Calcium in PDB 5kn9: Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair

The structure of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair, PDB code: 5kn9 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)	79.88 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.878, 38.759, 82.960, 90.00, 105.66, 90.00
R / Rfree (%)	16.9 / 22.9

The structure of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair 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 Dna Containing An Intrahelical Oxog:A Base-Pair (pdb code 5kn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair, PDB code: 5kn9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair


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 Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:52.7 occ:1.00 O A:SER118 2.3 31.4 1.0 O A:HOH432 2.3 32.4 1.0 O A:HOH497 2.5 44.5 1.0 O A:HOH477 2.5 39.7 1.0 O A:VAL123 2.5 27.8 1.0 OG A:SER118 2.8 42.3 1.0 C A:SER118 3.3 38.2 1.0 OP2 D:DA21 3.6 28.6 1.0 C A:VAL123 3.6 26.8 1.0 CA A:SER118 3.9 28.0 1.0 CB A:SER118 3.9 29.0 1.0 CA A:GLY124 4.2 25.1 1.0 N A:GLY124 4.3 24.6 1.0 O A:LEU120 4.4 29.1 1.0 N A:ARG119 4.5 30.7 1.0 CA A:VAL123 4.7 29.9 1.0 CA A:ARG119 4.8 32.5 1.0 N A:VAL123 4.9 25.7 1.0 CB A:VAL123 5.0 33.4 1.0

Calcium binding site 2 out of 2 in the Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Muty N-Terminal Domain in Complex with Dna Containing An Intrahelical Oxog:A Base-Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:61.3 occ:1.00 O C:HOH218 2.5 40.5 1.0 O A:HOH515 2.5 43.8 1.0 O C:HOH204 2.6 34.8 1.0 O A:HOH494 2.6 30.0 1.0 O C:HOH209 2.7 36.8 1.0 O A:HOH486 4.0 32.2 1.0 NZ A:LYS163 4.4 32.1 1.0 OP2 C:DC5 4.4 33.4 1.0 OP1 C:DT4 4.5 21.6 1.0 O C:HOH205 4.6 26.4 1.0 O A:HOH421 4.8 24.1 1.0 OP1 C:DC5 4.8 27.9 1.0 P C:DC5 5.0 30.4 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