Calcium in PDB 6p1h: Cryo-Em Structure of Dna Polymerase Delta Holoenzyme

All present enzymatic activity of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme:
2.7.7.7;

The structure of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme (pdb code 6p1h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme, PDB code: 6p1h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1103 b:65.0 occ:1.00 O1B A:DCP1102 2.3 64.0 1.0 OD2 A:ASP764 2.4 67.2 1.0 O A:PHE609 2.4 63.6 1.0 OD2 A:ASP608 2.6 66.8 1.0 O1G A:DCP1102 2.8 64.0 1.0 O1A A:DCP1102 3.1 64.0 1.0 CG A:ASP608 3.3 66.8 1.0 CG A:ASP764 3.5 67.2 1.0 C A:PHE609 3.5 63.6 1.0 CB A:ASP608 3.7 66.8 1.0 PB A:DCP1102 3.8 64.0 1.0 N A:PHE609 3.8 63.6 1.0 CA A:CA1104 3.9 87.0 1.0 PG A:DCP1102 3.9 64.0 1.0 O3G A:DCP1102 4.0 64.0 1.0 OD1 A:ASP764 4.2 67.2 1.0 CA A:PHE609 4.2 63.6 1.0 OD1 A:ASP608 4.3 66.8 1.0 C A:ASP608 4.4 66.8 1.0 CB A:ASP764 4.4 67.2 1.0 O3B A:DCP1102 4.4 64.0 1.0 PA A:DCP1102 4.4 64.0 1.0 N A:ASN610 4.6 63.5 1.0 CA A:ASP608 4.6 66.8 1.0 O3A A:DCP1102 4.6 64.0 1.0 O2B A:DCP1102 4.7 64.0 1.0 N A:SER611 4.7 62.1 1.0 CA A:ASN610 4.8 63.5 1.0 C5' A:DCP1102 4.8 64.0 1.0 CB A:PHE609 4.9 63.6 1.0

Calcium binding site 2 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:87.0 occ:1.00 O A:HOH1225 2.9 57.8 1.0 O1A A:DCP1102 3.5 64.0 1.0 OD1 A:ASP764 3.6 67.2 1.0 OD2 A:ASP608 3.8 66.8 1.0 CA A:CA1103 3.9 65.0 1.0 OD2 A:ASP764 3.9 67.2 1.0 CG A:ASP764 4.1 67.2 1.0 C5' P:DC30 4.1 65.4 1.0 CB A:ASP608 4.1 66.8 1.0 OG A:SER765 4.3 67.6 1.0 CB A:SER765 4.3 67.6 1.0 CG A:ASP608 4.4 66.8 1.0 C3' P:DC30 4.4 65.4 1.0 OE2 A:GLU802 4.5 69.5 1.0 O5' P:DC30 4.6 65.4 1.0 C4' P:DC30 4.6 65.4 1.0 PA A:DCP1102 4.8 64.0 1.0 O2A A:DCP1102 4.9 64.0 1.0

Calcium binding site 3 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:90.2 occ:1.00 OE1 A:GLU800 2.3 71.0 1.0 OD1 A:ASP608 3.1 66.8 1.0 OD2 A:ASP608 3.3 66.8 1.0 OD1 A:ASN610 3.4 63.5 1.0 CD A:GLU800 3.4 71.0 1.0 CG A:ASP608 3.6 66.8 1.0 CG A:GLU802 3.8 69.5 1.0 CG A:GLU800 3.8 71.0 1.0 CB A:GLU802 4.2 69.5 1.0 CD A:GLU802 4.5 69.5 1.0 OE2 A:GLU800 4.5 71.0 1.0 O1G A:DCP1102 4.6 64.0 1.0 CG A:ASN610 4.6 63.5 1.0 O3G A:DCP1102 4.6 64.0 1.0 CA A:GLU802 4.7 69.5 1.0 OE1 A:GLU802 4.8 69.5 1.0

Calcium binding site 4 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1106 b:95.6 occ:1.00 OD2 A:ASP321 1.9 74.1 1.0 CG A:ASP321 2.6 74.1 1.0 OD1 A:ASP321 2.6 74.1 1.0 O A:ILE322 3.3 74.7 1.0 OD2 A:ASP520 4.0 77.5 1.0 CB A:ASP321 4.1 74.1 1.0 OE2 A:GLU323 4.2 81.8 1.0 CD A:GLU323 4.3 81.8 1.0 N A:ILE322 4.3 74.7 1.0 C A:ILE322 4.4 74.7 1.0 O A:HOH1211 4.4 77.3 1.0 CB A:ASP520 4.5 77.5 1.0 OE1 A:GLU323 4.6 81.8 1.0 CG A:ASP520 4.6 77.5 1.0 OD1 A:ASP407 4.7 77.2 1.0 CG A:GLU323 4.8 81.8 1.0 CA A:ASP321 4.8 74.1 1.0 C A:ASP321 5.0 74.1 1.0

Calcium binding site 5 out of 5 in the Cryo-Em Structure of Dna Polymerase Delta Holoenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Dna Polymerase Delta Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca101 b:0.9 occ:1.00 O T:HOH201 3.2 81.7 1.0 OP2 T:DG10 3.2 72.6 1.0 C8 T:DG10 4.0 72.6 1.0 N7 T:DG10 4.2 72.6 1.0 N7 T:DG11 4.3 78.3 1.0 P T:DG10 4.6 72.6 1.0 C2' T:DG9 4.9 68.7 1.0 O5' T:DG10 4.9 72.6 1.0 C8 T:DG11 4.9 78.3 1.0

R.Jain, W.J.Rice, R.Malik, R.E.Johnson, L.Prakash, S.Prakash, I.Ubarretxena-Belandia, A.K.Aggarwal. Cryo-Em Structure and Dynamics of Eukaryotic Dna Polymerase Delta Holoenzyme. Nat.Struct.Mol.Biol. V. 26 955 2019.
ISSN: ESSN 1545-9985
PubMed: 31582849
DOI: 10.1038/S41594-019-0305-Z