Calcium in PDB 5ean: Crystal Structure of DNA2 in Complex with A 5' Overhang Dna

All present enzymatic activity of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna:
3.6.4.12;

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean was solved by C.Zhou, S.Pourmal, N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.36
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.153, 118.488, 149.260, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.6

The structure of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna (pdb code 5ean). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna, PDB code: 5ean:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:43.8 occ:1.00 OP2 B:DA12 2.1 77.3 1.0 O B:HOH201 2.2 49.0 1.0 O A:LEU300 2.3 45.1 1.0 OE1 A:GLU299 2.3 51.1 1.0 OD2 A:ASP278 2.3 49.1 1.0 NE2 A:HIS164 2.3 46.9 1.0 CG A:ASP278 3.2 47.1 1.0 CD A:GLU299 3.2 46.6 1.0 CE1 A:HIS164 3.3 42.7 1.0 CD2 A:HIS164 3.3 43.3 1.0 P B:DA12 3.3 0.8 1.0 C A:LEU300 3.4 41.0 1.0 OD1 A:ASP278 3.4 50.5 1.0 O5' B:DA12 3.6 93.0 1.0 N A:LEU300 3.7 38.8 1.0 OE2 A:GLU299 3.7 48.2 1.0 CA B:CA101 3.8 76.2 1.0 CA A:LEU300 3.9 39.2 1.0 O3' B:DG11 4.0 93.5 1.0 CB A:LEU300 4.2 38.4 1.0 CG A:GLU299 4.4 44.7 1.0 ND1 A:HIS164 4.4 41.5 1.0 CG A:HIS164 4.5 41.8 1.0 N A:LYS301 4.5 41.2 1.0 OP1 B:DA12 4.6 0.7 1.0 CB A:ASP278 4.6 45.9 1.0 C A:GLU299 4.7 39.1 1.0 NZ A:LYS301 4.7 41.9 1.0 CE A:LYS301 4.8 41.8 1.0 OP2 B:DG13 4.8 78.1 1.0 C5' B:DA12 4.9 85.7 1.0 O A:HOH1201 4.9 55.2 1.0 CD A:LYS301 5.0 41.8 1.0 CA A:LYS301 5.0 41.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of DNA2 in Complex with A 5' Overhang Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DNA2 in Complex with A 5' Overhang Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:76.2 occ:1.00 O B:HOH201 2.2 49.0 1.0 O A:HOH1202 2.2 71.4 1.0 O B:HOH202 2.2 62.9 1.0 O3' B:DG11 2.3 93.5 1.0 C3' B:DG11 3.0 87.9 1.0 NZ A:LYS301 3.1 41.9 1.0 C2' B:DG11 3.4 87.5 1.0 OP2 B:DG13 3.4 78.1 1.0 P B:DA12 3.4 0.8 1.0 OP2 B:DA12 3.5 77.3 1.0 OE1 A:GLU299 3.8 51.1 1.0 CA A:CA1102 3.8 43.8 1.0 O5' B:DA12 3.8 93.0 1.0 C5' B:DA12 4.1 85.7 1.0 CE A:LYS301 4.3 41.8 1.0 OE1 A:GLN314 4.5 50.9 1.0 C4' B:DG11 4.5 85.2 1.0 C1' B:DG11 4.5 97.0 1.0 C3' B:DA12 4.5 80.9 1.0 P B:DG13 4.7 75.0 1.0 OP1 B:DA12 4.7 0.7 1.0 N7 B:DG13 4.7 85.5 1.0 CD A:LYS301 4.7 41.8 1.0 CD A:GLU299 4.9 46.6 1.0 O3' B:DA12 4.9 81.2 1.0 C4' B:DA12 4.9 80.6 1.0 O A:LEU300 5.0 45.1 1.0

C.Zhou, S.Pourmal, N.P.Pavletich. DNA2 Nuclease-Helicase Structure, Mechanism and Regulation By Rpa. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26491943
DOI: 10.7554/ELIFE.09832