Calcium in PDB 4r49: Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex

The structure of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49 was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.25 / 1.28
Space group	P -1
Cell size a, b, c (Å), α, β, γ (°)	23.263, 33.604, 36.820, 103.32, 101.02, 109.78
R / Rfree (%)	21.7 / 26

The structure of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex (pdb code 4r49). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex, PDB code: 4r49:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:8.8 occ:1.00 O A:HOH201 2.3 10.0 1.0 O A:HOH217 2.4 9.9 1.0 O A:HOH209 2.4 10.7 1.0 O A:HOH202 2.5 9.7 1.0 O A:HOH203 2.5 10.3 1.0 OP1 A:DA6 4.3 14.2 1.0 O A:HOH258 4.3 15.7 0.7 O A:HOH207 4.5 11.0 0.8 O A:HOH212 4.7 10.9 0.9 OP2 A:DC7 4.7 11.8 1.0 O A:HOH257 4.8 17.7 1.0 O5' A:DA6 4.8 13.5 1.0 P A:DA6 5.0 12.9 1.0

Calcium binding site 2 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:10.2 occ:1.00 O A:HOH295 2.3 33.6 1.0 OP1 A:DT5 2.3 9.8 1.0 O A:HOH216 2.4 10.8 0.9 O A:HOH205 2.4 15.1 1.0 O A:HOH208 2.4 13.2 1.0 P A:DT5 3.6 9.2 1.0 O5' A:DT5 4.2 9.4 1.0 C5' A:DT5 4.3 9.0 1.0 OP2 A:DT5 4.3 11.0 1.0 O A:HOH264 4.3 32.2 0.5 O A:HOH279 4.4 34.1 1.0 O A:HOH274 4.5 25.0 1.0 O A:HOH271 4.7 18.4 1.0 O3' A:DG4 4.8 8.2 1.0

Calcium binding site 3 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:13.2 occ:0.84 O A:HOH233 2.3 17.6 0.6 O A:HOH214 2.4 12.6 1.0 O A:HOH243 2.4 22.9 0.7 O A:HOH239 2.4 22.0 0.7 O A:HOH238 2.5 17.3 0.7 N4 B:DC7 4.1 8.9 1.0 O A:HOH227 4.5 14.6 0.7 O A:HOH261 4.7 28.3 0.8 O B:HOH255 4.7 23.2 0.7 O A:HOH262 4.7 21.8 0.6 N7 A:DG3 4.7 11.8 1.0 C6 A:DC2 4.9 11.0 1.0 O6 A:DG3 4.9 9.1 1.0

Calcium binding site 4 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:10.7 occ:1.00 OP1 B:DT5 2.3 10.3 1.0 O B:HOH216 2.4 13.0 1.0 O B:HOH261 2.5 23.0 1.0 P B:DT5 3.6 9.4 1.0 O5' B:DT5 4.2 9.4 1.0 OP2 B:DT5 4.3 11.4 1.0 O B:HOH240 4.3 21.1 0.6 C5' B:DT5 4.4 10.1 1.0 O B:HOH231 4.7 13.3 0.6 O3' B:DG4 4.8 9.2 1.0

Calcium binding site 5 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:12.3 occ:0.86 O B:HOH220 2.4 16.5 1.0 O B:HOH227 2.4 23.1 0.8 O B:HOH254 2.5 12.2 1.0 O B:HOH250 4.4 26.6 0.8 OP1 B:DG10 4.4 12.7 1.0 OP2 B:DG10 4.6 17.2 1.0 O B:HOH256 4.6 22.8 1.0 O B:HOH246 4.6 19.3 0.8

Calcium binding site 6 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:9.0 occ:1.00 O B:HOH203 2.4 10.2 1.0 O B:HOH201 2.5 10.7 1.0 O B:HOH205 2.5 11.7 1.0 OP1 B:DA6 4.2 28.3 1.0 O B:HOH207 4.5 11.9 0.9 O B:HOH217 4.7 12.5 1.0 OP2 B:DC7 4.7 11.1 1.0 O5' B:DA6 4.9 12.4 1.0 P B:DA6 4.9 16.9 1.0

Calcium binding site 7 out of 7 in the Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Racemic Crystal Structure of A Calcium-Bound B-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:14.2 occ:0.66 O B:HOH245 2.9 16.1 0.8 N4 B:DC8 3.3 8.3 1.0 O A:HOH234 3.4 21.9 0.9 O B:HOH248 3.4 16.8 0.6 C5 B:DC8 3.7 8.8 1.0 C6 B:DC7 3.8 8.6 1.0 N4 A:DC2 3.9 10.4 1.0 C4 B:DC8 4.0 7.6 1.0 O B:HOH263 4.0 33.9 1.0 C2' B:DC7 4.1 10.6 1.0 C5 B:DC7 4.2 8.3 1.0 O B:HOH207 4.3 11.9 0.9 N1 B:DC7 4.5 8.2 1.0 O6 B:DG9 4.6 10.1 1.0 C1' B:DC7 4.8 9.7 1.0 C6 B:DC8 5.0 9.7 1.0

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014