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Magnesium in PDB 5c53: Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma

Enzymatic activity of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma

All present enzymatic activity of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma:
2.7.7.7;

Protein crystallography data

The structure of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma, PDB code: 5c53 was solved by C.D.Sohl, M.R.Szymanski, A.C.Mislak, C.K.Shumate, S.Amiralaei, R.F.Schinazi, K.S.Anderson, Y.W.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 3.57
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 217.447, 217.447, 163.593, 90.00, 90.00, 90.00
R / Rfree (%) 30 / 33.8

Other elements in 5c53:

The structure of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma (pdb code 5c53). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma, PDB code: 5c53:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5c53

Go back to Magnesium Binding Sites List in 5c53
Magnesium binding site 1 out of 2 in the Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4001

b:71.0
occ:1.00
 O2A A:4Y34003 2.0 0.5 1.0
C5' A:4Y34003 2.4 95.4 1.0
C3' P:DOC101 2.5 97.4 1.0
CB A:ASP1135 2.5 66.4 1.0
PA A:4Y34003 2.7 0.9 1.0
O5' A:4Y34003 2.8 98.2 1.0
OD2 A:ASP1135 3.0 61.0 1.0
C2' P:DOC101 3.0 94.0 1.0
CG A:ASP1135 3.1 66.3 1.0
O1A A:4Y34003 3.3 0.3 1.0
C4' A:4Y34003 3.6 91.3 1.0
C4' P:DOC101 3.8 96.3 1.0
O4' A:4Y34003 3.9 93.7 1.0
CA A:ASP1135 3.9 54.7 1.0
MG A:MG4002 4.0 60.2 1.0
O3A A:4Y34003 4.2 0.1 1.0
OD1 A:ASP1135 4.2 63.6 1.0
O2B A:4Y34003 4.2 80.8 1.0
N A:ASP1135 4.2 53.5 1.0
NE2 A:GLN894 4.2 67.7 1.0
OD2 A:ASP890 4.5 63.2 1.0
C1' P:DOC101 4.5 91.8 1.0
C5' P:DOC101 4.6 92.7 1.0
O4' P:DOC101 4.8 94.0 1.0
O5' P:DOC101 4.8 94.4 1.0
PB A:4Y34003 4.9 88.0 1.0
S A:4Y34003 4.9 92.3 1.0
C A:ASP1135 5.0 66.0 1.0

Magnesium binding site 2 out of 2 in 5c53

Go back to Magnesium Binding Sites List in 5c53
Magnesium binding site 2 out of 2 in the Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4002

b:60.2
occ:1.00
 O A:VAL891 2.2 62.2 1.0
OD2 A:ASP1135 2.4 61.0 1.0
O2A A:4Y34003 2.5 0.5 1.0
O3B A:4Y34003 2.6 100.0 1.0
O2B A:4Y34003 2.6 80.8 1.0
OD1 A:ASP890 2.7 72.9 1.0
O1G A:4Y34003 2.8 0.7 1.0
PB A:4Y34003 2.9 88.0 1.0
CG A:ASP1135 3.0 66.3 1.0
OD1 A:ASP1135 3.1 63.6 1.0
PG A:4Y34003 3.2 0.6 1.0
O3A A:4Y34003 3.3 0.1 1.0
C A:VAL891 3.4 69.8 1.0
PA A:4Y34003 3.5 0.9 1.0
CG A:ASP890 3.6 69.9 1.0
O2G A:4Y34003 3.8 0.1 1.0
OD2 A:ASP890 3.8 63.2 1.0
MG A:MG4001 4.0 71.0 1.0
CA A:ASP892 4.2 71.9 1.0
CB A:ASP1135 4.2 66.4 1.0
N A:ASP892 4.2 78.5 1.0
O5' A:4Y34003 4.4 98.2 1.0
O1B A:4Y34003 4.4 89.6 1.0
N A:VAL891 4.4 68.0 1.0
CA A:VAL891 4.4 62.5 1.0
C5' A:4Y34003 4.5 95.4 1.0
O3G A:4Y34003 4.5 0.5 1.0
CB A:ASP892 4.6 78.9 1.0
CA A:SER893 4.6 65.7 1.0
O1A A:4Y34003 4.7 0.3 1.0
C A:ASP890 4.7 60.0 1.0
CB A:SER893 4.9 64.9 1.0
CB A:VAL891 4.9 69.8 1.0
CB A:ASP890 4.9 63.6 1.0

Reference:

C.D.Sohl, M.R.Szymanski, A.C.Mislak, C.K.Shumate, S.Amiralaei, R.F.Schinazi, K.S.Anderson, Y.W.Yin. Probing the Structural and Molecular Basis of Nucleotide Selectivity By Human Mitochondrial Dna Polymerase Gamma. Proc.Natl.Acad.Sci.Usa V. 112 8596 2015.
ISSN: ESSN 1091-6490
PubMed: 26124101
DOI: 10.1073/PNAS.1421733112
Page generated: Tue Aug 12 06:17:03 2025

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