Calcium in PDB 9f6l: Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State)

All present enzymatic activity of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State):
2.7.7.7;

The structure of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State) (pdb code 9f6l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State), PDB code: 9f6l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:111.5 occ:1.00 OP1 P:DC31 2.2 105.9 1.0 O3' P:DT30 2.4 105.5 1.0 P P:DC31 2.8 105.9 1.0 OD1 A:ASP275 2.9 73.3 1.0 OD2 A:ASP368 3.0 80.1 1.0 OD1 A:ASP368 3.0 80.1 1.0 CG A:ASP368 3.4 80.1 1.0 CA A:CA1303 3.5 89.6 1.0 CG A:ASP275 3.6 73.3 1.0 OD2 A:ASP275 3.6 73.3 1.0 C3' P:DT30 3.7 105.5 1.0 O5' P:DC31 3.7 105.9 1.0 OP2 P:DC31 4.1 105.9 1.0 C4' P:DT30 4.1 105.5 1.0 O A:TYR362 4.1 70.4 1.0 C2' P:DT30 4.3 105.5 1.0 CD2 A:PHE367 4.6 83.0 1.0 C5' P:DC31 4.8 105.9 1.0 C4' P:DC31 4.9 105.9 1.0 CB A:ASP368 4.9 80.1 1.0 CB A:ASP275 4.9 73.3 1.0 CE2 A:PHE367 5.0 83.0 1.0

Calcium binding site 2 out of 2 in the Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Dna Polymerase Epsilon Bound to T-C Mismatched Dna (Mismatch Excision State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:89.6 occ:1.00 OP1 P:DC31 2.1 105.9 1.0 O5' P:DC31 2.2 105.9 1.0 OD2 A:ASP275 2.4 73.3 1.0 OD2 A:ASP462 2.6 75.9 1.0 OE2 A:GLU277 2.6 88.5 1.0 P P:DC31 2.7 105.9 1.0 CA A:CA1302 3.5 111.5 1.0 CG A:ASP275 3.5 73.3 1.0 C5' P:DC31 3.5 105.9 1.0 OP2 P:DC31 3.7 105.9 1.0 CG A:ASP462 3.8 75.9 1.0 CD A:GLU277 3.8 88.5 1.0 O3' P:DT30 3.8 105.5 1.0 OD1 A:ASP275 4.0 73.3 1.0 OE1 A:GLU277 4.3 88.5 1.0 CB A:ASP462 4.4 75.9 1.0 C4' P:DC31 4.4 105.9 1.0 O A:ILE276 4.7 73.9 1.0 CB A:ASP275 4.7 73.3 1.0 OD1 A:ASP462 4.8 75.9 1.0 O3' P:DC31 4.9 105.9 1.0 C3' P:DC31 4.9 105.9 1.0 CG A:GLU277 5.0 88.5 1.0

J.J.Roske, J.T.P.Yeeles. Structural Basis For Processive Daughter-Strand Synthesis and Proofreading By the Human Leading-Strand Dna Polymerase Pol Epsilon. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01370-Y