Magnesium in PDB 423d: 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'

The structure of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3', PDB code: 423d was solved by H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.60 / 1.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	64.067, 64.067, 44.679, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.6

The binding sites of Magnesium atom in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' (pdb code 423d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3', PDB code: 423d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg26 b:16.7 occ:1.00 O B:HOH164 2.0 15.9 1.0 O B:HOH163 2.0 14.0 1.0 O A:HOH166 2.1 16.3 1.0 O A:HOH168 2.1 16.8 1.0 O A:HOH165 2.1 15.7 1.0 O B:HOH167 2.1 15.5 1.0 O A:HOH46 4.0 21.5 1.0 O A:HOH82 4.1 17.7 1.0 O B:HOH48 4.1 12.9 1.0 O4' B:DG19 4.2 9.7 1.0 O B:HOH94 4.2 28.5 1.0 O B:HOH56 4.3 16.1 1.0 O A:HOH64 4.4 26.5 1.0 O2 B:DC18 4.4 10.7 1.0 O2 A:DT8 4.6 11.5 1.0 C4' B:DG19 4.6 8.2 1.0 N2 A:DG7 4.8 11.3 1.0 C5' B:DG19 4.8 9.1 1.0 O4' A:DC9 4.9 17.8 1.0 C4' A:DC9 5.0 15.7 1.0

Magnesium binding site 2 out of 5 in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg29 b:24.2 occ:1.00 O A:HOH185 2.0 26.3 1.0 O A:HOH186 2.0 32.6 1.0 O A:HOH183 2.0 23.6 1.0 O A:HOH181 2.0 18.6 1.0 O A:HOH184 2.0 27.5 1.0 O A:HOH182 2.2 29.3 1.0 O A:HOH68 3.9 36.7 1.0 O A:HOH129 4.1 30.5 1.0 O6 A:DG11 4.2 18.0 1.0 N7 A:DG10 4.2 18.4 1.0 O B:HOH147 4.3 27.4 1.0 N4 B:DC14 4.3 18.0 1.0 O A:HOH145 4.4 51.4 1.0 O6 A:DG10 4.4 12.7 1.0 O A:HOH84 4.6 28.1 1.0 O A:HOH39 4.8 13.0 1.0 O A:HOH125 4.8 40.4 1.0 C5 A:DC9 4.9 11.8 1.0

Magnesium binding site 3 out of 5 in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg25 b:11.5 occ:1.00 O B:HOH159 2.0 8.5 1.0 O B:HOH158 2.1 9.9 1.0 O B:HOH162 2.1 10.4 1.0 O A:HOH161 2.1 10.5 1.0 O A:HOH160 2.1 10.1 1.0 O B:HOH157 2.2 10.9 1.0 O A:HOH51 4.1 18.3 1.0 O B:HOH40 4.2 14.9 1.0 O A:HOH50 4.2 14.3 1.0 N6 A:DA5 4.3 9.3 1.0 O B:HOH65 4.4 15.3 1.0 O6 B:DG19 4.4 11.5 1.0 N7 B:DG19 4.4 9.6 1.0 O4 B:DT20 4.4 14.2 1.0 N7 A:DG4 4.5 11.3 1.0 C6 B:DC18 4.9 11.1 1.0 O A:HOH37 4.9 15.1 1.0 C5 B:DC18 5.0 9.5 1.0

Magnesium binding site 4 out of 5 in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg27 b:17.1 occ:1.00 O A:HOH171 1.9 16.3 1.0 O A:HOH170 2.0 25.0 1.0 O A:HOH172 2.0 19.8 1.0 O B:HOH173 2.1 18.1 1.0 O B:HOH174 2.1 15.3 1.0 O B:HOH169 2.2 17.5 1.0 O A:HOH60 3.7 22.9 1.0 O A:HOH144 4.2 30.9 1.0 O B:HOH88 4.2 24.4 1.0 O B:HOH67 4.2 30.9 1.0 N7 B:DG16 4.4 13.2 1.0 O B:HOH32 4.4 9.9 1.0 O6 B:DG16 4.4 12.7 1.0 O B:HOH42 4.4 16.4 1.0 C5 B:DC15 4.5 9.3 1.0 O A:HOH108 4.7 31.8 1.0 C6 B:DC15 5.0 16.8 1.0

Magnesium binding site 5 out of 5 in the 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3'


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 5'-D(*Ap*Cp*Cp*Gp*Ap*Cp*Gp*Tp*Cp*Gp*Gp*T)-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg28 b:21.5 occ:1.00 O B:HOH179 1.9 24.8 1.0 O B:HOH175 1.9 24.2 1.0 O B:HOH176 2.1 18.0 1.0 O A:HOH178 2.1 25.1 1.0 O A:HOH180 2.1 24.4 1.0 O B:HOH177 2.1 28.3 1.0 O B:HOH152 3.5 33.1 1.0 O B:HOH131 4.0 38.6 1.0 O B:HOH93 4.1 24.6 0.7 O B:HOH58 4.1 20.2 1.0 O A:HOH97 4.2 28.4 1.0 O B:HOH115 4.3 38.8 1.0 O2 B:DT20 4.3 13.6 1.0 O A:HOH85 4.3 23.1 1.0 O A:HOH139 4.4 41.6 1.0 O B:HOH35 4.4 11.4 1.0 O2 A:DC6 4.5 14.2 1.0 C5' B:DC21 4.7 11.6 1.0 C5' A:DG7 4.7 13.8 1.0 C4' A:DG7 4.9 16.2 1.0 N2 B:DG19 4.9 12.5 1.0 O A:HOH102 4.9 31.8 1.0 C4' B:DC21 5.0 14.8 1.0

H.Rozenberg, D.Rabinovich, F.Frolow, R.S.Hegde, Z.Shakked. Structural Code For Dna Recognition Revealed in Crystal Structures of Papillomavirus E2-Dna Targets. Proc.Natl.Acad.Sci.Usa V. 95 15194 1998.
ISSN: ISSN 0027-8424
PubMed: 9860945
DOI: 10.1073/PNAS.95.26.15194