Calcium in PDB 5e5o: I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions

The structure of I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions, PDB code: 5e5o was solved by B.W.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.00 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.327, 67.993, 97.743, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 27.4

The binding sites of Calcium atom in the I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions (pdb code 5e5o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions, PDB code: 5e5o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:42.1 occ:1.00 O B:HOH203 2.2 41.0 1.0 OP1 C:DC16 2.3 38.6 1.0 OE2 A:GLU20 2.4 31.8 1.0 O A:GLY178 2.4 26.9 1.0 OD1 A:ASP179 2.5 30.0 1.0 O B:HOH201 2.7 28.3 1.0 CD A:GLU20 3.1 33.2 1.0 OE1 A:GLU20 3.2 35.2 1.0 O3' C:DT15 3.2 33.9 1.0 P C:DC16 3.3 36.7 1.0 C A:GLY178 3.4 26.4 1.0 CG A:ASP179 3.7 28.2 1.0 O C:HOH205 3.8 38.6 1.0 CA A:CA402 3.9 37.4 1.0 CA A:ASP179 3.9 29.0 1.0 N A:ASP179 4.0 27.7 1.0 O3' B:DA14 4.2 41.5 1.0 C4' B:DA14 4.3 43.6 1.0 OP2 C:DC16 4.4 34.4 1.0 CB A:ASP179 4.4 29.0 1.0 CG A:GLU20 4.4 32.1 1.0 O5' B:DA14 4.4 52.2 1.0 C3' C:DT15 4.5 34.6 1.0 CA A:GLY178 4.5 27.1 1.0 OP1 B:DA14 4.5 50.4 1.0 O5' C:DC16 4.5 36.8 1.0 OD2 A:ASP179 4.5 29.1 1.0 C5' C:DC16 4.6 39.5 1.0 C3' B:DA14 4.8 42.4 1.0 C2 B:EDO101 4.8 51.9 1.0 O2 B:EDO101 4.8 53.1 1.0 OP1 B:DT15 4.9 41.1 1.0 C4' C:DT15 5.0 35.6 1.0

Calcium binding site 2 out of 3 in the I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:37.4 occ:1.00 OP1 C:DT15 2.2 40.0 1.0 O C:HOH203 2.3 36.4 1.0 O A:ALA19 2.3 23.8 1.0 OP1 B:DT15 2.3 41.1 1.0 OD2 A:ASP179 2.6 29.1 1.0 O B:HOH201 2.6 28.3 1.0 OD1 A:ASP179 2.7 30.0 1.0 OE2 A:GLU20 2.9 31.8 1.0 CG A:ASP179 3.0 28.2 1.0 C A:ALA19 3.5 25.0 1.0 P B:DT15 3.7 41.0 1.0 P C:DT15 3.7 37.5 1.0 O B:HOH211 3.7 38.0 1.0 CA A:CA401 3.9 42.1 1.0 O3' B:DA14 3.9 41.5 1.0 CD A:GLU20 4.0 33.2 1.0 CA A:ALA19 4.2 24.5 1.0 N A:GLU20 4.4 27.9 1.0 CA A:GLU20 4.4 30.1 1.0 CB A:ASP179 4.5 29.0 1.0 O3' C:DA14 4.5 36.9 1.0 OP2 C:DT15 4.6 39.7 1.0 O5' C:DT15 4.6 37.7 1.0 CB A:ALA19 4.6 25.2 1.0 C5' B:DT15 4.6 41.4 1.0 OE1 A:GLU20 4.6 35.2 1.0 O5' B:DT15 4.7 40.3 1.0 OP2 B:DT15 4.7 41.5 1.0 OE1 A:GLN206 4.8 27.0 1.0 C4' C:DT15 4.8 35.6 1.0 CG A:GLU20 4.9 32.1 1.0

Calcium binding site 3 out of 3 in the I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of I-Smami Bound to Uncleaved Dna Target in the Presence of Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:54.5 occ:1.00 O A:HOH503 2.2 42.8 1.0 O A:ILE138 2.5 42.3 1.0 O A:HOH526 2.6 50.2 1.0 OD2 A:ASP106 2.7 43.5 1.0 O A:HOH541 2.8 34.3 1.0 OD1 A:ASP106 2.9 41.1 1.0 CG A:ASP106 3.2 37.8 1.0 NH2 A:ARG209 3.3 60.3 1.0 C A:ILE138 3.7 42.9 1.0 CZ A:ARG209 4.1 64.1 1.0 NH1 A:ARG209 4.3 69.4 1.0 NH1 A:ARG158 4.4 45.3 1.0 CA A:ASN139 4.5 51.7 1.0 OD1 A:ASN139 4.5 56.9 1.0 NH2 A:ARG158 4.5 40.3 1.0 OP2 B:DG16 4.5 38.7 1.0 N A:ASN139 4.6 47.5 1.0 CB A:ASP106 4.6 35.5 1.0 CA A:ILE138 4.7 40.6 1.0 CZ A:ARG158 4.7 44.2 1.0 O B:HOH210 4.8 30.1 1.0 CB A:ASN139 4.9 52.3 1.0 OP1 B:DG16 4.9 42.1 1.0 CG2 A:ILE138 5.0 36.9 1.0

B.W.Shen, A.Lambert, B.C.Walker, B.L.Stoddard, B.K.Kaiser. The Structural Basis of Asymmetry in Dna Binding and Cleavage As Exhibited By the I-Smami Laglidadg Meganuclease. J.Mol.Biol. V. 428 206 2016.
ISSN: ESSN 1089-8638
PubMed: 26705195
DOI: 10.1016/J.JMB.2015.12.005