Calcium in PDB 3i5l: Allosteric Modulation of Dna By Small Molecules

The structure of Allosteric Modulation of Dna By Small Molecules, PDB code: 3i5l was solved by D.M.Chenoweth, P.B.Dervan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.47 / 1.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	22.500, 25.140, 29.090, 66.53, 79.28, 79.57
R / Rfree (%)	9.9 / 13.8

The structure of Allosteric Modulation of Dna By Small Molecules also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Calcium atom in the Allosteric Modulation of Dna By Small Molecules (pdb code 3i5l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Allosteric Modulation of Dna By Small Molecules, PDB code: 3i5l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:5.5 occ:1.00 O A:HOH116 2.4 7.1 1.0 O B:HOH137 2.4 7.3 1.0 O A:HOH117 2.4 7.4 1.0 O A:HOH427 2.4 5.8 1.0 O A:HOH191 2.4 8.1 1.0 O6 A:DG10 2.5 5.1 1.0 C6 A:DG10 3.5 5.4 1.0 N4 B:DC1 4.0 4.1 0.5 N7 A:DG10 4.2 5.9 1.0 C5 A:DG10 4.2 5.8 1.0 N4 B:DC1 4.3 3.7 0.5 N7 A:DG9 4.4 4.9 1.0 O A:HOH218 4.5 16.5 1.0 O A:HOH161 4.5 14.3 1.0 O A:HOH138 4.6 8.9 1.0 N1 A:DG10 4.6 4.8 1.0 O B:HOH240 4.7 24.4 1.0 O A:HOH144 4.8 12.3 1.0 C8 A:DG9 4.9 5.3 1.0 C4 B:DC1 4.9 3.4 0.5

Calcium binding site 2 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:5.9 occ:1.00 O B:HOH141 2.2 18.8 1.0 OP2 B:DT8 2.3 6.4 1.0 O B:HOH120 2.3 11.8 1.0 O B:HOH114 2.4 10.4 1.0 O B:HOH166 2.4 9.4 1.0 P B:DT8 3.6 4.8 1.0 OP1 B:DT8 4.1 6.9 1.0 O B:HOH260 4.3 17.7 1.0 O3' B:DC7 4.3 5.0 1.0 O B:HOH267 4.3 18.1 1.0 C3' B:DC7 4.4 4.5 1.0 O B:HOH160 4.5 10.4 1.0 O B:HOH147 4.5 8.8 1.0 O5' B:DT8 4.7 4.5 1.0 O B:HOH305 4.9 24.0 1.0

Calcium binding site 3 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:5.1 occ:1.00 OP1 B:DA3 2.3 5.0 1.0 O B:HOH139 2.4 7.4 1.0 O B:HOH125 2.4 8.5 1.0 O B:HOH135 2.4 8.5 1.0 O B:HOH110 2.4 6.8 1.0 O B:HOH129 2.4 8.6 1.0 O B:HOH115 2.5 7.3 1.0 P B:DA3 3.8 4.3 1.0 O B:HOH121 4.4 8.9 1.0 C5' B:DA3 4.4 4.9 1.0 O5' B:DA3 4.5 4.5 1.0 O3' B:DC2 4.6 4.3 0.5 O B:HOH200 4.6 15.6 1.0 OP2 B:DA3 4.6 4.7 1.0 O B:HOH127 4.6 9.8 1.0 O B:HOH188 4.7 16.0 1.0 O3' B:DC2 4.7 4.3 0.5 O B:HOH393 4.7 20.9 1.0

Calcium binding site 4 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:23.8 occ:0.50 CA B:CA604 0.0 23.8 0.5 CA B:CA604 1.7 19.9 0.5 O B:HOH334 2.3 18.2 1.0 O B:HOH160 2.8 10.4 1.0 O2 B:1P1500 2.8 6.0 1.0 O B:HOH231 3.0 16.4 1.0 C8 B:1P1500 3.4 6.2 1.0 C5' B:DC7 3.7 5.4 1.0 C12 B:1P1500 3.9 4.3 1.0 C4' B:DC7 4.1 4.7 1.0 N3 B:1P1500 4.2 5.4 1.0 C7 B:1P1500 4.2 4.6 1.0 O B:HOH166 4.3 9.4 1.0 C9 B:1P1500 4.4 7.9 1.0 C15 B:1P1500 4.4 8.0 1.0 O B:HOH402 4.5 26.5 1.0 N4 B:1P1500 4.5 4.1 1.0 O B:HOH319 4.6 28.0 1.0 O B:HOH277 4.8 30.8 1.0 O3' B:DC7 4.8 5.0 1.0 OP1 B:DC7 4.9 6.8 1.0 O5' B:DC7 4.9 4.7 1.0 C3' B:DC7 5.0 4.5 1.0

Calcium binding site 5 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:19.9 occ:0.50 CA B:CA604 0.0 19.9 0.5 CA B:CA604 1.7 23.8 0.5 O B:HOH160 2.7 10.4 1.0 O B:HOH334 2.7 18.2 1.0 O A:HOH292 3.5 28.6 1.0 O B:HOH319 3.9 28.0 1.0 C9 B:1P1500 3.9 7.9 1.0 C8 B:1P1500 4.0 6.2 1.0 O2 B:1P1500 4.1 6.0 1.0 O B:HOH231 4.2 16.4 1.0 O B:HOH221 4.2 20.6 1.0 N3 B:1P1500 4.3 5.4 1.0 O B:HOH402 4.4 26.5 1.0 O B:HOH166 4.6 9.4 1.0

Calcium binding site 6 out of 6 in the Allosteric Modulation of Dna By Small Molecules


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Allosteric Modulation of Dna By Small Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca605 b:10.1 occ:1.00 OP1 B:DT8 2.3 6.9 1.0 O B:HOH206 2.3 18.3 1.0 O B:HOH212 2.3 19.1 1.0 O B:HOH173 2.3 20.1 1.0 O B:HOH126 2.4 11.2 1.0 O B:HOH221 2.5 20.6 1.0 P B:DT8 3.7 4.8 1.0 O B:HOH114 4.1 10.4 1.0 O5' B:DT8 4.2 4.5 1.0 C5' B:DT8 4.2 5.4 1.0 O B:HOH333 4.3 19.1 1.0 O B:HOH211 4.5 17.3 1.0 O B:HOH201 4.5 11.7 1.0 O B:HOH160 4.5 10.4 1.0 OP2 B:DT8 4.5 6.4 1.0 O3' B:DC7 4.6 5.0 1.0 O B:HOH255 4.6 25.9 1.0 O B:HOH260 4.7 17.7 1.0 C9 B:1P1500 4.9 7.9 1.0 O1 B:1P1500 4.9 5.3 1.0

D.M.Chenoweth, P.B.Dervan. Allosteric Modulation of Dna By Small Molecules Proc.Natl.Acad.Sci.Usa V. 106 13175 2009.
ISSN: ISSN 0027-8424
PubMed: 19666554
DOI: 10.1073/PNAS.0906532106