Sodium in PDB 1g5h: Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma

The structure of Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma, PDB code: 1g5h was solved by J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.623, 133.422, 135.038, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.4

The binding sites of Sodium atom in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma (pdb code 1g5h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma, PDB code: 1g5h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:28.6 occ:1.00 O A:ARG96 2.3 27.2 1.0 O A:HOH920 2.3 33.4 1.0 O A:VAL93 2.3 26.3 1.0 O A:HOH911 2.4 31.9 1.0 O A:VAL99 2.5 27.7 1.0 O A:HOH977 2.6 44.9 1.0 C A:ARG96 3.4 31.5 1.0 C A:VAL93 3.4 27.9 1.0 C A:VAL99 3.6 27.6 1.0 CG1 A:VAL93 3.9 30.6 1.0 N A:VAL99 4.1 26.7 1.0 CA A:GLU97 4.1 33.0 1.0 CA A:VAL93 4.1 24.8 1.0 N A:GLU97 4.2 30.8 1.0 CA A:VAL99 4.2 26.0 1.0 N A:ARG96 4.2 28.1 1.0 C A:GLU97 4.3 28.6 1.0 CA A:ARG96 4.3 28.1 1.0 O A:VAL94 4.4 30.5 1.0 CB A:VAL99 4.4 22.6 1.0 N A:VAL94 4.4 29.8 1.0 O A:GLU97 4.5 35.0 1.0 O B:HOH1130 4.5 78.1 1.0 O B:HOH955 4.6 40.7 1.0 C A:VAL94 4.6 29.7 1.0 CA A:VAL94 4.6 30.5 1.0 CB A:VAL93 4.7 25.7 1.0 N A:PHE100 4.7 22.6 1.0 CB A:ARG96 4.8 31.2 1.0 N A:GLN98 4.9 27.0 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:39.3 occ:1.00 O B:HOH944 2.3 38.8 1.0 O B:ARG96 2.3 37.6 1.0 O B:VAL93 2.5 35.2 1.0 O B:VAL99 2.5 25.9 1.0 O B:HOH992 2.5 47.1 1.0 O A:HOH1010 2.7 49.8 1.0 C B:ARG96 3.4 45.9 1.0 C B:VAL93 3.5 38.7 1.0 C B:VAL99 3.6 26.6 1.0 CG1 B:VAL93 4.0 40.2 1.0 N B:VAL99 4.0 29.1 1.0 CA B:GLU97 4.1 41.0 1.0 CA B:VAL93 4.2 34.2 1.0 N B:GLU97 4.2 48.1 1.0 CA B:VAL99 4.2 25.2 1.0 C B:GLU97 4.3 37.8 1.0 O B:GLU97 4.3 49.4 1.0 CB B:VAL99 4.4 28.2 1.0 N B:ARG96 4.4 42.5 1.0 O B:VAL94 4.4 43.0 1.0 CA B:ARG96 4.4 46.0 1.0 N B:VAL94 4.5 34.3 1.0 N B:PHE100 4.7 22.7 1.0 CA B:VAL94 4.7 35.6 1.0 C B:VAL94 4.7 43.2 1.0 CB B:VAL93 4.7 34.9 1.0 O A:HOH1024 4.8 51.4 1.0 N B:GLN98 4.9 33.6 1.0 O A:HOH1115 5.0 78.7 1.0 O A:HOH1078 5.0 64.2 1.0 CA B:PHE100 5.0 23.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:29.3 occ:1.00 O C:ARG96 2.2 30.8 1.0 O C:VAL93 2.3 33.7 1.0 O C:HOH953 2.3 42.0 1.0 O C:VAL99 2.4 26.9 1.0 O C:HOH968 2.5 45.3 1.0 O C:HOH982 2.6 47.4 1.0 C C:ARG96 3.4 31.0 1.0 C C:VAL93 3.4 36.9 1.0 C C:VAL99 3.5 29.3 1.0 N C:VAL99 4.0 25.0 1.0 CG1 C:VAL93 4.1 40.6 1.0 CA C:GLU97 4.1 30.7 1.0 CA C:VAL93 4.2 30.1 1.0 CA C:VAL99 4.2 27.3 1.0 N C:GLU97 4.2 31.1 1.0 C C:GLU97 4.3 30.6 1.0 CA C:ARG96 4.3 31.9 1.0 N C:ARG96 4.3 32.6 1.0 CB C:VAL99 4.3 23.1 1.0 O C:GLU97 4.5 36.5 1.0 N C:VAL94 4.5 37.9 1.0 O C:VAL94 4.5 40.7 1.0 CB C:ARG96 4.6 36.5 1.0 N C:PHE100 4.6 23.9 1.0 CA C:VAL94 4.7 33.6 1.0 C C:VAL94 4.8 29.7 1.0 CB C:VAL93 4.8 35.4 1.0 N C:GLN98 4.8 27.2 1.0 CA C:PHE100 4.9 24.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Accessory Subunit of Murine Mitochondrial Polymerase Gamma within 5.0Å range: probe atom residue distance (Å) B Occ D:Na904 b:50.2 occ:1.00 O D:ARG96 2.1 46.4 1.0 O D:VAL93 2.4 61.6 1.0 O D:VAL99 2.5 33.2 1.0 C D:ARG96 3.2 49.6 1.0 C D:VAL93 3.4 59.0 1.0 C D:VAL99 3.6 30.7 1.0 N D:VAL99 3.9 32.5 1.0 CG1 D:VAL93 4.0 46.5 1.0 N D:GLU97 4.0 56.4 1.0 CA D:GLU97 4.0 57.9 1.0 CA D:VAL99 4.1 29.2 1.0 CA D:VAL93 4.1 47.6 1.0 O C:HOH1052 4.1 58.1 1.0 CB D:VAL99 4.1 29.2 1.0 O C:HOH1030 4.2 54.2 1.0 CA D:ARG96 4.2 60.0 1.0 N D:ARG96 4.3 57.4 1.0 C D:GLU97 4.3 58.9 1.0 N D:VAL94 4.3 55.7 1.0 O D:VAL94 4.5 58.4 1.0 CA D:VAL94 4.6 50.7 1.0 C D:VAL94 4.6 47.2 1.0 N D:GLN98 4.6 44.3 1.0 CB D:ARG96 4.7 57.6 1.0 N D:PHE100 4.7 25.4 1.0 CB D:VAL93 4.7 50.3 1.0 O D:GLU97 4.8 65.3 1.0 CG1 D:VAL99 4.9 32.5 1.0 O C:HOH1035 5.0 55.1 1.0

J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, C.Kisker. Crystal Structure and Deletion Analysis Show That the Accessory Subunit of Mammalian Dna Polymerase Gamma, Pol Gamma B, Functions As A Homodimer. Mol.Cell V. 7 43 2001.
ISSN: ISSN 1097-2765
PubMed: 11172710
DOI: 10.1016/S1097-2765(01)00153-8