Calcium in PDB 4yit: Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna

The structure of Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna, PDB code: 4yit was solved by J.P.Hallinan, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.24
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.960, 61.536, 88.621, 97.18, 99.10, 101.89
R / Rfree (%)	22.5 / 29.9

The binding sites of Calcium atom in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna (pdb code 4yit). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna, PDB code: 4yit:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved 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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:50.3 occ:1.00 O A:GLY12 2.0 37.5 1.0 OP1 B:DA14 2.4 34.9 1.0 OP1 C:DA16 2.6 45.8 1.0 OE2 A:GLU169 2.8 51.2 1.0 C A:GLY12 3.2 37.7 1.0 CD A:GLU169 3.3 49.6 1.0 P C:DA16 3.3 45.4 1.0 O5' C:DA16 3.4 43.9 1.0 OE1 A:GLU169 3.4 49.8 1.0 NE2 A:GLN196 3.6 37.4 1.0 C5' C:DA16 3.6 45.3 1.0 OP2 C:DA16 3.7 47.4 1.0 CA A:GLY12 3.9 36.5 1.0 P B:DA14 3.9 36.7 1.0 NZ A:LYS93 4.0 64.1 1.0 OE1 A:GLN196 4.1 37.7 1.0 N A:GLU13 4.2 38.8 1.0 CD A:GLN196 4.3 37.1 1.0 C4' B:DA14 4.4 36.1 1.0 CG A:GLU169 4.4 48.9 1.0 CA A:GLU13 4.5 40.9 1.0 C5' B:DA14 4.5 35.1 1.0 O A:ASP11 4.7 31.4 1.0 O3' B:DA13 4.7 37.3 1.0 O5' B:DA14 4.7 35.9 1.0 OP2 B:DA14 4.7 34.5 1.0 O3' C:DA15 4.8 40.0 1.0 C4' C:DA16 4.9 48.0 1.0 C3' C:DA16 5.0 49.4 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved 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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:43.5 occ:1.00 OP1 C:DA15 2.1 37.6 1.0 OE1 A:GLU13 2.4 41.7 1.0 OP2 B:DA15 2.4 39.1 1.0 O A:ALA168 2.4 55.6 1.0 CD A:GLU13 3.4 42.5 1.0 C A:ALA168 3.4 50.9 1.0 P C:DA15 3.6 37.8 1.0 CA A:ALA168 3.8 49.2 1.0 OE2 A:GLU13 3.8 45.2 1.0 P B:DA15 3.8 40.1 1.0 C5' C:DA15 3.9 38.7 1.0 O5' C:DA15 4.2 38.4 1.0 O3' C:DA14 4.3 38.8 1.0 CB A:ALA168 4.4 49.4 1.0 NZ A:LYS249 4.5 40.0 1.0 OP1 B:DA15 4.6 38.2 1.0 N A:GLU169 4.7 49.8 1.0 OP2 C:DA15 4.7 35.0 1.0 CG A:GLU13 4.7 41.2 1.0 O5' B:DA15 4.7 40.0 1.0 C5' B:DA15 4.7 39.4 1.0 O3' B:DA14 4.8 37.1 1.0 C4' C:DA15 4.8 36.9 1.0 OE1 A:GLU169 4.9 49.8 1.0 O A:SER167 5.0 47.3 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:56.7 occ:1.00 OD2 