterium Tuberculosis Biochemistry V. 46 436 2007.
ISSN: ISSN 0006-2960
PubMed: 17209554
DOI: 10.1021/BI0609826