Calcium in PDB 9ibz: Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite)

All present enzymatic activity of Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite):
2.7.7.7;

The binding sites of Calcium atom in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite) (pdb code 9ibz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite), PDB code: 9ibz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-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 Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1300 b:167.9 occ:1.00 O A:VAL869 2.5 122.1 1.0 OD2 A:ASP868 3.0 125.9 1.0 OD2 A:ASP1113 3.3 128.7 1.0 CG A:ASP868 3.4 128.6 1.0 OD1 A:ASP868 3.5 131.9 1.0 C A:VAL869 3.7 123.0 1.0 O3A A:DCP1301 4.0 173.8 1.0 N A:SER871 4.1 135.7 1.0 CG A:ASP1113 4.1 128.2 1.0 O1B A:DCP1301 4.2 175.4 1.0 CA A:ASP870 4.2 132.3 1.0 N A:ASP870 4.4 134.0 1.0 OD1 A:ASP1113 4.5 127.3 1.0 CB A:ASP868 4.5 119.4 1.0 PB A:DCP1301 4.6 175.9 1.0 O3B A:DCP1301 4.6 175.1 1.0 N A:VAL869 4.6 118.0 1.0 C A:ASP870 4.7 132.8 1.0 CA A:VAL869 4.8 117.3 1.0 C5' A:DCP1301 4.8 177.1 1.0 C A:ASP868 4.8 116.9 1.0 O1A A:DCP1301 4.8 175.2 1.0 PA A:DCP1301 4.9 175.1 1.0 O5' A:DCP1301 5.0 176.7 1.0

Calcium binding site 2 out of 2 in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-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 Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Mahb) in Human-Like Error-Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:120.0 occ:1.00 O A:HIS252 2.4 122.8 1.0 OD1 A:ASP257 2.5 120.4 1.0 OD2 A:ASP257 2.6 121.1 1.0 OP1 P:DT25 2.8 156.6 1.0 CG A:ASP257 2.9 116.2 1.0 OD1 A:ASP181 3.2 128.1 1.0 C A:HIS252 3.6 118.1 1.0 P P:DT25 3.9 166.0 1.0 O A:ASN253 3.9 123.7 1.0 O3' P:DC24 4.0 177.9 1.0 CG A:ASP181 4.2 126.7 1.0 C A:ASN253 4.3 119.7 1.0 N A:HIS252 4.3 104.1 1.0 CB A:ASP257 4.4 108.7 1.0 C4' P:DC24 4.4 177.0 1.0 CA A:HIS252 4.4 105.8 1.0 CD2 A:PHE256 4.6 126.8 1.0 CA A:ASP181 4.6 125.2 1.0 N A:ASN253 4.6 124.8 1.0 CB A:ASN253 4.6 123.1 1.0 O A:PHE180 4.6 118.7 1.0 OP2 P:DT25 4.7 160.2 1.0 CB A:HIS252 4.7 106.8 1.0 C3' P:DC24 4.7 177.2 1.0 N A:ASP257 4.8 109.9 1.0 CA A:ASN253 4.8 119.3 1.0 CB A:ASP181 4.8 120.3 1.0 C5' P:DC24 4.9 176.5 1.0 N A:VAL254 4.9 111.3 1.0 OD2 A:ASP181 5.0 125.7 1.0 CB A:PHE256 5.0 120.4 1.0

S.Corra, A.Zuppardo, S.Valenzuela, L.Jenninger, R.Cerutti, S.Sillamaa, E.Hoberg, K.A.S.Johansson, U.Rovsnik, S.Volta, P.Silva-Pinheiro, H.Davis, A.Trifunovic, M.Minczuk, C.M.Gustafsson, A.Suomalainen, M.Zeviani, B.Macao, X.Zhu, M.Falkenberg, C.Viscomi. Modelling Polg Mutations in Mice Unravels A Critical Role of Pol Gamma Beta in Regulating Phenotypic Severity. Nat Commun V. 16 4782 2025.
ISSN: ESSN 2041-1723
PubMed: 40404629
DOI: 10.1038/S41467-025-60059-Y