Calcium in PDB 2fld: I-Msoi Re-Designed For Altered Dna Cleavage Specificity

The structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity, PDB code: 2fld was solved by J.Ashworth, C.M.Duarte, J.J.Havranek, D.Sussman, R.J.Monnat, B.L.Stoddard, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.50 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.961, 42.981, 71.545, 72.29, 72.30, 70.51
R / Rfree (%)	22.9 / 27.1

The structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (pdb code 2fld). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity, PDB code: 2fld:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:26.2 occ:1.00 OP1 C:DA514 2.3 31.8 1.0 O B:HOH9 2.3 21.0 1.0 OD2 A:ASP22 2.4 21.5 1.0 OP2 D:DG565 2.4 30.0 1.0 O B:GLY221 2.5 27.8 1.0 OD1 A:ASP22 2.8 25.2 1.0 CG A:ASP22 2.9 25.4 1.0 C B:GLY221 3.5 25.2 1.0 P C:DA514 3.7 31.1 1.0 P D:DG565 3.7 26.4 1.0 NA C:NA603 3.8 31.0 1.0 CA B:GLY221 3.9 24.2 1.0 O B:ASP220 4.0 23.6 1.0 OE1 A:GLN50 4.0 35.3 1.0 NE2 A:GLN50 4.1 27.6 1.0 O3' C:DG513 4.2 32.0 1.0 O5' D:DG565 4.3 25.6 1.0 C5' D:DG565 4.3 25.6 1.0 CB A:ASP22 4.4 24.6 1.0 CD A:GLN50 4.5 30.6 1.0 OP1 D:DG565 4.5 29.6 1.0 OP2 C:DA514 4.6 29.6 1.0 N B:ASP222 4.6 27.2 1.0 C5' C:DA514 4.6 28.7 1.0 O5' C:DA514 4.7 30.1 1.0 C4' C:DA514 4.7 27.1 1.0 C B:ASP220 4.8 24.2 1.0 O3' D:DC564 4.9 26.5 1.0 N B:GLY221 4.9 24.0 1.0

Calcium binding site 2 out of 2 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:28.0 occ:1.00 O A:HOH607 2.2 33.1 1.0 OP1 D:DC564 2.2 37.5 1.0 OP2 C:DG515 2.4 29.3 1.0 O C:HOH34 2.4 25.8 1.0 O A:GLY21 2.5 25.3 1.0 OD2 B:ASP222 2.6 20.5 1.0 OD1 B:ASP222 2.8 26.4 1.0 CG B:ASP222 3.0 24.4 1.0 P D:DC564 3.5 35.8 1.0 C A:GLY21 3.6 23.0 1.0 NA C:NA603 3.6 31.0 1.0 P C:DG515 3.6 28.2 1.0 O3' D:DA563 3.9 36.0 1.0 OE1 B:GLN250 4.2 32.1 1.0 CA A:GLY21 4.2 23.4 1.0 OP1 C:DG515 4.2 30.0 1.0 NE2 B:GLN250 4.3 32.6 1.0 O5' C:DG515 4.3 29.4 1.0 OP2 D:DC564 4.3 33.8 1.0 C5' C:DG515 4.4 29.9 1.0 O A:HOH626 4.4 56.9 1.0 O A:ASP20 4.4 22.7 1.0 CB B:ASP222 4.5 26.8 1.0 CD B:GLN250 4.6 32.0 1.0 O5' D:DC564 4.7 28.9 1.0 N A:ASP22 4.7 23.4 1.0 C4' D:DC564 4.7 27.6 1.0 C5' D:DC564 4.8 29.1 1.0 O3' C:DA514 4.9 30.9 1.0 NZ B:LYS254 5.0 45.2 1.0

J.Ashworth, J.J.Havranek, C.M.Duarte, D.Sussman, R.J.Monnat, B.L.Stoddard, D.Baker. Computational Redesign of Endonuclease Dna Binding and Cleavage Specificity. Nature V. 441 656 2006.
ISSN: ISSN 0028-0836
PubMed: 16738662
DOI: 10.1038/NATURE04818