D:ASP209 2.1 69.5 1.0 OD2 A:ASP209 3.1 68.2 1.0 CG D:ASP209 3.3 67.0 1.0 O A:ASP209 3.5 51.1 1.0 CA A:ASP209 3.5 58.8 1.0 CG A:ASP209 3.6 66.2 1.0 CB A:ASP209 3.6 62.1 1.0 OD1 A:ASN212 3.7 64.7 1.0 CB D:ASP209 3.9 65.2 1.0 C A:ASP209 4.0 55.0 1.0 CG A:ASN212 4.0 63.4 1.0 CA A:ASN212 4.0 59.2 1.0 CB A:ASN212 4.1 61.8 1.0 OD1 D:ASP209 4.3 59.8 1.0 O D:ASP209 4.5 59.7 1.0 OD1 A:ASP209 4.6 67.8 1.0 N A:ASN212 4.6 57.3 1.0 N A:ASP209 4.8 59.3 1.0 C D:ASP209 4.9 59.7 1.0 ND2 A:ASN212 5.0 61.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:33.5 occ:1.00 OP1 E:DA14 2.1 32.2 1.0 O D:GLY12 2.5 33.2 1.0 OP1 F:DA16 2.6 42.4 1.0 OE2 D:GLU169 2.7 30.9 1.0 OE1 D:GLU169 3.3 29.6 1.0 P F:DA16 3.3 45.2 1.0 C5' F:DA16 3.4 49.7 1.0 CD D:GLU169 3.4 30.5 1.0 OP2 F:DA16 3.5 46.6 1.0 P E:DA14 3.6 32.6 1.0 C D:GLY12 3.7 31.9 1.0 O5' F:DA16 3.8 45.9 1.0 C4' F:DA16 4.0 52.5 1.0 NZ D:LYS93 4.1 51.5 1.0 OE1 D:GLN196 4.3 46.6 1.0 O3' E:DA13 4.3 33.4 1.0 OP2 E:DA14 4.4 32.1 1.0 C4' E:DA14 4.4 34.0 1.0 NE2 D:GLN196 4.5 50.1 1.0 C5' E:DA14 4.5 34.5 1.0 O D:ASP11 4.5 26.2 1.0 CA D:GLY12 4.5 30.2 1.0 O5' E:DA14 4.6 33.0 1.0 N D:GLU13 4.7 34.1 1.0 CG D:GLU169 4.8 29.4 1.0 CA D:GLU13 4.8 36.3 1.0 CD D:GLN196 4.8 47.2 1.0 O3' F:DA15 4.8 40.4 1.0 C3' F:DA16 4.9 51.4 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:40.8 occ:1.00 OP2 E:DA15 2.2 31.6 1.0 OP1 F:DA15 2.3 37.1 1.0 OE1 D:GLU13 2.4 39.1 1.0 O D:ALA168 2.4 31.7 1.0 CD D:GLU13 3.3 38.7 1.0 OE2 D:GLU13 3.5 36.4 1.0 C D:ALA168 3.5 30.9 1.0 P E:DA15 3.5 31.4 1.0 P F:DA15 3.8 34.5 1.0 CA D:ALA168 4.1 32.8 1.0 NZ D:LYS249 4.1 53.1 1.0 OP1 E:DA15 4.1 31.9 1.0 C5' F:DA15 4.3 36.6 1.0 C5' E:DA15 4.3 38.4 1.0 O5' E:DA15 4.4 34.1 1.0 O3' F:DA14 4.4 32.5 1.0 O5' F:DA15 4.5 34.9 1.0 O D:SER167 4.5 36.2 1.0 CG D:GLU13 4.6 38.8 1.0 N D:GLU169 4.6 29.1 1.0 O3' E:DA14 4.7 31.4 1.0 OP2 F:DA15 4.7 34.4 1.0 CD2 D:LEU39 4.8 54.6 1.0 O E:HOH101 4.8 4.5 1.0 C4' F:DA15 4.8 37.6 1.0 CA D:GLU169 5.0 29.1 1.0 C4' E:DA15 5.0 40.3 1.0

A.R.Lambert, J.P.Hallinan, B.W.Shen, J.K.Chik, J.M.Bolduc, N.Kulshina, L.I.Robins, B.K.Kaiser, J.Jarjour, K.Havens, A.M.Scharenberg, B.L.Stoddard. Indirect Dna Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure V. 24 862 2016.
ISSN: ISSN 0969-2126
PubMed: 27133026
DOI: 10.1016/J.STR.2016.03.024