Calcium in PDB 1sk5: The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition

The structure of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition, PDB code: 1sk5 was solved by G.W.Han, D.Langs, M.L.Kopka, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 0.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	22.665, 35.664, 28.289, 90.00, 101.69, 90.00
R / Rfree (%)	12.6 / 14.4

The binding sites of Calcium atom in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition (pdb code 1sk5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition, PDB code: 1sk5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:6.8 occ:1.00 O B:HOH1112 2.3 8.0 1.0 O A:HOH1115 2.4 9.1 1.0 O B:HOH1113 2.4 9.4 1.0 O B:HOH1116 2.4 7.9 1.0 O B:HOH1118 2.4 9.1 1.0 O A:HOH1117 2.4 7.0 1.0 O B:HOH1114 2.4 10.0 1.0 O B:HOH1017 4.4 10.3 1.0 O4' A:DA8 4.4 6.1 1.0 O B:HOH1016 4.4 9.4 1.0 O A:HOH1080 4.5 28.2 1.0 O B:HOH1044 4.5 13.4 1.0 O2 B:DT15 4.6 6.3 1.0 O4' B:DA16 4.7 7.7 1.0 C4' A:DA8 4.7 6.9 1.0 C4' B:DA16 4.8 7.8 1.0 C5' B:DA16 4.8 8.8 1.0 O A:HOH1050 4.9 18.5 1.0 O B:HOH1075 4.9 21.8 1.0 N3 A:DA7 5.0 4.7 1.0 C2' A:DA7 5.0 5.6 1.0

Calcium binding site 2 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:14.5 occ:1.00 O A:HOH1131 2.2 25.3 1.0 O A:HOH1127 2.4 14.4 1.0 OP2 A:DA8 2.4 7.3 1.0 O A:HOH1128 2.4 23.2 1.0 O A:HOH1132 2.4 34.1 1.0 O A:HOH1129 2.5 17.1 1.0 O A:HOH1130 2.5 22.3 1.0 O A:HOH1133 2.8 11.2 1.0 P A:DA8 3.6 6.5 1.0 O A:HOH1055 4.0 19.7 1.0 OP1 A:DA8 4.1 7.7 1.0 O3' A:DA7 4.2 6.2 1.0 O A:HOH1136 4.4 18.4 1.0 C3' A:DA7 4.4 5.5 1.0 C5' A:DA7 4.6 5.9 1.0 O A:HOH1061 4.7 23.4 1.0 O5' A:DA8 4.8 6.8 1.0 O A:HOH1033 4.9 13.3 1.0

Calcium binding site 3 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:32.5 occ:0.57 O B:HOH1134 2.1 14.5 1.0 O A:HOH1136 2.2 18.4 1.0 O A:HOH1137 2.4 16.6 1.0 O A:HOH1138 2.6 52.2 1.0 O B:HOH1135 2.7 13.5 1.0 N6 A:DA8 3.0 5.2 1.0 N7 A:DA8 3.9 6.1 1.0 N7 A:DA7 4.0 5.3 1.0 C6 A:DA8 4.1 4.7 1.0 C5 A:DA8 4.3 4.9 1.0 O4 B:DT12 4.3 6.4 1.0 O B:HOH1102 4.5 13.0 1.0 O A:HOH1107 4.5 27.4 1.0 O A:HOH1127 4.5 14.4 1.0 C5 A:DA7 4.6 4.6 1.0 C8 A:DA7 4.6 5.0 1.0 O A:HOH1041 4.7 14.8 1.0 N6 A:DA7 4.8 5.4 1.0 O4 B:DT13 4.9 6.2 1.0 N6 A:DA9 5.0 5.9 1.0 C6 A:DA7 5.0 4.5 1.0

Calcium binding site 4 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca307 b:18.0 occ:1.00 O A:HOH1143 2.1 24.3 1.0 OP1 A:DT4 2.2 12.2 1.0 O A:HOH1141 2.2 24.8 1.0 O A:HOH1139 2.3 22.8 1.0 O A:HOH1140 2.3 24.2 1.0 O A:HOH1142 2.8 10.7 1.0 O A:HOH1051 3.6 20.6 1.0 P A:DT4 3.7 9.0 1.0 O5' A:DT4 4.3 8.0 1.0 C5' A:DT4 4.3 7.5 1.0 OP2 A:DT4 4.5 11.7 1.0 O A:HOH1085 4.6 23.2 1.0 O3' A:DT3 4.7 8.0 1.0 O A:HOH1076 4.7 23.8 1.0 O A:HOH1152 5.0 36.3 1.0

