Calcium in PDB 5esp: Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions

The structure of Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions, PDB code: 5esp 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)	30.97 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.555, 78.442, 101.023, 90.00, 92.38, 90.00
R / Rfree (%)	22.6 / 26.9

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

Calcium binding site 1 out of 4 in the Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions


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-Panmi with Coordinated Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.6 occ:1.00 OP1 H:DT16 2.2 52.3 1.0 O A:ALA176 2.3 35.4 1.0 OE1 A:GLU20 2.4 48.9 1.0 OP2 G:DC17 2.6 33.3 1.0 CD A:GLU20 3.3 44.1 1.0 C A:ALA176 3.4 31.6 1.0 P H:DT16 3.6 44.5 1.0 P G:DC17 3.8 76.8 1.0 OE2 A:GLU20 3.9 44.6 1.0 CA A:ALA176 4.0 32.0 1.0 CG A:GLU20 4.3 37.5 1.0 C5' G:DC17 4.3 33.8 1.0 OP1 G:DC17 4.3 45.9 1.0 O3' H:DT15 4.3 46.5 1.0 O5' G:DC17 4.4 36.6 1.0 C5' H:DT16 4.4 53.6 1.0 O A:ASP175 4.5 31.4 1.0 N A:GLU177 4.5 30.8 1.0 OP2 H:DT16 4.5 50.8 1.0 C4' H:DT16 4.6 50.1 1.0 O5' H:DT16 4.6 57.5 1.0 NZ A:LYS259 4.6 34.0 1.0 CA A:GLU177 4.8 31.6 1.0 CB A:ALA176 4.9 32.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions


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-Panmi with Coordinated Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:45.4 occ:1.00 O A:GLY19 2.2 41.7 1.0 OE2 A:GLU177 2.3 41.6 1.0 OP1 G:DC16 2.5 51.1 1.0 OP1 H:DA17 3.1 49.5 1.0 C A:GLY19 3.2 38.6 1.0 CD A:GLU177 3.5 42.8 1.0 C5' H:DA17 3.6 53.4 1.0 CA A:GLY19 3.7 36.9 1.0 P H:DA17 3.7 50.8 1.0 O5' H:DA17 3.8 52.9 1.0 P G:DC16 3.8 46.6 1.0 OP2 H:DA17 3.9 43.2 1.0 OE1 A:GLU177 4.2 48.4 1.0 NE2 A:GLN204 4.3 41.7 1.0 O A:ASP18 4.3 29.2 1.0 OE2 A:GLU20 4.4 44.6 1.0 OE1 A:GLN204 4.4 47.4 1.0 N A:GLU20 4.4 36.0 1.0 OP2 G:DC16 4.4 50.4 1.0 O3' G:DT15 4.5 47.9 1.0 CG A:GLU177 4.6 39.3 1.0 CD A:GLN204 4.8 46.3 1.0 N A:GLY19 4.8 31.1 1.0 C4' H:DA17 4.8 48.5 1.0 CA A:GLU20 4.9 37.4 1.0 O5' G:DC16 4.9 43.6 1.0 C A:ASP18 5.0 26.7 1.0 C5' G:DC16 5.0 44.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions


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-Panmi with Coordinated Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:57.3 occ:1.00 OP1 C:DC16 2.3 73.0 1.0 OE2 B:GLU177 2.4 55.8 1.0 O B:GLY19 2.4 43.7 1.0 OE1 B:GLU177 2.5 63.7 1.0 CD B:GLU177 2.6 54.8 1.0 OP1 D:DA17 2.8 63.2 1.0 C B:GLY19 3.3 39.5 1.0 P D:DA17 3.7 60.0 1.0 CA B:GLY19 3.7 33.1 1.0 P C:DC16 3.8 82.1 1.0 OE1 B:GLU20 3.8 61.4 1.0 O5' D:DA17 3.9 62.8 1.0 CG B:GLU177 4.0 42.4 1.0 OP2 D:DA17 4.0 60.1 1.0 C5' D:DA17 4.1 57.6 1.0 OE1 B:GLN204 4.3 60.2 1.0 NE2 B:GLN204 4.3 51.4 1.0 N B:GLU20 4.4 46.2 1.0 C5' C:DC16 4.5 71.9 1.0 C4' C:DC16 4.5 76.2 1.0 OP2 C:DC16 4.6 79.6 1.0 O3' C:DT15 4.6 84.9 1.0 O B:ASP18 4.6 32.9 1.0 O5' C:DC16 4.7 69.6 1.0 O3' C:DC16 4.7 75.1 1.0 CD B:GLN204 4.8 60.5 1.0 CA B:GLU20 4.9 48.4 1.0 N B:GLY19 5.0 29.4 1.0 CD B:GLU20 5.0 56.6 1.0 C3' C:DC16 5.0 77.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Laglidadg Meganuclease I-Panmi with Coordinated Calcium Ions


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-Panmi with Coordinated Calcium Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:65.4 occ:1.00 OE2 B:GLU20 2.3 55.0 1.0 O B:ALA176 2.4 56.3 1.0 OP1 D:DT16 2.5 84.9 1.0 OP1 C:DC17 2.6 71.8 1.0 CD B:GLU20 3.2 56.6 1.0 C B:ALA176 3.4 45.9 1.0 P C:DC17 3.5 0.7 1.0 OP2 C:DC17 3.7 63.7 1.0 OE1 B:GLU20 3.8 61.4 1.0 C5' C:DC17 3.9 74.0 1.0 O5' C:DC17 3.9 73.1 1.0 P D:DT16 3.9 78.5 1.0 CA B:ALA176 4.0 46.3 1.0 CG B:GLU20 4.1 50.0 1.0 NZ B:LYS259 4.3 49.5 1.0 O B:ASP175 4.4 39.6 1.0 N B:GLU177 4.5 43.2 1.0 O3' D:DT15 4.6 73.8 1.0 C5' D:DT16 4.6 69.4 1.0 C4' D:DT16 4.7 72.3 1.0 OP2 D:DT16 4.8 74.5 1.0 CA B:GLU177 4.8 47.8 1.0 O5' D:DT16 4.8 80.4 1.0 CB B:ALA176 4.9 45.5 1.0 O3' C:DC16 4.9 75.1 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