Calcium in PDB 3bse: Crystal Structure Analysis of A 16-Base-Pair B-Dna

The structure of Crystal Structure Analysis of A 16-Base-Pair B-Dna, PDB code: 3bse was solved by N.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	38.740, 38.740, 161.327, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 27.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of A 16-Base-Pair B-Dna (pdb code 3bse). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure Analysis of A 16-Base-Pair B-Dna, PDB code: 3bse:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca37 b:15.7 occ:1.00 O B:HOH71 2.4 14.9 1.0 O B:HOH196 2.9 30.6 1.0 O A:HOH55 4.4 10.4 1.0 O4' B:DG24 4.5 14.1 1.0 O2 B:DT23 4.6 15.6 1.0 O B:HOH99 4.7 20.1 1.0 C4' B:DG24 4.7 13.6 1.0 N3 A:DA17 4.8 9.4 1.0 O4' A:DT18 4.9 10.9 1.0 C5' A:DT18 5.0 10.1 1.0 C4' A:DT18 5.0 12.0 1.0

Calcium binding site 2 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca38 b:15.1 occ:1.00 O A:HOH86 2.4 17.2 1.0 O A:HOH195 2.9 26.2 1.0 O B:HOH56 4.4 12.8 1.0 O4' A:DA6 4.4 12.8 1.0 O2 A:DT5 4.5 17.8 1.0 C4' A:DA6 4.6 12.4 1.0 N2 B:DG35 4.7 13.4 1.0 N3 B:DG35 4.7 10.5 1.0 C5' A:DA6 5.0 13.5 1.0

Calcium binding site 3 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca39 b:15.7 occ:1.00 O B:HOH76 2.4 14.8 1.0 O A:HOH131 2.5 19.4 1.0 O A:HOH152 2.5 20.9 1.0 O A:HOH58 2.6 21.9 1.0 O B:HOH72 2.6 22.7 1.0 O A:HOH81 2.6 28.6 1.0 O A:HOH141 2.8 27.7 1.0 O A:HOH104 4.3 18.7 1.0 O4' A:DC15 4.6 12.5 1.0 N2 A:DG14 4.6 11.9 1.0 O A:HOH157 4.6 37.5 1.0 C4' A:DC15 4.6 13.6 1.0 C5' B:DA27 4.6 16.7 1.0 C4' B:DA27 4.6 16.7 1.0 O4' B:DA27 4.6 16.0 1.0 O B:HOH189 4.7 26.9 1.0 C5' A:DC15 4.7 15.2 1.0 O A:HOH108 4.8 20.5 1.0 O A:HOH135 4.8 24.8 1.0 N3 A:DG14 4.9 14.7 1.0 N3 B:DA26 5.0 8.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca41 b:10.1 occ:0.33 OP1 A:DA8 2.3 10.2 1.0 O A:HOH54 2.3 9.4 1.0 P A:DA8 3.6 11.2 1.0 C5' A:DA8 4.0 12.7 1.0 O5' A:DA8 4.1 11.5 1.0 C5' A:DC7 4.4 11.0 1.0 OP2 A:DA8 4.4 11.2 1.0 C4' A:DC7 4.7 11.8 1.0 O A:HOH140 4.8 28.2 1.0 O3' A:DC7 4.8 11.1 1.0 OP1 A:DC7 5.0 15.3 1.0 C3' A:DC7 5.0 12.0 1.0

Calcium binding site 5 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca42 b:10.1 occ:0.33 OP2 A:DA8 2.4 11.2 1.0 O A:HOH75 2.5 18.9 1.0 P A:DA8 3.5 11.2 1.0 O5' A:DA8 3.8 11.5 1.0 O A:HOH123 3.9 22.2 1.0 OP1 A:DA8 4.1 10.2 1.0 O3' A:DC7 4.8 11.1 1.0 C5' A:DA8 5.0 12.7 1.0

Calcium binding site 6 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca45 b:19.8 occ:0.33 OP1 A:DC4 2.3 7.1 1.0 O A:HOH68 2.4 10.4 1.0 P A:DC4 3.5 9.2 1.0 O A:HOH52 4.0 5.9 1.0 OP2 A:DC4 4.0 9.7 1.0 O5' A:DC4 4.2 9.9 1.0 C5' A:DC4 4.6 11.8 1.0 O A:HOH82 4.6 21.4 1.0 O3' A:DA3 4.7 8.5 1.0

Calcium binding site 7 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca47 b:30.3 occ:0.33 OP1 A:DT18 2.3 9.1 1.0 P A:DT18 3.6 8.6 1.0 O5' A:DT18 4.1 8.5 1.0 O A:HOH88 4.3 13.1 1.0 C5' A:DT18 4.4 10.1 1.0 O A:HOH50 4.4 7.3 1.0 OP2 A:DT18 4.4 8.5 1.0 O3' A:DA17 4.7 8.5 1.0

Calcium binding site 8 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca40 b:17.1 occ:1.00 O B:HOH132 2.4 20.6 1.0 O B:HOH138 2.4 16.3 1.0 O B:HOH59 2.4 20.2 1.0 O A:HOH69 2.5 16.4 1.0 O A:HOH66 2.6 25.8 1.0 O B:HOH74 2.7 19.4 1.0 O B:HOH111 4.3 21.2 1.0 O4' B:DT33 4.5 11.7 1.0 O B:HOH199 4.6 31.9 1.0 N2 B:DG32 4.6 14.6 1.0 C4' B:DT33 4.6 14.5 1.0 C4' A:DA9 4.6 15.8 1.0 O4' A:DA9 4.7 16.6 1.0 C5' B:DT33 4.7 16.4 1.0 C5' A:DA9 4.8 15.1 1.0 O B:HOH101 4.8 23.3 1.0 N3 B:DG32 4.8 15.3 1.0 N3 A:DA8 4.9 11.2 1.0 O B:HOH136 4.9 21.7 1.0

Calcium binding site 9 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca43 b:10.1 occ:0.33 OP2 B:DA26 2.4 11.4 1.0 O B:HOH172 2.6 16.5 1.0 P B:DA26 3.5 10.6 1.0 O5' B:DA26 3.7 12.2 1.0 O B:HOH125 3.9 28.0 1.0 OP1 B:DA26 4.1 11.4 1.0 O3' B:DC25 4.8 11.5 1.0 C5' B:DA26 4.9 12.7 1.0 CA B:CA44 4.9 10.1 0.3

Calcium binding site 10 out of 12 in the Crystal Structure Analysis of A 16-Base-Pair B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure Analysis of A 16-Base-Pair B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca44 b:10.1 occ:0.33 OP1 B:DA26 2.3 11.4 1.0 O B:HOH53 2.5 10.2 1.0 P B:DA26 3.6 10.6 1.0 C5' B:DA26 4.0 12.7 1.0 O5' B:DA26 4.1 12.2 1.0 OP2 B:DA26 4.3 11.4 1.0 C5' B:DC25 4.5 9.8 1.0 O B:HOH153 4.6 24.0 1.0 C4' B:DC25 4.7 10.6 1.0 O3' B:DC25 4.7 11.5 1.0 CA B:CA43 4.9 10.1 0.3 C3' B:DC25 5.0 11.0 1.0

N.Narayana, M.A.Weiss. Crystallographic Analysis of A Sex-Specific Enhancer Element: Sequence-Dependent Dna Structure, Hydration, and Dynamics J.Mol.Biol. V. 385 469 2009.
ISSN: ISSN 0022-2836
PubMed: 18992257
DOI: 10.1016/J.JMB.2008.10.041