Calcium in PDB 9ic3: Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-Like Error-Editing Conformer (Composite)

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

The binding sites of Calcium atom in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-Like Error-Editing Conformer (Composite) (pdb code 9ic3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-Like Error-Editing Conformer (Composite), PDB code: 9ic3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-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 (Hamb) in Mouse-Like Error-Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:54.6 occ:1.00 OD1 A:ASP890 2.3 25.4 1.0 O A:VAL891 2.4 28.3 1.0 OD2 A:ASP1135 2.4 35.0 1.0 O2A A:DCP1304 2.4 68.7 1.0 O1A A:DCP1304 3.1 68.7 1.0 PA A:DCP1304 3.2 68.7 1.0 O1B A:DCP1304 3.3 68.7 1.0 CG A:ASP890 3.4 25.4 1.0 CG A:ASP1135 3.5 35.0 1.0 C A:VAL891 3.6 28.3 1.0 N A:SER893 3.6 34.9 1.0 OD2 A:ASP890 3.7 25.4 1.0 OD1 A:ASP1135 4.1 35.0 1.0 O3A A:DCP1304 4.3 68.7 1.0 CA A:ASP892 4.3 31.7 1.0 O5' A:DCP1304 4.4 68.7 1.0 CA A:SER893 4.4 34.9 1.0 PB A:DCP1304 4.4 68.7 1.0 N A:VAL891 4.4 28.3 1.0 N A:ASP892 4.4 31.7 1.0 C A:ASP892 4.5 31.7 1.0 CA A:VAL891 4.5 28.3 1.0 CB A:ASP1135 4.6 35.0 1.0 N A:GLN894 4.6 32.1 1.0 CB A:ASP890 4.7 25.4 1.0 C A:ASP890 4.8 25.4 1.0 C5' A:DCP1304 4.8 68.7 1.0

Calcium binding site 2 out of 3 in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-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 (Hamb) in Mouse-Like Error-Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:29.9 occ:1.00 O A:HIS269 2.4 31.0 1.0 OD1 A:ASP198 2.5 31.1 1.0 OD1 A:ASP274 3.3 25.8 1.0 CG A:ASP198 3.4 31.1 1.0 C A:HIS269 3.7 31.0 1.0 O A:ASN270 3.9 33.5 1.0 OD2 A:ASP274 4.0 25.8 1.0 CG A:ASP274 4.0 25.8 1.0 OD2 A:ASP198 4.1 31.1 1.0 CA A:ASP198 4.2 31.1 1.0 N A:HIS269 4.3 31.0 1.0 O A:PHE197 4.4 28.5 1.0 CB A:ASP198 4.4 31.1 1.0 C A:ASN270 4.4 33.5 1.0 CA A:HIS269 4.5 31.0 1.0 O3' P:DC24 4.5 74.7 1.0 C4' P:DC24 4.6 74.7 1.0 CB A:ASN270 4.6 33.5 1.0 CD2 A:PHE273 4.6 30.4 1.0 N A:ASN270 4.6 33.5 1.0 N A:VAL199 4.7 32.6 1.0 CB A:HIS269 4.7 31.0 1.0 CA A:ASN270 4.8 33.5 1.0 C2' P:DC24 5.0 74.7 1.0 C3' P:DC24 5.0 74.7 1.0 C A:ASP198 5.0 31.1 1.0

Calcium binding site 3 out of 3 in the Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-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 3 of Chimeric Mitochondrial Dna Polymerase Gamma Ternary Complex (Hamb) in Mouse-Like Error-Editing Conformer (Composite) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1303 b:51.0 occ:1.00 OD2 A:ASP198 2.3 31.1 1.0 OE2 A:GLU200 2.4 40.8 1.0 OP1 P:DT25 2.4 69.5 1.0 OD2 A:ASP399 2.8 46.0 1.0 CD A:GLU200 3.5 40.8 1.0 CG A:ASP198 3.5 31.1 1.0 CG A:ASP399 3.6 46.0 1.0 P P:DT25 3.6 69.5 1.0 CB A:ASP399 3.7 46.0 1.0 O5' P:DT25 3.8 69.5 1.0 OE1 A:GLU200 3.9 40.8 1.0 CA A:CYS396 4.1 48.3 1.0 SG A:CYS396 4.1 48.3 1.0 CB A:ASP198 4.3 31.1 1.0 CB A:CYS396 4.4 48.3 1.0 OD1 A:ASP198 4.4 31.1 1.0 O3' P:DC24 4.6 74.7 1.0 OP2 P:DT25 4.7 69.5 1.0 CG A:GLU200 4.7 40.8 1.0 O A:CYS396 4.7 48.3 1.0 OD1 A:ASP399 4.8 46.0 1.0 N A:CYS396 4.9 48.3 1.0 C A:CYS396 4.9 48.3 1.0 O A:TYR395 5.0 54.0 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