Calcium in PDB 5kn8: Muty N-Terminal Domain in Complex with Undamaged Dna

The structure of Muty N-Terminal Domain in Complex with Undamaged Dna, PDB code: 5kn8 was solved by L.Wang, S.Chakravarthy, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.35 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.200, 38.618, 83.796, 90.00, 104.00, 90.00
R / Rfree (%)	16.7 / 22

The structure of Muty N-Terminal Domain in Complex with Undamaged Dna also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Muty N-Terminal Domain in Complex with Undamaged Dna (pdb code 5kn8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Muty N-Terminal Domain in Complex with Undamaged Dna, PDB code: 5kn8:

Calcium binding site 1 out of 1 in the Muty N-Terminal Domain in Complex with Undamaged Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Muty N-Terminal Domain in Complex with Undamaged Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:40.8 occ:1.00 O A:HOH507 2.3 39.8 1.0 O A:SER118 2.3 33.6 1.0 O A:HOH415 2.4 33.7 1.0 O A:VAL123 2.4 22.3 1.0 O A:HOH499 2.4 39.9 1.0 OP2 D:DA21 2.8 20.6 1.0 OG A:SER118 3.4 48.4 1.0 C A:SER118 3.5 37.1 1.0 C A:VAL123 3.6 26.8 1.0 O D:HOH122 4.1 51.0 1.0 P D:DA21 4.2 29.5 1.0 O A:LEU120 4.2 29.2 1.0 CA A:SER118 4.3 22.7 1.0 CA A:GLY124 4.3 19.5 1.0 CB A:SER118 4.4 26.5 1.0 N A:GLY124 4.4 19.2 1.0 N A:ARG119 4.5 27.2 1.0 CA A:VAL123 4.6 21.5 1.0 N A:VAL123 4.6 18.4 1.0 CA A:ARG119 4.7 30.9 1.0 OP1 D:DA21 4.8 30.8 1.0 C A:ARG119 4.9 23.4 1.0 CB A:VAL123 4.9 30.3 1.0

L.Wang, S.Chakravarthy, G.L.Verdine. Structural Basis For the Lesion-Scanning Mechanism of the Muty Dna Glycosylase. J. Biol. Chem. V. 292 5007 2017.
ISSN: ESSN 1083-351X
PubMed: 28130451
DOI: 10.1074/JBC.M116.757039