Calcium in PDB 1en8: 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium

The structure of 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium, PDB code: 1en8 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 (°)	31.847, 25.100, 34.144, 90.00, 114.87, 90.00
R / Rfree (%)	n/a / 14.1

The binding sites of Calcium atom in the 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium (pdb code 1en8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium, PDB code: 1en8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 1 A 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 Calcium with other atoms in the Ca binding site number 1 of 1 A 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:Ca111 b:4.2 occ:0.50 O A:HOH1062 2.4 6.8 0.5 O A:HOH1063 2.4 4.7 0.5 O A:HOH1064 2.4 5.1 0.5 O A:HOH1061 2.4 5.8 0.5 O A:EOH115 2.4 4.9 0.5 O A:HOH1059 2.5 4.4 0.5 O A:HOH1060 2.5 5.1 0.5 O A:HOH269 2.7 8.2 0.5 O A:HOH1058 2.8 10.6 0.5 C1 A:EOH115 3.0 4.7 0.5 O A:HOH248 3.4 7.7 0.5 C2 A:EOH115 4.1 3.0 0.5 O A:HOH212 4.3 13.6 1.0 H21 A:DG10 4.6 5.6 1.0 O A:HOH200 4.6 5.4 1.0 H22 A:DG10 5.0 5.6 1.0

Calcium binding site 2 out of 4 in the 1 A 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 Calcium with other atoms in the Ca binding site number 2 of 1 A 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:Ca112 b:9.0 occ:0.64 O A:HOH1068 2.4 7.9 0.6 O A:HOH1069 2.4 11.9 0.6 O A:HOH1070 2.4 11.2 0.6 O A:HOH1067 2.4 13.7 0.6 O A:HOH1066 2.4 9.8 0.6 O A:HOH1065 2.5 8.5 0.6 O A:HOH1071 2.5 10.7 0.6 O A:HOH246 3.2 8.8 0.4 H1' A:DC5 4.0 7.4 0.4 H2 A:DA4 4.2 7.3 1.0 H4' A:DC5 4.2 7.3 0.6 H5' A:DC5 4.3 7.7 0.6 N3 A:DA4 4.5 5.5 1.0 O4' A:DC5 4.6 5.8 0.6 O A:HOH215 4.6 13.5 0.5 H2'' A:DC5 4.7 7.8 0.4 O A:HOH230 4.7 11.3 0.6 C2 A:DA4 4.8 6.1 1.0 O A:HOH246 4.8 13.5 0.6 C4' A:DC5 4.8 6.1 0.6 H1' A:DA4 4.9 7.8 1.0 O A:HOH1052 4.9 29.4 0.5 C1' A:DC5 5.0 6.2 0.4 C5' A:DC5 5.0 6.4 0.6

Calcium binding site 3 out of 4 in the 1 A 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 Calcium with other atoms in the Ca binding site number 3 of 1 A 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:Ca113 b:4.8 occ:0.62 O A:HOH1075 2.4 5.6 0.6 O A:HOH1076 2.4 6.6 0.6 O A:HOH1072 2.4 7.4 0.6 O A:HOH1073 2.4 7.2 0.6 O A:HOH1074 2.5 6.0 0.6 O6 A:DG10 2.5 5.2 1.0 N7 A:DG9 2.6 4.5 1.0 O A:HOH245 2.7 3.4 0.4 O A:HOH214 3.3 5.9 0.4 C8 A:DG9 3.5 4.4 1.0 C6 A:DG10 3.5 3.7 1.0 H8 A:DG9 3.5 5.2 1.0 H2'' A:DT8 3.6 6.5 1.0 C5 A:DG9 3.6 3.4 1.0 N7 A:DG10 3.9 3.9 1.0 O6 A:DG9 3.9 4.3 1.0 C5 A:DG10 4.0 3.0 1.0 C6 A:DG9 4.1 3.7 1.0 O A:HOH245 4.4 14.4 0.6 O A:HOH263 4.5 15.2 0.6 C2' A:DT8 4.6 5.4 1.0 N1 A:DG10 4.6 3.6 1.0 N9 A:DG9 4.7 3.8 1.0 O A:HOH214 4.7 11.2 0.6 C4 A:DG9 4.7 3.7 1.0 H2' A:DT8 4.8 6.5 1.0 H1 A:DG10 4.8 4.3 1.0

Calcium binding site 4 out of 4 in the 1 A 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 Calcium with other atoms in the Ca binding site number 4 of 1 A 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:Ca114 b:7.7 occ:0.50 O A:HOH241 1.9 12.9 0.5 OP1 A:DT7 2.4 9.3 0.5 O A:HOH1078 2.4 9.3 0.5 O A:HOH1077 2.4 8.4 0.5 O A:HOH1079 2.4 8.1 0.5 O A:HOH1080 2.4 10.1 0.5 O A:HOH252 3.0 12.8 0.5 OP1 A:DT7 3.0 12.5 0.5 H5'' A:DT7 3.6 9.2 0.5 P A:DT7 3.7 8.1 0.5 P A:DT7 3.8 10.7 0.5 OP2 A:DT7 3.9 10.3 0.5 O5' A:DT7 4.2 7.7 0.5 O A:HOH250 4.2 18.0 0.5 O A:HOH241 4.3 10.1 0.5 O5' A:DT7 4.3 9.0 0.5 C5' A:DT7 4.3 7.7 0.5 OP2 A:DT7 4.3 8.8 0.5 H3' A:DT7 4.4 8.6 0.5 H5'' A:DT7 4.5 9.9 0.5 H5' A:DT7 4.7 9.2 0.5 O3' A:DG6 4.8 9.6 0.5 H3' A:DT7 4.9 9.6 0.5 C5' A:DT7 5.0 8.3 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