Magnesium in PDB 1en3: 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium

The structure of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium, PDB code: 1en3 was solved by T.K.Chiu, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 0.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	32.001, 25.369, 33.633, 90.00, 112.98, 90.00
R / Rfree (%)	14.1 / 15.9

The binding sites of Magnesium atom in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium (pdb code 1en3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium, PDB code: 1en3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg111 b:10.2 occ:0.50 O A:HOH1318 2.0 13.2 1.0 O A:HOH1319 2.1 13.6 1.0 O A:HOH1320 2.1 13.9 1.0 H5' A:DC2 3.5 9.8 1.0 O A:HOH216 4.0 13.3 1.0 O A:HOH206 4.0 12.7 1.0 H1' A:DC1 4.1 8.8 1.0 O A:HOH214 4.2 15.9 1.0 O A:HOH231 4.3 16.9 1.0 O2 A:DC1 4.4 6.8 1.0 H4' A:DC2 4.4 9.1 1.0 C5' A:DC2 4.4 8.2 1.0 O4' A:DC2 4.6 6.7 1.0 H5'' A:DC2 4.6 9.8 1.0 C4' A:DC2 4.7 7.6 1.0

Magnesium binding site 2 out of 5 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg112 b:11.7 occ:0.66 O A:HOH1323 2.1 10.5 0.7 O A:HOH1324 2.1 17.0 0.7 O A:HOH1326 2.1 10.3 0.7 O A:HOH1321 2.1 14.1 0.7 O A:HOH1322 2.1 12.9 0.7 O A:HOH1325 2.1 16.3 0.7 H5' A:DG6 3.8 15.7 1.0 O A:HOH235 3.9 9.2 0.3 H4' A:DG6 4.0 13.5 1.0 O A:HOH247 4.0 14.8 0.3 O A:HOH245 4.1 19.4 0.5 O A:HOH205 4.2 14.4 1.0 O A:HOH232 4.2 15.5 1.0 O4' A:DG6 4.3 11.2 1.0 O2 A:DC5 4.3 12.1 1.0 O A:HOH238 4.4 17.5 1.0 O A:HOH208 4.4 18.5 1.0 H2 A:DA4 4.4 13.1 1.0 C4' A:DG6 4.5 11.3 1.0 H1' A:DC5 4.5 16.5 1.0 C5' A:DG6 4.5 13.1 1.0 H4' A:DC5 4.6 16.4 1.0 H5'' A:DG6 4.8 15.7 1.0

Magnesium binding site 3 out of 5 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg114 b:18.4 occ:1.00 O A:HOH1328 2.1 18.7 1.0 O A:HOH1329 2.1 25.9 1.0 O A:HOH1327 2.1 24.8 1.0 O A:HOH1330 2.1 25.0 1.0 O A:HOH1331 2.1 16.1 1.0 O A:HOH1332 2.1 29.3 1.0 O A:HOH210 3.9 22.9 0.5

Magnesium binding site 4 out of 5 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg113 b:11.2 occ:0.61 MG A:MG113 0.0 11.2 0.6 O A:HOH1334 1.5 14.7 0.4 O A:HOH1337 1.8 11.1 0.4 O A:HOH1335 2.1 14.6 0.6 O A:HOH1334 2.1 13.4 0.6 O A:HOH1336 2.1 11.6 0.6 O A:HOH1333 2.1 18.4 0.6 O A:HOH1338 2.1 16.6 0.6 O A:HOH1337 2.1 8.3 0.6 MG A:MG113 2.3 9.3 0.4 O A:HOH1335 3.0 12.1 0.4 O A:HOH1336 3.2 16.7 0.4 O A:HOH201 3.9 8.5 1.0 O A:HOH1338 4.0 12.8 0.4 H42 A:DC1 4.0 7.6 1.0 O A:HOH234 4.1 25.4 1.0 O A:HOH1333 4.1 13.1 0.4 H41 A:DC1 4.3 7.6 1.0 O A:HOH202 4.3 10.7 1.0 N4 A:DC1 4.5 6.3 1.0 O A:HOH233 4.5 14.5 0.6

Magnesium binding site 5 out of 5 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg113 b:9.3 occ:0.39 MG A:MG113 0.0 9.3 0.4 O A:HOH1338 1.9 16.6 0.6 O A:HOH1333 2.0 18.4 0.6 O A:HOH1333 2.1 13.1 0.4 O A:HOH1338 2.1 12.8 0.4 O A:HOH1337 2.1 11.1 0.4 O A:HOH1336 2.1 16.7 0.4 O A:HOH1334 2.1 14.7 0.4 O A:HOH1335 2.1 12.1 0.4 O A:HOH1335 2.3 14.6 0.6 MG A:MG113 2.3 11.2 0.6 O A:HOH1336 3.8 11.6 0.6 O A:HOH1334 3.9 13.4 0.6 O A:HOH1337 4.0 8.3 0.6 O A:HOH234 5.0 25.4 1.0

T.K.Chiu, R.E.Dickerson. 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. J.Mol.Biol. V. 301 915 2000.
ISSN: ISSN 0022-2836
PubMed: 10966796
DOI: 10.1006/JMBI.2000.4012