Magnesium in PDB 4q45: Dna Polymerase- Damaged Dna Complex

All present enzymatic activity of Dna Polymerase- Damaged Dna Complex:
2.7.7.7;

The structure of Dna Polymerase- Damaged Dna Complex, PDB code: 4q45 was solved by J.Kottur, A.Sharma, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.34 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.500, 57.900, 111.040, 90.00, 90.44, 90.00
R / Rfree (%)	21.2 / 25.7

The binding sites of Magnesium atom in the Dna Polymerase- Damaged Dna Complex (pdb code 4q45). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase- Damaged Dna Complex, PDB code: 4q45:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna Polymerase- Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase- Damaged Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:11.2 occ:1.00 OD1 F:ASP8 2.0 30.7 1.0 O2A F:1FZ401 2.1 26.6 1.0 O1B F:1FZ401 2.1 23.5 1.0 O F:MET9 2.3 27.7 1.0 O1G F:1FZ401 2.3 23.2 1.0 OD1 F:ASP103 2.3 29.5 1.0 CG F:ASP8 3.1 29.7 1.0 MG F:MG403 3.3 47.1 1.0 PB F:1FZ401 3.4 20.9 1.0 PA F:1FZ401 3.4 25.0 1.0 C F:MET9 3.5 24.2 1.0 CG F:ASP103 3.5 28.1 1.0 PG F:1FZ401 3.6 27.2 1.0 OD2 F:ASP8 3.6 32.8 1.0 O F:HOH673 3.8 35.9 1.0 O F:HOH635 3.8 30.8 1.0 N3A F:1FZ401 3.9 23.1 1.0 N F:MET9 3.9 20.9 1.0 O3B F:1FZ401 3.9 33.4 1.0 C5' F:1FZ401 4.1 24.8 1.0 OD2 F:ASP103 4.1 25.7 1.0 O5' F:1FZ401 4.2 31.1 1.0 C F:ASP8 4.2 28.2 1.0 CA F:MET9 4.2 23.7 1.0 O2G F:1FZ401 4.3 31.5 1.0 CB F:ASP8 4.4 28.3 1.0 O1A F:1FZ401 4.5 18.7 1.0 N F:ASP10 4.5 26.6 1.0 O2B F:1FZ401 4.6 24.2 1.0 CA F:ASP8 4.6 29.5 1.0 CB F:ASP103 4.7 29.3 1.0 O F:ASP8 4.7 26.1 1.0 CA F:ASP10 4.7 27.2 1.0 O3G F:1FZ401 4.7 28.3 1.0 OE1 F:GLU104 4.8 37.0 1.0 CB F:MET9 4.8 24.6 1.0 N F:CYS11 4.8 21.1 1.0 CB F:PHE12 4.8 24.7 1.0 N F:PHE12 4.9 23.5 1.0 C F:ASP10 5.0 22.5 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase- Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase- Damaged Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:47.1 occ:1.00 OD2 F:ASP103 2.1 25.7 1.0 OE1 F:GLU104 2.2 37.0 1.0 CG F:GLU104 2.5 34.9 1.0 O2A F:1FZ401 2.6 26.6 1.0 CD F:GLU104 2.7 36.9 1.0 OD1 F:ASP103 2.8 29.5 1.0 CG F:ASP103 2.8 28.1 1.0 O3' H:DC873 2.8 29.5 1.0 O F:HOH673 3.0 35.9 1.0 MG F:MG402 3.3 11.2 1.0 OD1 F:ASP8 3.4 30.7 1.0 C3' H:DC873 3.4 26.5 1.0 OD2 F:ASP8 3.5 32.8 1.0 O5' F:1FZ401 3.5 31.1 1.0 PA F:1FZ401 3.5 25.0 1.0 CG F:ASP8 3.7 29.7 1.0 C5' F:1FZ401 3.7 24.8 1.0 OE2 F:GLU104 3.8 36.9 1.0 CB F:GLU104 3.9 26.1 1.0 O1A F:1FZ401 3.9 18.7 1.0 OG F:SER101 4.0 32.6 1.0 CB F:ASP103 4.3 29.3 1.0 C F:ASP103 4.4 27.6 1.0 C4' H:DC873 4.5 29.3 1.0 N F:GLU104 