Magnesium in PDB 1en9: 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: 1en9 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 (°)	32.243, 25.352, 34.190, 90.00, 117.17, 90.00
R / Rfree (%)	14.1 / 15.1

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 1en9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 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: 1en9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 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:6.8 occ:0.50 O A:HOH1280 2.1 9.7 1.0 O A:HOH1279 2.1 9.5 1.0 O A:HOH1278 2.1 10.0 1.0 H5' A:DC2 3.7 7.2 1.0 O A:HOH209 4.0 11.3 1.0 H1' A:DC1 4.0 9.4 1.0 O A:HOH204 4.1 12.0 1.0 O A:HOH225 4.2 17.6 1.0 O A:HOH214 4.2 12.6 1.0 O2 A:DC1 4.3 6.6 1.0 H4' A:DC2 4.3 7.2 1.0 C5' A:DC2 4.5 6.0 1.0 O4' A:DC2 4.6 5.3 1.0 C4' A:DC2 4.7 6.0 1.0 H5'' A:DC2 4.7 7.2 1.0

Magnesium binding site 2 out of 8 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:Mg116 b:14.5 occ:0.41 O A:HOH1116 1.7 16.0 0.6 O A:HOH1282 2.0 10.6 0.4 O A:HOH1281 2.1 13.5 0.4 O A:HOH1283 2.1 11.5 0.4 O A:HOH1284 2.1 16.9 0.4 N7 A:DG10 4.3 5.6 1.0 H8 A:DG9 4.6 7.5 1.0 H8 A:DG10 4.8 6.9 1.0 C8 A:DG10 5.0 5.7 1.0

Magnesium binding site 3 out of 8 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:Mg112 b:10.7 occ:0.36 MG A:MG112 0.0 10.7 0.4 O A:HOH1288 1.7 17.2 0.4 O A:HOH1286 2.0 11.9 0.3 O A:HOH1289 2.1 12.9 0.4 O A:HOH1286 2.1 10.9 0.4 O A:HOH1287 2.1 18.4 0.4 O A:HOH1288 2.1 11.3 0.4 O A:HOH1285 2.1 6.2 0.4 MG A:MG112 2.2 15.5 0.4 O A:HOH1285 2.6 12.9 0.4 O A:HOH1286 3.4 13.6 0.4 O A:HOH1288 3.4 12.3 0.3 H4' A:DG6 3.6 15.7 0.5 MG A:MG112 3.7 11.7 0.3 H21 A:DG4 3.8 9.3 1.0 O A:HOH1289 3.9 16.7 0.4 O A:HOH1287 3.9 11.7 0.4 H4' A:DG6 4.0 16.8 0.2 O A:HOH1114 4.1 11.4 0.7 H5' A:DG6 4.1 16.1 0.2 H5' A:DG6 4.2 15.9 0.5 O A:HOH1285 4.2 17.9 0.3 H22 A:DG4 4.2 9.3 1.0 O A:HOH212 4.3 15.3 1.0 N2 A:DG4 4.4 7.8 1.0 C4' A:DG6 4.4 13.1 0.5 O4' A:DG6 4.4 15.1 0.5 H5' A:DG6 4.4 15.6 0.3 O4' A:DG6 4.4 15.2 0.2 O2 A:DC5 4.5 12.8 1.0 C4' A:DG6 4.5 14.0 0.2 O4' A:DG6 4.7 15.6 0.3 C5' A:DG6 4.7 13.4 0.2 H4' A:DG6 4.7 16.7 0.3 H5'' A:DG6 4.7 16.1 0.2 C5' A:DG6 4.8 13.3 0.5 O A:HOH232 4.8 31.3 1.0 O A:HOH1289 4.9 12.2 0.3 H5'' A:DG6 5.0 15.9 0.5

Magnesium binding site 4 out of 8 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:Mg112 b:15.5 occ:0.37 MG A:MG112 0.0 15.5 0.4 O A:HOH1287 1.8 18.4 0.4 O A:HOH1288 1.9 12.3 0.3 O A:HOH1286 1.9 11.9 0.3 O A:HOH1289 2.1 16.7 0.4 O A:HOH1285 2.1 12.9 0.4 O A:HOH1288 2.1 17.2 0.4 O A:HOH1286 2.1 13.6 0.4 O A:HOH1287 2.1 11.7 0.4 MG A:MG112 2.2 10.7 0.4 O A:HOH1289 2.2 12.9 0.4 MG A:MG112 2.4 11.7 0.3 O A:HOH1288 3.6 11.3 0.4 H5' A:DG6 3.7 15.9 0.5 O A:HOH1285 3.7 17.9 0.3 H5' A:DG6 3.8 16.1 0.2 O A:HOH1114 3.8 11.4 0.7 O A:HOH1286 3.8 10.9 0.4 O A:HOH1285 3.8 6.2 0.4 H5' A:DG6 3.9 15.6 0.3 O A:HOH1289 4.0 12.2 0.3 O A:HOH1287 4.1 13.5 0.3 H4' A:DG6 4.1 15.7 0.5 H5'' A:DG6 4.1 16.1 0.2 O A:HOH257 4.2 21.1 0.6 H21 A:DG4 4.3 9.3 1.0 C5' A:DG6 4.4 13.4 0.2 H4' A:DG6 4.4 16.8 0.2 H5'' A:DG6 4.4 15.9 0.5 O A:HOH256 4.4 18.5 0.7 C5' A:DG6 4.4 13.3 0.5 H1' A:DC5 4.6 15.7 1.0 O A:HOH212 4.6 15.3 1.0 C4' A:DG6 4.7 13.1 0.5 H4' A:DC5 4.8 15.4 1.0 C5' A:DG6 4.8 13.0 0.3 C4' A:DG6 4.9 14.0 0.2 O2 A:DC5 4.9 12.8 1.0

