Calcium in PDB 7lo5: Cryoem Structure Drdv-Dna Complex

All present enzymatic activity of Cryoem Structure Drdv-Dna Complex:
2.1.1.72;

The binding sites of Calcium atom in the Cryoem Structure Drdv-Dna Complex (pdb code 7lo5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryoem Structure Drdv-Dna Complex, PDB code: 7lo5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryoem Structure Drdv-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryoem Structure Drdv-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1102 b:133.0 occ:1.00 OE2 A:GLU79 1.8 132.1 1.0 OE2 A:GLU25 2.2 142.4 1.0 OP1 G:DC23 2.2 141.4 1.0 OD2 A:ASP64 2.4 129.5 1.0 O A:SER80 2.4 136.2 1.0 CD A:GLU79 3.0 132.1 1.0 CD A:GLU25 3.0 142.4 1.0 CG A:ASP64 3.1 129.5 1.0 OD1 A:ASP64 3.2 129.5 1.0 OE1 A:GLU25 3.4 142.4 1.0 P G:DC23 3.4 141.4 1.0 C A:SER80 3.6 136.2 1.0 OE1 A:GLU79 3.7 132.1 1.0 OP2 G:DC23 3.8 141.4 1.0 N A:SER80 4.0 136.2 1.0 CG A:GLU79 4.0 132.1 1.0 O5' G:DC23 4.1 141.4 1.0 CG A:GLU25 4.2 142.4 1.0 CA A:SER80 4.4 136.2 1.0 CB A:ASP64 4.5 129.5 1.0 NH2 A:ARG29 4.6 133.7 1.0 N A:LYS81 4.6 141.0 1.0 O3' G:DC22 4.7 135.9 1.0 C A:GLU79 4.7 132.1 1.0 CA A:LYS81 4.8 141.0 1.0 CB A:SER80 4.8 136.2 1.0 CZ A:ARG29 4.9 133.7 1.0 CA A:GLU79 5.0 132.1 1.0

Calcium binding site 2 out of 4 in the Cryoem Structure Drdv-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryoem Structure Drdv-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1102 b:30.0 occ:1.00 OD2 B:ASP64 1.8 74.4 1.0 OE2 B:GLU25 1.9 90.7 1.0 OE2 B:GLU79 2.0 77.7 1.0 O B:SER80 2.4 81.9 1.0 OP1 E:DC23 2.6 86.5 1.0 CG B:ASP64 2.6 74.4 1.0 OD1 B:ASP64 2.8 74.4 1.0 CD B:GLU79 3.0 77.7 1.0 CD B:GLU25 3.1 90.7 1.0 C B:SER80 3.4 81.9 1.0 N B:SER80 3.6 81.9 1.0 OE1 B:GLU79 3.6 77.7 1.0 OE1 B:GLU25 3.8 90.7 1.0 P E:DC23 3.9 86.5 1.0 CA B:SER80 4.0 81.9 1.0 CB B:ASP64 4.0 74.4 1.0 CG B:GLU79 4.0 77.7 1.0 NH2 B:ARG29 4.1 79.5 1.0 CG B:GLU25 4.1 90.7 1.0 CB B:SER80 4.3 81.9 1.0 C B:GLU79 4.3 77.7 1.0 O5' E:DC23 4.4 86.5 1.0 OP2 E:DC23 4.5 86.5 1.0 N B:LYS81 4.6 89.0 1.0 CZ B:ARG29 4.6 79.5 1.0 CA B:GLU79 4.6 77.7 1.0 NE B:ARG29 4.9 79.5 1.0 CA B:LYS81 4.9 89.0 1.0 CB B:GLU79 4.9 77.7 1.0

Calcium binding site 3 out of 4 in the Cryoem Structure Drdv-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryoem Structure Drdv-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1102 b:79.4 occ:1.00 OE1 C:GLU25 2.0 88.2 1.0 OD2 C:ASP64 2.1 75.6 1.0 OP1 F:DG9 2.1 81.5 1.0 O C:SER80 2.4 80.1 1.0 OE2 C:GLU79 2.8 77.2 1.0 CG C:ASP64 2.9 75.6 1.0 CD C:GLU25 2.9 88.2 1.0 OD1 C:ASP64 3.0 75.6 1.0 OE1 C:GLU79 3.1 77.2 1.0 CD C:GLU79 3.2 77.2 1.0 OE2 C:GLU25 3.4 88.2 1.0 P F:DG9 3.4 81.5 1.0 C C:SER80 3.5 80.1 1.0 N C:SER80 3.8 80.1 1.0 OP2 F:DG9 4.0 81.5 1.0 O5' F:DG9 4.0 81.5 1.0 CG C:GLU25 4.1 88.2 1.0 CA C:SER80 4.1 80.1 1.0 CB C:ASP64 4.3 75.6 1.0 C5' F:DG9 4.4 81.5 1.0 CB C:SER80 4.6 80.1 1.0 CG C:GLU79 4.6 77.2 1.0 N C:LYS81 4.6 86.3 1.0 O3' F:DT8 4.7 80.6 1.0 C C:GLU79 4.7 77.2 1.0 CD C:ARG29 4.8 81.4 1.0 CA C:LYS81 4.9 86.3 1.0 CA C:GLU79 5.0 77.2 1.0

Calcium binding site 4 out of 4 in the Cryoem Structure Drdv-Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryoem Structure Drdv-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1101 b:30.0 occ:1.00 OE2 D:GLU25 1.9 134.5 1.0 OE1 D:GLU79 2.1 138.5 1.0 OD2 D:ASP64 2.2 136.9 1.0 OP1 H:DG9 2.2 130.8 1.0 O D:SER80 2.3 138.4 1.0 CD D:GLU25 2.7 134.5 1.0 CG D:ASP64 3.0 136.9 1.0 OD1 D:ASP64 3.1 136.9 1.0 OE1 D:GLU25 3.2 134.5 1.0 CD D:GLU79 3.2 138.5 1.0 C D:SER80 3.5 138.4 1.0 P H:DG9 3.5 130.8 1.0 OE2 D:GLU79 3.8 138.5 1.0 N D:SER80 3.8 138.4 1.0 CG D:GLU25 3.9 134.5 1.0 O5' H:DG9 4.0 130.8 1.0 CA D:SER80 4.2 138.4 1.0 OP2 H:DG9 4.2 130.8 1.0 CB D:ASP64 4.4 136.9 1.0 CG D:GLU79 4.4 138.5 1.0 CB D:SER80 4.5 138.4 1.0 NH2 D:ARG29 4.5 132.1 1.0 N D:LYS81 4.5 140.6 1.0 CZ D:ARG29 4.6 132.1 1.0 C5' H:DG9 4.7 130.8 1.0 CA D:LYS81 4.7 140.6 1.0 O3' H:DT8 4.7 132.6 1.0 C D:GLU79 4.7 138.5 1.0 NH1 D:ARG29 4.9 132.1 1.0 NE D:ARG29 4.9 132.1 1.0 CG D:LYS81 5.0 140.6 1.0

B.W.Shen, B.L.Stoddard. Coordination of Phage Genome Degradation Versus Host Genome Protection By A Bifunctional Restriction-Modification Enzyme Visualized By Cryoem To Be Published.