Calcium binding site 5 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca308 b:14.8 occ:1.00 O A:HOH1147 2.3 40.1 1.0 O A:HOH1144 2.3 10.5 1.0 O A:HOH1148 2.3 19.1 1.0 O A:HOH1145 2.5 24.0 1.0 O A:HOH1149 2.5 35.7 1.0 O A:HOH1146 2.6 18.3 1.0 O A:HOH1108 3.6 47.3 1.0 OP2 A:DA6 4.1 7.8 1.0 O A:HOH1059 4.5 17.4 1.0 OP2 A:DT5 4.5 13.4 1.0 O A:HOH1058 4.6 26.9 1.0 O A:HOH1052 4.6 20.1 1.0 O5' A:DT5 4.8 9.1 1.0 OP1 A:DT5 4.9 16.5 1.0 C3' A:DT5 4.9 6.5 1.0 P A:DT5 5.0 10.8 1.0

Calcium binding site 6 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:14.3 occ:1.00 O A:HOH1151 2.3 34.7 1.0 O B:HOH1153 2.3 20.4 1.0 O B:HOH1150 2.4 16.1 1.0 O A:HOH1157 2.4 22.3 1.0 O A:HOH1154 2.4 22.7 1.0 O B:HOH1156 2.5 10.5 1.0 O A:HOH1155 2.5 23.5 1.0 O A:HOH1152 2.8 36.3 1.0 O B:HOH1043 3.9 14.7 1.0 OP1 A:DT5 4.1 16.5 1.0 O B:HOH1020 4.5 10.5 1.0 O A:HOH1092 4.5 28.5 1.0 O A:HOH1072 4.6 25.4 1.0 OP1 B:DG20 4.8 9.2 1.0 O A:HOH1058 5.0 26.9 1.0

Calcium binding site 7 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:14.7 occ:1.00 O B:HOH1122 2.3 33.9 1.0 OP1 B:DA18 2.3 7.5 0.5 O B:HOH1123 2.4 13.8 1.0 O B:HOH1120 2.4 15.3 1.0 O B:HOH1121 2.5 14.5 1.0 O B:HOH1119 2.6 33.6 1.0 OP1 B:DA18 3.3 16.8 0.5 P B:DA18 3.7 7.3 0.5 O B:HOH1021 4.1 15.4 1.0 C5' B:DA18 4.1 8.3 0.5 C5' B:DA18 4.2 11.0 0.5 O3' B:DA17 4.3 8.7 0.5 O5' B:DA18 4.4 7.5 0.5 O3' B:DA17 4.4 10.5 0.5 P B:DA18 4.4 13.7 0.5 O A:HOH1091 4.8 26.2 1.0 O5' B:DA18 4.8 11.2 0.5 OP2 B:DA18 4.9 9.3 0.5

Calcium binding site 8 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:11.3 occ:0.51 CA B:CA303 0.0 11.3 0.5 CA B:CA303 1.1 10.7 0.5 O B:HOH1126 2.2 16.3 1.0 OP1 B:DA19 2.3 10.2 1.0 O B:HOH1124 2.8 31.5 1.0 O B:HOH1125 3.1 14.7 1.0 P B:DA19 3.5 8.4 1.0 O3' B:DA18 3.6 9.5 0.5 O3' B:DA18 3.7 8.6 0.5 O B:HOH1078 4.0 31.2 1.0 O A:HOH1028 4.3 12.8 1.0 OP2 B:DA19 4.5 12.2 1.0 O5' B:DA19 4.6 7.5 1.0 C5' B:DA19 4.7 7.3 1.0 O B:HOH1063 4.8 23.4 1.0 C3' B:DA18 4.9 8.8 0.5 C3' B:DA18 4.9 9.7 0.5

Calcium binding site 9 out of 9 in the The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:10.7 occ:0.49 CA B:CA303 0.0 10.7 0.5 CA B:CA303 1.1 11.3 0.5 O B:HOH1125 2.3 14.7 1.0 O B:HOH1124 2.4 31.5 1.0 OP1 B:DA19 2.5 10.2 1.0 O B:HOH1126 2.6 16.3 1.0 O3' B:DA18 3.1 9.5 0.5 O3' B:DA18 3.1 8.6 0.5 P B:DA19 3.5 8.4 1.0 O A:HOH1028 4.1 12.8 1.0 C3' B:DA18 4.3 8.8 0.5 C3' B:DA18 4.3 9.7 0.5 C4' B:DA18 4.5 8.5 0.5 C5' B:DA19 4.5 7.3 1.0 O5' B:DA19 4.5 7.5 1.0 OP2 B:DA19 4.6 12.2 1.0 C4' B:DA18 4.6 9.5 0.5 O B:HOH1078 4.7 31.2 1.0 O B:HOH1027 4.8 11.2 1.0 C5' B:DA18 4.9 8.3 0.5

G.W.Han, D.Langs, M.L.Kopka, R.E.Dickerson. The Ultra-High Resolution Structure of D(Cttttaaaag)2: Modulation of Bending By T-A Steps and Its Role in Dna Recognition To Be Published.