Magnesium binding site 5 out of 8 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:Mg112 b:11.7 occ:0.28 MG A:MG112 0.0 11.7 0.3 O A:HOH1285 1.7 12.9 0.4 O A:HOH1287 1.9 11.7 0.4 O A:HOH1289 2.1 12.2 0.3 O A:HOH1287 2.1 13.5 0.3 O A:HOH1286 2.1 11.9 0.3 O A:HOH1285 2.1 17.9 0.3 O A:HOH1288 2.1 12.3 0.3 O A:HOH1114 2.2 11.4 0.7 O A:HOH1287 2.3 18.4 0.4 MG A:MG112 2.4 15.5 0.4 O A:HOH1289 3.1 16.7 0.4 O A:HOH1289 3.1 12.9 0.4 O A:HOH1288 3.3 17.2 0.4 O A:HOH215 3.4 15.0 0.7 O A:HOH257 3.6 21.1 0.6 MG A:MG112 3.7 10.7 0.4 O A:HOH256 3.8 18.5 0.7 H21 A:DG4 3.9 9.3 1.0 O A:HOH1286 4.1 13.6 0.4 O A:HOH1285 4.4 6.2 0.4 N2 A:DG4 4.7 7.8 1.0 O A:HOH219 4.8 17.0 1.0 H2 A:DA3 4.8 6.8 1.0 H22 A:DG4 5.0 9.3 1.0

Magnesium binding site 6 out of 8 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 6 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:10.4 occ:0.76 O A:HOH1292 2.1 8.2 0.8 O A:HOH1295 2.1 14.0 0.8 O A:HOH1290 2.1 10.0 0.8 O A:HOH1293 2.1 12.9 0.8 O A:HOH1291 2.1 14.1 0.8 O A:HOH1294 2.1 12.3 0.8 O A:HOH202 3.8 10.4 1.0 O A:HOH201 3.9 8.3 1.0 O A:HOH239 4.0 25.6 0.8 H42 A:DC1 4.1 6.6 1.0 O A:HOH208 4.2 11.2 1.0 O A:HOH228 4.3 20.9 0.5 H41 A:DC1 4.5 6.6 1.0 N4 A:DC1 4.6 5.5 1.0

Magnesium binding site 7 out of 8 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 7 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:17.0 occ:1.00 O A:HOH1297 2.1 16.9 1.0 O A:HOH1299 2.1 16.9 1.0 O A:HOH1300 2.1 21.9 1.0 O A:HOH1296 2.1 14.1 1.0 O A:HOH1301 2.1 21.2 1.0 O A:HOH1298 2.1 16.5 1.0 O A:HOH226 3.9 20.0 1.0 OP2 A:DA3 4.1 6.0 0.5 O A:HOH207 4.2 12.8 1.0 O A:HOH1233 4.2 18.4 1.0 N7 A:DA3 4.3 5.5 1.0 H8 A:DA3 4.4 7.2 1.0 O6 A:DG4 4.4 6.5 1.0 O A:HOH252 4.4 30.9 1.0 N7 A:DG4 4.4 7.3 1.0 C8 A:DA3 4.7 6.0 1.0 OP2 A:DA3 4.8 10.5 0.5 H2'' A:DC2 5.0 5.8 1.0

Magnesium binding site 8 out of 8 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 8 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:Mg115 b:7.1 occ:0.21 O A:HOH1305 2.1 10.8 0.2 O A:HOH1304 2.1 6.6 0.2 O A:HOH1302 2.1 6.2 0.2 O A:HOH1307 2.1 8.0 0.2 O A:HOH1303 2.1 9.2 0.2 O A:HOH1306 2.1 5.4 0.2 OP2 A:DA3 4.2 10.5 0.5 OP2 A:DA3 4.3 6.0 0.5 OP1 A:DA3 4.4 6.2 0.5 O A:HOH252 4.5 30.9 1.0 O A:HOH1239 4.6 19.7 1.0 P A:DA3 4.7 5.3 0.5 O5' A:DA3 4.7 5.6 0.5 P A:DA3 4.9 7.5 0.5 OP1 A:DA3 5.0 11.6 0.5

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