4.5 34.0 1.0 O1B F:1FZ401 4.5 23.5 1.0 C2' H:DC873 4.5 23.3 1.0 O F:ASP103 4.5 31.1 1.0 CA F:GLU104 4.7 30.1 1.0 O H:HOH902 4.7 27.6 1.0 O5' H:DC873 4.7 29.7 1.0 C5' H:DC873 4.7 21.0 1.0 CA F:ASP103 4.9 31.7 1.0 CB F:ASP8 4.9 28.3 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase- Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase- Damaged Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:21.7 occ:1.00 O1A A:1FZ401 2.0 38.4 1.0 OD1 A:ASP8 2.1 38.3 1.0 O1G A:1FZ401 2.1 20.8 1.0 O2B A:1FZ401 2.1 30.2 1.0 O A:MET9 2.3 39.0 1.0 OD2 A:ASP103 2.4 34.0 1.0 CG A:ASP8 3.2 40.7 1.0 PB A:1FZ401 3.3 29.2 1.0 PA A:1FZ401 3.4 33.3 1.0 C A:MET9 3.4 39.0 1.0 PG A:1FZ401 3.5 28.1 1.0 CG A:ASP103 3.5 37.9 1.0 NZ A:LYS157 3.5 39.9 1.0 OD2 A:ASP8 3.8 47.4 1.0 O3B A:1FZ401 3.8 40.0 1.0 N3A A:1FZ401 3.8 28.6 1.0 MG A:MG403 3.9 45.4 1.0 N A:MET9 3.9 35.0 1.0 C5' A:1FZ401 4.0 32.9 1.0 OD1 A:ASP103 4.1 36.2 1.0 O5' A:1FZ401 4.1 35.0 1.0 O3G A:1FZ401 4.2 37.5 1.0 CA A:MET9 4.2 36.7 1.0 C A:ASP8 4.2 41.3 1.0 O A:HOH586 4.3 49.7 1.0 CB A:ASP8 4.4 36.2 1.0 N A:ASP10 4.5 33.8 1.0 O2A A:1FZ401 4.5 28.9 1.0 O2G A:1FZ401 4.6 27.4 1.0 O1B A:1FZ401 4.6 37.6 1.0 CE A:LYS157 4.6 40.8 1.0 O A:ASP8 4.6 39.6 1.0 CA A:ASP10 4.7 37.3 1.0 CA A:ASP8 4.7 41.1 1.0 N A:CYS11 4.7 36.8 1.0 CB A:ASP103 4.7 36.7 1.0 CB A:MET9 4.7 34.8 1.0 CB A:PHE12 4.8 33.7 1.0 N A:PHE12 4.8 31.9 1.0 C A:ASP10 4.9 33.1 1.0 OE2 A:GLU104 4.9 39.6 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase- Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Polymerase- Damaged Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.4 occ:1.00 OE2 A:GLU104 2.2 39.6 1.0 O1A A:1FZ401 2.5 38.4 1.0 OD2 A:ASP8 2.7 47.4 1.0 O2A A:1FZ401 2.7 28.9 1.0 O A:HOH586 2.8 49.7 1.0 PA A:1FZ401 3.2 33.3 1.0 CD A:GLU104 3.4 43.2 1.0 CG A:ASP8 3.5 40.7 1.0 O A:HOH592 3.6 40.0 1.0 OD1 A:ASP8 3.6 38.3 1.0 MG A:MG402 3.9 21.7 1.0 OP2 C:DC873 4.1 39.9 1.0 CG A:GLU104 4.1 50.7 1.0 O1G A:1FZ401 4.2 20.8 1.0 O5' C:DC873 4.2 39.2 1.0 O5' A:1FZ401 4.2 35.0 1.0 C3' C:DC873 4.3 35.8 1.0 OE1 A:GLU104 4.3 36.5 1.0 N3A A:1FZ401 4.5 28.6 1.0 P C:DC873 4.5 41.1 1.0 O3' C:DC873 4.5 31.1 1.0 O A:HOH510 4.6 42.6 1.0 OP1 C:DC873 4.7 42.1 1.0 CE A:LYS150 4.8 47.6 1.0 C5' C:DC873 4.9 32.3 1.0 CB A:ASP8 5.0 36.2 1.0 OD2 A:ASP103 5.0 34.0 1.0

J.Kottur, A.Sharma, K.R.Gore, N.Narayanan, B.Samanta, P.I.Pradeepkumar, D.T.Nair. Unique Structural Features in Dna Polymerase IV Enable Efficient Bypass of the N2 Adduct Induced By the Nitrofurazone Antibiotic Structure V. 23 56 2015.
ISSN: ISSN 0969-2126
PubMed: 25497730
DOI: 10.1016/J.STR.2014.10.019