Magnesium in PDB 4ztu: Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase

The structure of Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase, PDB code: 4ztu was solved by M.R.Szymanski, V.B.Kuznestov, C.K.Shumate, Q.Meng, Y.-S.Lee, G.Patel, S.S.Patel, Y.W.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.67 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	217.575, 217.575, 168.277, 90.00, 90.00, 90.00
R / Rfree (%)	31.6 / 31.6

The binding sites of Magnesium atom in the Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase (pdb code 4ztu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase, PDB code: 4ztu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:73.9 occ:1.00 O1A A:DCT4003 2.1 87.4 1.0 CB A:ASP1135 2.5 71.5 1.0 C3' P:DOC24 2.6 77.6 1.0 O5' A:DCT4003 2.7 69.0 1.0 PA A:DCT4003 2.7 77.8 1.0 C5' A:DCT4003 2.9 73.5 1.0 CG A:ASP1135 3.0 70.3 1.0 OD2 A:ASP1135 3.2 74.6 1.0 O2A A:DCT4003 3.3 68.4 1.0 MG A:MG4002 3.5 35.3 1.0 C2' P:DOC24 3.5 76.9 1.0 C4' P:DOC24 3.6 0.5 1.0 OD2 A:ASP890 3.8 69.7 1.0 CA A:ASP1135 3.9 46.3 1.0 OD1 A:ASP1135 3.9 76.8 1.0 C5' P:DOC24 4.1 70.0 1.0 O3A A:DCT4003 4.2 96.5 1.0 N A:ASP1135 4.2 47.8 1.0 C4' A:DCT4003 4.3 68.1 1.0 OD1 A:ASP890 4.5 77.4 1.0 CG A:ASP890 4.5 75.2 1.0 O5' P:DOC24 4.5 72.7 1.0 O2B A:DCT4003 4.7 98.4 1.0 C A:ASP1135 4.7 91.5 1.0 O4' A:DCT4003 4.7 100.0 1.0 O4' P:DOC24 4.8 0.1 1.0 N A:GLU1136 4.8 48.8 1.0 C1' P:DOC24 4.8 0.3 1.0 PB A:DCT4003 5.0 74.9 1.0 O2G A:DCT4003 5.0 72.4 1.0

Magnesium binding site 2 out of 2 in the Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4002 b:35.3 occ:1.00 O2G A:DCT4003 1.7 72.4 1.0 OD2 A:ASP1135 2.2 74.6 1.0 O1A A:DCT4003 2.2 87.4 1.0 OD1 A:ASP890 2.3 77.4 1.0 O A:VAL891 2.3 49.7 1.0 CG A:ASP1135 2.5 70.3 1.0 O2B A:DCT4003 2.6 98.4 1.0 OD1 A:ASP1135 2.7 76.8 1.0 PG A:DCT4003 3.1 81.6 1.0 CG A:ASP890 3.2 75.2 1.0 O3B A:DCT4003 3.4 77.1 1.0 C A:VAL891 3.5 66.7 1.0 PB A:DCT4003 3.5 74.9 1.0 MG A:MG4001 3.5 73.9 1.0 OD2 A:ASP890 3.5 69.7 1.0 PA A:DCT4003 3.6 77.8 1.0 CB A:ASP1135 3.7 71.5 1.0 O3G A:DCT4003 3.9 86.8 1.0 O3A A:DCT4003 4.0 96.5 1.0 N A:VAL891 4.2 56.0 1.0 O1G A:DCT4003 4.2 75.2 1.0 CA A:VAL891 4.3 60.2 1.0 N A:ASP892 4.4 74.6 1.0 C A:ASP890 4.4 64.6 1.0 CA A:ASP892 4.4 77.0 1.0 C5' A:DCT4003 4.5 73.5 1.0 CB A:ASP890 4.5 68.1 1.0 O2A A:DCT4003 4.6 68.4 1.0 O5' A:DCT4003 4.6 69.0 1.0 O A:ASP890 4.7 73.5 1.0 CB A:VAL891 4.8 69.0 1.0 CB A:ASP892 4.9 72.4 1.0 O1B A:DCT4003 4.9 0.0 1.0 CA A:SER893 5.0 67.6 1.0 CA A:ASP890 5.0 68.2 1.0 CA A:ASP1135 5.0 46.3 1.0

M.R.Szymanski, V.B.Kuznestov, C.K.Shumate, Q.Meng, Y.-S.Lee, G.Patel, S.S.Patel, Y.W.Yin. Structural Basis For Processivity and Antiviral Drug Toxicity in Human Mitochondrial Dna Replicase Embo J. V. 34 1959 2015.
ISSN: ISSN 0261-4189
PubMed: 26056153
DOI: 10.15252/EMBJ.201591520