Calcium in PDB 1sgs: Crystal Structure of A Free Kb Dna

The structure of Crystal Structure of A Free Kb Dna, PDB code: 1sgs was solved by D.B.Huang, C.B.Phelps, A.J.Fusco, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.37 / 1.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	38.916, 38.916, 158.910, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 21.8

The binding sites of Calcium atom in the Crystal Structure of A Free Kb Dna (pdb code 1sgs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A Free Kb Dna, PDB code: 1sgs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:17.4 occ:0.33 O A:HOH297 2.2 19.4 1.0 OP1 A:DC3 2.4 15.9 1.0 P A:DC3 3.6 16.4 1.0 OP2 A:DC3 4.0 16.9 1.0 O5' A:DC3 4.2 15.9 1.0 O A:HOH211 4.5 31.9 1.0 C5' A:DC3 4.6 17.4 1.0 O3' A:DG2 4.9 15.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:16.9 occ:0.33 O A:HOH298 2.2 19.4 1.0 OP1 A:DA7 2.5 17.1 1.0 P A:DA7 3.8 16.8 1.0 C5' A:DA7 4.0 17.3 1.0 O5' A:DA7 4.2 17.5 1.0 C5' A:DG6 4.4 18.7 1.0 O A:HOH285 4.4 38.2 1.0 OP2 A:DA7 4.6 17.5 1.0 O A:HOH235 4.7 33.4 1.0 C4' A:DG6 4.7 17.7 1.0 O3' A:DG6 4.9 17.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:19.2 occ:0.33 O A:HOH299 2.3 21.5 1.0 OP2 A:DA7 2.4 17.5 1.0 P A:DA7 3.6 16.8 1.0 O5' A:DA7 3.9 17.5 1.0 O A:HOH217 4.2 27.3 1.0 OP1 A:DA7 4.3 17.1 1.0 O3' A:DG6 4.9 17.0 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:14.2 occ:0.33 O A:HOH300 2.2 13.7 1.0 OP1 A:DC17 2.4 14.8 1.0 P A:DC17 3.7 15.3 1.0 O5' A:DC17 4.1 16.1 1.0 C5' A:DC17 4.3 16.6 1.0 O A:HOH229 4.4 17.0 1.0 OP2 A:DC17 4.4 15.9 1.0 O A:HOH245 4.5 19.2 1.0 O3' A:DG16 4.8 14.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:22.6 occ:1.00 O A:HOH302 2.2 40.2 1.0 O A:HOH301 2.3 16.9 1.0 OP1 A:DG16 2.3 17.2 1.0 O A:HOH304 2.4 25.8 1.0 O A:HOH305 2.4 22.7 1.0 O A:HOH303 2.6 36.3 1.0 P A:DG16 3.5 17.2 1.0 OP2 A:DG16 4.1 18.8 1.0 O5' A:DG16 4.2 15.4 1.0 C5' A:DG16 4.3 15.4 1.0 O A:HOH245 4.5 19.2 1.0 O A:HOH228 4.7 21.3 1.0 O3' A:DA15 4.8 16.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of A Free Kb 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 of A Free Kb Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:26.1 occ:0.50 O A:HOH312 1.9 15.4 0.5 O A:HOH309 2.0 35.0 0.5 O A:HOH313 2.2 17.6 0.5 O A:HOH311 2.3 25.0 0.5 O A:HOH307 2.4 37.6 0.5 O A:HOH308 2.5 33.3 0.5 O A:HOH310 2.6 19.8 0.5 O A:HOH276 4.2 33.0 1.0 O A:HOH243 4.5 38.3 1.0 O4' A:DC14 4.5 21.5 1.0 C4' A:DC14 4.6 22.7 1.0 C5' A:DC14 4.8 25.2 1.0

D.B.Huang, C.B.Phelps, A.J.Fusco, G.Ghosh. Crystal Structure of A Free Kappab Dna: Insights Into Dna Recognition By Transcription Factor Nf-Kappab. J.Mol.Biol. V. 346 147 2005.
ISSN: ISSN 0022-2836
PubMed: 15663934
DOI: 10.1016/J.JMB.2004.11.042