Calcium in PDB 8d42: Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite)

All present enzymatic activity of Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite):
2.7.7.7;

The binding sites of Calcium atom in the Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite) (pdb code 8d42). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite), PDB code: 8d42:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:60.6 occ:1.00 OD2 A:ASP890 2.3 61.2 1.0 O2A A:DCP1304 2.4 66.1 1.0 O1B A:DCP1304 2.8 73.2 1.0 CG A:ASP890 3.3 62.3 1.0 PA A:DCP1304 3.6 70.8 1.0 OD1 A:ASP890 3.6 68.9 1.0 OD2 A:ASP1135 3.7 68.3 1.0 PB A:DCP1304 3.8 70.3 1.0 O3A A:DCP1304 3.9 59.4 1.0 HZ2 A:LYS1191 3.9 70.4 1.0 O3G A:DCP1304 4.0 64.5 1.0 HZ1 A:LYS1191 4.0 70.6 1.0 H5'2 A:DCP1304 4.2 65.0 1.0 NZ A:LYS1191 4.3 77.7 1.0 HZ3 A:LYS1191 4.3 69.6 1.0 O3B A:DCP1304 4.3 63.6 1.0 O A:VAL891 4.4 57.0 1.0 H A:SER893 4.5 56.1 1.0 O1A A:DCP1304 4.5 66.8 1.0 CG A:ASP1135 4.6 65.7 1.0 CB A:ASP890 4.6 53.9 1.0 OD1 A:ASP1135 4.7 61.6 1.0 HB3 A:ASP890 4.7 56.2 1.0 O5' A:DCP1304 4.7 65.3 1.0 PG A:DCP1304 4.9 57.5 1.0 HB2 A:ASP890 5.0 56.8 1.0 C5' A:DCP1304 5.0 65.2 1.0

Calcium binding site 2 out of 3 in the Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:60.7 occ:1.00 OD1 A:ASP198 2.2 65.6 1.0 CG A:ASP198 2.9 67.6 1.0 OD2 A:ASP198 3.3 66.8 1.0 O3' P:DA23 3.4 40.2 1.0 H4' P:DA23 3.5 41.8 1.0 OP1 P:DT24 3.5 46.9 1.0 HA A:ASP198 3.7 64.4 1.0 H A:VAL199 3.8 60.7 1.0 CB A:ASP198 3.9 64.8 1.0 HB2 A:ASP198 4.0 64.6 1.0 P P:DT24 4.2 52.8 1.0 O A:HIS269 4.2 60.5 1.0 H5' P:DT24 4.3 44.0 1.0 OD1 A:ASP274 4.3 75.6 1.0 C4' P:DA23 4.3 40.6 1.0 OD2 A:ASP274 4.3 70.9 1.0 CA A:ASP198 4.3 63.2 1.0 O A:VAL199 4.4 61.2 1.0 H5'' P:DA23 4.4 41.9 1.0 C3' P:DA23 4.4 44.4 1.0 N A:VAL199 4.5 61.4 1.0 CA A:CA1303 4.5 69.5 1.0 HB3 A:HIS269 4.6 57.2 1.0 HB3 A:ASP198 4.8 65.3 1.0 CG A:ASP274 4.8 72.2 1.0 H A:HIS269 4.8 55.9 1.0 C5' P:DA23 4.9 41.5 1.0 H5'' P:DT24 4.9 44.7 1.0 C A:ASP198 4.9 65.6 1.0 C5' P:DT24 5.0 46.3 1.0 H2'' P:DA23 5.0 42.6 1.0

Calcium binding site 3 out of 3 in the Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Mitochondrial Dna Polymerase Gamma Ternary Complex with Gt Basepair in Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:69.5 occ:1.00 OE2 A:GLU200 2.2 68.6 1.0 OD2 A:ASP198 2.2 66.8 1.0 OP1 P:DT24 2.7 46.9 1.0 OD2 A:ASP399 2.9 81.0 1.0 HA A:CYS396 3.0 66.4 1.0 HB2 A:ASP399 3.2 72.1 1.0 CG A:ASP198 3.4 67.6 1.0 CD A:GLU200 3.4 71.7 1.0 HB3 A:ASP399 3.7 71.8 1.0 CG A:ASP399 3.7 81.1 1.0 CB A:ASP399 3.7 73.8 1.0 OD1 A:ASP198 3.9 65.6 1.0 SG A:CYS396 3.9 81.7 1.0 CA A:CYS396 4.0 59.2 1.0 P P:DT24 4.1 52.8 1.0 HG2 A:GLU200 4.2 66.0 1.0 OE1 A:GLU200 4.3 75.0 1.0 HB2 A:CYS396 4.3 67.1 1.0 CB A:CYS396 4.3 67.2 1.0 CG A:GLU200 4.3 69.8 1.0 CA A:CA1302 4.5 60.7 1.0 HG3 A:GLU200 4.5 66.3 1.0 HB3 A:ASP198 4.5 65.3 1.0 CB A:ASP198 4.6 64.8 1.0 O A:CYS396 4.6 71.1 1.0 HG A:CYS396 4.7 67.4 1.0 H5'' P:DT24 4.7 44.7 1.0 N A:CYS396 4.8 68.0 1.0 OP2 P:DT24 4.8 49.9 1.0 O A:TYR395 4.8 67.9 1.0 C A:CYS396 4.8 61.5 1.0 O5' P:DT24 4.9 50.7 1.0 OD1 A:ASP399 4.9 80.5 1.0 HB2 A:ASP198 4.9 64.6 1.0 O A:VAL199 5.0 61.2 1.0

J.Park, G.K.Herrmann, P.G.Mitchell, M.B.Sherman, Y.W.Yin. Pol-Gamma Coordinates Dna Synthesis and Proofreading to Ensure Mitochondrial Genome Integrity Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00980-2