Sodium in PDB 1mdg: An Alternating Antiparallel Octaplex in An Rna Crystal Structure

The structure of An Alternating Antiparallel Octaplex in An Rna Crystal Structure, PDB code: 1mdg was solved by B.C.Pan, Y.Xiong, K.Shi, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	35.956, 35.956, 38.045, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.4

The structure of An Alternating Antiparallel Octaplex in An Rna Crystal Structure also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Bromine	(Br)	1 atom

The binding sites of Sodium atom in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure (pdb code 1mdg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure, PDB code: 1mdg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An Alternating Antiparallel Octaplex in An Rna Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:15.7 occ:0.25 O6 A:BGM2 2.9 10.0 1.0 NA A:NA102 3.4 17.8 0.2 C6 A:BGM2 3.7 10.2 1.0 N1 A:BGM2 4.1 9.8 1.0 C5 A:BGM2 4.9 9.4 1.0

Sodium binding site 2 out of 5 in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of An Alternating Antiparallel Octaplex in An Rna Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:17.8 occ:0.25 O6 A:BGM2 2.8 10.0 1.0 NA A:NA103 3.1 21.0 0.2 NA A:NA101 3.4 15.7 0.2 N1 A:A3 3.5 10.5 1.0 C2 A:A3 3.6 8.2 1.0 C6 A:BGM2 3.7 10.2 1.0 N1 A:BGM2 4.0 9.8 1.0 C6 A:A3 4.7 12.0 1.0 N3 A:A3 4.8 11.1 1.0 C5 A:BGM2 4.9 9.4 1.0

Sodium binding site 3 out of 5 in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of An Alternating Antiparallel Octaplex in An Rna Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:21.0 occ:0.25 O6 A:G4 3.0 9.8 1.0 NA A:NA102 3.1 17.8 0.2 NA A:NA104 3.3 8.2 0.2 C2 A:A3 3.5 8.2 1.0 N1 A:A3 3.5 10.5 1.0 C6 A:G4 3.8 10.3 1.0 N1 A:G4 4.1 11.3 1.0 N3 A:A3 4.6 11.1 1.0 C6 A:A3 4.8 12.0 1.0

Sodium binding site 4 out of 5 in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of An Alternating Antiparallel Octaplex in An Rna Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:8.2 occ:0.25 O6 A:G5 2.7 10.8 1.0 O6 A:G4 2.8 9.8 1.0 NA A:NA103 3.3 21.0 0.2 NA A:NA105 3.4 8.5 0.2 C6 A:G4 3.6 10.3 1.0 C6 A:G5 3.7 10.2 1.0 N1 A:G4 3.9 11.3 1.0 N1 A:G5 4.0 10.6 1.0 C5 A:G4 4.9 10.2 1.0 C5 A:G5 5.0 9.8 1.0

Sodium binding site 5 out of 5 in the An Alternating Antiparallel Octaplex in An Rna Crystal Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of An Alternating Antiparallel Octaplex in An Rna Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:8.5 occ:0.25 O4 A:U6 2.7 12.8 1.0 O6 A:G5 2.8 10.8 1.0 NA A:NA104 3.4 8.2 0.2 C6 A:G5 3.6 10.2 1.0 C4 A:U6 3.6 14.4 1.0 N3 A:U6 3.9 12.2 1.0 N1 A:G5 3.9 10.6 1.0 C5 A:G5 4.8 9.8 1.0 C5 A:U6 5.0 13.7 1.0

B.C.Pan, Y.Xiong, K.Shi, M.Sundaralingam. An Eight-Stranded Helical Fragment in Rna Crystal Structure: Implications For Tetraplex Interaction Structure V. 11 825 2003.
ISSN: ISSN 0969-2126
PubMed: 12842045
DOI: 10.1016/S0969-2126(03)00108-4