Calcium in PDB 7lvv: 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 7lvv). 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: 7lvv:
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:30.0 occ:1.00 OP1 G:DC23 2.3 141.4 1.0 OE2 A:GLU79 2.4 132.1 1.0 O A:SER80 2.9 136.2 1.0 OD2 A:ASP64 2.9 129.5 1.0 P G:DC23 3.2 141.4 1.0 OP2 G:DC23 3.2 141.4 1.0 CD A:GLU79 3.5 132.1 1.0 OE2 A:GLU25 3.6 142.4 1.0 OD1 A:ASP64 3.6 129.5 1.0 CG A:ASP64 3.6 129.5 1.0 CD A:GLU25 3.7 142.4 1.0 OE1 A:GLU25 3.9 142.4 1.0 NZ A:LYS94 4.0 137.8 1.0 C A:SER80 4.0 136.2 1.0 O5' G:DC23 4.1 141.4 1.0 OE1 A:GLU79 4.2 132.1 1.0 NH1 A:ARG29 4.4 133.7 1.0 CG A:GLU25 4.4 142.4 1.0 O3' G:DC22 4.5 135.9 1.0 CG A:GLU79 4.5 132.1 1.0 CA A:LYS81 4.6 141.0 1.0 N A:LYS81 4.7 141.0 1.0 N A:SER80 4.9 136.2 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 OD1 B:ASP64 1.8 74.4 1.0 CG B:ASP64 2.3 74.4 1.0 OD2 B:ASP64 2.4 74.4 1.0 OE2 B:GLU79 2.4 77.7 1.0 OP1 E:DC23 2.5 86.5 1.0 O B:SER80 2.7 81.9 1.0 OE2 B:GLU25 3.2 90.7 1.0 CD B:GLU79 3.3 77.7 1.0 CD B:GLU25 3.5 90.7 1.0 OE1 B:GLU25 3.6 90.7 1.0 CB B:ASP64 3.6 74.4 1.0 OE1 B:GLU79 3.6 77.7 1.0 N B:SER80 3.7 81.9 1.0 C B:SER80 3.7 81.9 1.0 P E:DC23 4.0 86.5 1.0 CA B:SER80 4.1 81.9 1.0 CB B:SER80 4.4 81.9 1.0 CA B:ASP64 4.4 74.4 1.0 CG B:GLU25 4.5 90.7 1.0 CG B:GLU79 4.5 77.7 1.0 O5' E:DC23 4.6 86.5 1.0 N B:ASP64 4.6 74.4 1.0 C B:GLU79 4.7 77.7 1.0 O3' E:DC22 4.8 83.6 1.0 OP2 E:DC23 4.8 86.5 1.0 NH1 B:ARG29 4.9 79.5 1.0 N B:LYS81 4.9 89.0 1.0 CA B:GLU79 5.0 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:Ca1101 b:79.4 occ:1.00 OP1 F:DG9 1.9 81.5 1.0 OD2 C:ASP64 2.5 75.6 1.0 O C:SER80 2.5 80.1 1.0 OE1 C:GLU25 2.6 88.2 1.0 OE2 C:GLU79 2.9 77.2 1.0 CG C:ASP64 3.2 75.6 1.0 P F:DG9 3.3 81.5 1.0 OD1 C:ASP64 3.3 75.6 1.0 CD C:GLU25 3.6 88.2 1.0 CD C:GLU79 3.7 77.2 1.0 C C:SER80 3.7 80.1 1.0 OE2 C:GLU25 3.9 88.2 1.0 OP2 F:DG9 4.0 81.5 1.0 O5' F:DG9 4.0 81.5 1.0 N C:SER80 4.2 80.1 1.0 OE1 C:GLU79 4.3 77.2 1.0 O3' F:DT8 4.3 80.6 1.0 NZ C:LYS81 4.3 86.3 1.0 CD C:ARG29 4.3 81.4 1.0 CD C:LYS81 4.5 86.3 1.0 CA C:SER80 4.5 80.1 1.0 CG C:GLU79 4.6 77.2 1.0 C5' F:DG9 4.7 81.5 1.0 CB C:ASP64 4.7 75.6 1.0 N C:LYS81 4.7 86.3 1.0 CA C:LYS81 4.8 86.3 1.0 CB C:SER80 4.9 80.1 1.0 CG C:GLU25 5.0 88.2 1.0 NE C:ARG29 5.0 81.4 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 1.7 134.5 1.0 OP1 H:DG9 2.0 130.8 1.0 OE1 D:GLU79 2.4 138.5 1.0 CD D:GLU25 2.7 134.5 1.0 OD2 D:ASP64 2.9 136.9 1.0 O D:SER80 2.9 138.4 1.0 OE1 D:GLU25 3.2 134.5 1.0 P H:DG9 3.3 130.8 1.0 CD D:GLU79 3.5 138.5 1.0 C D:SER80 3.6 138.4 1.0 OP2 H:DG9 3.7 130.8 1.0 N D:SER80 3.8 138.4 1.0 CG D:ASP64 3.8 136.9 1.0 O5' H:DG9 4.0 130.8 1.0 CG D:GLU25 4.0 134.5 1.0 CA D:SER80 4.0 138.4 1.0 CB D:SER80 4.1 138.4 1.0 OD1 D:ASP64 4.1 136.9 1.0 NH2 D:ARG29 4.1 132.1 1.0 OE2 D:GLU79 4.1 138.5 1.0 CG D:GLU79 4.4 138.5 1.0 O3' H:DT8 4.5 132.6 1.0 N D:LYS81 4.6 140.6 1.0 C D:GLU79 4.7 138.5 1.0 C5' H:DG9 4.7 130.8 1.0 CZ D:ARG29 4.8 132.1 1.0 CA 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.