Calcium in PDB 5cfe: Bacillus Subtilis Ap Endonuclease Exoa

All present enzymatic activity of Bacillus Subtilis Ap Endonuclease Exoa:
3.1.11.2;

The structure of Bacillus Subtilis Ap Endonuclease Exoa, PDB code: 5cfe was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.57 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.280, 61.920, 73.360, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.8

The binding sites of Calcium atom in the Bacillus Subtilis Ap Endonuclease Exoa (pdb code 5cfe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Bacillus Subtilis Ap Endonuclease Exoa, PDB code: 5cfe:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Bacillus Subtilis Ap Endonuclease Exoa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacillus Subtilis Ap Endonuclease Exoa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:17.8 occ:1.00 OE1 A:GLU36 2.2 31.3 1.0 O A:HOH415 2.3 20.2 1.0 O A:HOH529 2.3 32.7 1.0 O A:HOH462 2.4 12.4 1.0 O A:HOH557 2.4 37.4 1.0 OD1 A:ASN9 2.5 20.0 1.0 OE2 A:GLU36 2.5 25.8 1.0 CD A:GLU36 2.7 23.1 1.0 CG A:ASN9 3.5 22.9 1.0 O A:HOH426 3.9 15.9 1.0 CG A:GLU36 4.2 21.0 1.0 CB A:ASN9 4.2 10.0 1.0 CA A:ASN9 4.3 9.9 1.0 OD2 A:ASP242 4.4 14.1 1.0 ND2 A:ASN9 4.5 15.0 1.0 OD1 A:ASP242 4.5 11.8 1.0 ND2 A:ASN7 4.6 8.2 1.0 OH A:TYR106 4.7 19.0 1.0 NZ A:LYS38 4.7 28.6 1.0 CE A:LYS38 4.7 24.8 1.0 CG A:ASP242 4.9 11.9 1.0 OD1 A:ASN7 4.9 14.5 1.0 CB A:GLU36 5.0 12.2 1.0

Calcium binding site 2 out of 3 in the Bacillus Subtilis Ap Endonuclease Exoa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacillus Subtilis Ap Endonuclease Exoa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:21.5 occ:1.00 O A:HOH549 2.4 23.9 1.0 OE1 A:GLU98 2.4 17.6 1.0 OE2 A:GLU98 2.4 23.5 1.0 CD A:GLU98 2.7 25.6 1.0 CG A:GLU98 4.2 25.7 1.0 O A:HOH416 4.4 30.1 1.0 ND2 A:ASN99 4.6 22.7 1.0 O A:HOH429 4.7 21.8 1.0 OD1 A:ASN99 4.8 25.7 1.0

Calcium binding site 3 out of 3 in the Bacillus Subtilis Ap Endonuclease Exoa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bacillus Subtilis Ap Endonuclease Exoa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:27.4 occ:1.00 O A:HOH548 2.4 28.8 1.0 OE2 A:GLU195 2.5 35.6 1.0 OE1 A:GLU195 2.5 29.3 1.0 O A:HOH562 2.6 26.5 1.0 CD A:GLU195 2.8 40.0 1.0 O A:HOH572 3.0 50.1 1.0 CG A:GLU195 4.4 31.0 1.0 O A:HOH409 4.4 26.4 1.0 CG2 A:ILE153 4.7 17.4 1.0 O A:HOH442 4.9 26.0 1.0

M.Redrejo-Rodriguez, A.Vigouroux, A.Mursalimov, I.Grin, D.Alili, Z.Koshenov, Z.Akishev, A.Maksimenko, A.K.Bissenbaev, B.T.Matkarimov, M.Saparbaev, A.A.Ishchenko, S.Morera. Structural Comparison of Ap Endonucleases From the Exonuclease III Family Reveals New Amino Acid Residues in Human Ap Endonuclease 1 That Are Involved in Incision of Damaged Dna. Biochimie V.-129 20 2016.
ISSN: ISSN 0300-9084
PubMed: 27343627
DOI: 10.1016/J.BIOCHI.2016.06.011