Sodium in PDB 7p0j: Crystal Structure of S.Pombe MDB1 Brct Domains

The structure of Crystal Structure of S.Pombe MDB1 Brct Domains, PDB code: 7p0j was solved by M.Day, A.W.Oliver, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.18, 44.12, 49.86, 90, 92.37, 90
R / Rfree (%)	17 / 19.7

The structure of Crystal Structure of S.Pombe MDB1 Brct Domains also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of S.Pombe MDB1 Brct Domains (pdb code 7p0j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of S.Pombe MDB1 Brct Domains, PDB code: 7p0j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of S.Pombe MDB1 Brct Domains


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 S.Pombe MDB1 Brct Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:12.9 occ:0.49 HO7 A:CIT601 1.9 17.1 1.0 O5 A:CIT601 2.3 14.9 1.0 O7 A:CIT601 2.3 14.3 1.0 O3 A:CIT601 2.4 19.1 1.0 C6 A:CIT601 2.9 15.4 1.0 C3 A:CIT601 3.0 14.7 1.0 HA A:SER393 3.2 15.6 0.7 HA A:SER393 3.2 15.7 0.3 H A:SER393 3.3 16.4 0.3 H A:SER393 3.3 16.4 0.7 C5 A:CIT601 3.4 18.7 1.0 HH12 A:ARG430 3.6 17.5 1.0 C4 A:CIT601 3.7 14.2 1.0 N A:SER393 3.9 13.6 1.0 CA A:SER393 4.0 13.0 0.7 CA A:SER393 4.0 13.1 0.3 O A:HOH722 4.0 25.3 0.9 O6 A:CIT601 4.1 14.7 1.0 H41 A:CIT601 4.2 17.1 1.0 NH1 A:ARG430 4.3 14.6 1.0 C2 A:CIT601 4.4 16.3 1.0 O2 A:CIT601 4.4 26.8 1.0 HH11 A:ARG430 4.5 17.5 1.0 O4 A:CIT601 4.5 21.0 1.0 H42 A:CIT601 4.6 17.1 1.0 HB2 A:SER393 4.6 17.8 0.7 H A:PHE394 4.7 15.5 1.0 H21 A:CIT601 4.7 19.6 1.0 CB A:SER393 4.8 14.8 0.7 OG A:SER393 4.8 15.8 0.3 C1 A:CIT601 4.8 23.8 1.0 OG A:SER393 4.9 15.2 0.7 HA A:SER392 4.9 14.6 1.0 CB A:SER393 5.0 14.8 0.3 C A:SER393 5.0 12.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of S.Pombe MDB1 Brct Domains


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 S.Pombe MDB1 Brct Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:39.9 occ:1.00 O A:HOH818 2.1 20.2 0.7 OG A:SER552 2.6 20.5 0.8 O A:HOH864 2.7 17.3 0.6 O A:SER552 2.8 17.9 1.0 HB3 A:SER552 2.9 21.2 0.2 C A:SER552 3.5 15.9 1.0 O A:HOH879 3.6 27.9 0.7 O A:HOH774 3.7 23.2 0.6 CB A:SER552 3.7 17.7 0.2 CB A:SER552 3.7 17.8 0.8 HA A:SER552 3.8 17.4 0.2 HA A:SER552 3.8 17.2 0.8 CA A:SER552 3.9 14.5 0.2 CA A:SER552 3.9 14.3 0.8 HB3 A:SER552 4.1 21.4 0.8 HA A:ALA553 4.3 17.6 1.0 HA2 A:GLY555 4.3 21.6 1.0 HB2 A:SER552 4.4 21.2 0.2 HB2 A:SER552 4.4 21.4 0.8 OG A:SER552 4.4 16.0 0.2 N A:ALA553 4.4 14.2 1.0 H A:GLY555 4.5 18.9 1.0 O A:LEU556 4.6 17.1 1.0 HG A:SER552 4.6 19.2 0.2 O A:HOH713 4.7 17.8 0.7 O A:HOH849 4.7 23.1 0.7 CA A:ALA553 4.9 14.7 1.0

M.Day, A.W.Oliver, L.H.Pearl. The Role of TOPBP1 in Phosphorylation-Dependent Assembly of Dna Damage Response Systems To Be Published.