Calcium in PDB 3fd2: Crystal Structure of Mmsoi/Dna Complex with Calcium

The structure of Crystal Structure of Mmsoi/Dna Complex with Calcium, PDB code: 3fd2 was solved by H.Li, R.J.Monnat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.932, 41.933, 70.960, 107.21, 95.43, 109.44
R / Rfree (%)	21.1 / 28.1

The binding sites of Calcium atom in the Crystal Structure of Mmsoi/Dna Complex with Calcium (pdb code 3fd2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Mmsoi/Dna Complex with Calcium, PDB code: 3fd2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Mmsoi/Dna Complex with Calcium


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 Mmsoi/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca374 b:57.9 occ:1.00 OP2 B:DG515 2.2 70.1 1.0 OP1 C:DC564 2.3 73.8 1.0 O A:GLY21 2.3 48.8 1.0 O A:HOH386 2.6 31.4 1.0 OD2 A:ASP225 2.6 46.5 1.0 OD1 A:ASP225 2.8 47.4 1.0 O A:HOH394 2.8 61.5 1.0 CG A:ASP225 3.1 47.6 1.0 P B:DG515 3.2 70.7 1.0 OP1 B:DG515 3.5 70.5 1.0 C A:GLY21 3.5 48.5 1.0 P C:DC564 3.6 73.3 1.0 O B:HOH34 3.8 45.5 1.0 O3' C:DA563 3.8 73.0 1.0 OE1 A:GLN253 4.0 56.6 1.0 O5' B:DG515 4.0 71.1 1.0 C5' B:DG515 4.2 71.7 1.0 CA A:GLY21 4.2 48.4 1.0 O A:ASP20 4.5 47.3 1.0 N A:ASP22 4.5 48.6 1.0 O3' B:DA514 4.6 71.4 1.0 OP2 C:DC564 4.6 73.9 1.0 CB A:ASP225 4.6 47.7 1.0 NE2 A:GLN253 4.7 55.6 1.0 C5' C:DC564 4.7 72.6 1.0 O5' C:DC564 4.7 72.9 1.0 OD2 A:ASP22 4.7 50.6 1.0 CD A:GLN253 4.7 55.5 1.0 CA A:ASP22 4.7 48.7 1.0 C4' B:DG515 4.8 70.6 1.0 C4' C:DC564 4.8 72.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Mmsoi/Dna Complex with Calcium


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 Mmsoi/Dna Complex with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca375 b:50.7 occ:1.00 OP2 C:DG565 2.2 71.0 1.0 OP1 B:DA514 2.3 73.3 1.0 OD1 A:ASP22 2.4 50.5 1.0 O A:GLY224 2.4 47.8 1.0 O A:HOH395 2.5 57.4 1.0 O A:HOH383 2.6 34.5 1.0 OD2 A:ASP22 2.7 50.6 1.0 CG A:ASP22 2.9 49.7 1.0 O B:HOH34 3.3 45.5 1.0 C A:GLY224 3.5 47.7 1.0 P C:DG565 3.6 71.3 1.0 P B:DA514 3.6 73.4 1.0 OE1 A:GLN50 3.9 55.0 1.0 O3' B:DG513 3.9 73.4 1.0 CA A:GLY224 4.1 47.5 1.0 NE2 A:GLN50 4.3 53.3 1.0 OP1 C:DG565 4.3 72.2 1.0 C5' B:DA514 4.4 72.5 1.0 O5' C:DG565 4.4 70.6 1.0 O A:ASP223 4.4 46.8 1.0 CB A:ASP22 4.4 48.7 1.0 C4' B:DA514 4.5 71.9 1.0 CD A:GLN50 4.5 54.1 1.0 O5' B:DA514 4.5 72.6 1.0 N A:ASP225 4.6 47.8 1.0 C5' C:DG565 4.6 70.1 1.0 O3' C:DC564 4.6 71.7 1.0 OP2 B:DA514 4.7 73.7 1.0 CA A:ASP225 4.9 47.8 1.0 OD1 A:ASP225 4.9 47.4 1.0

H.Li, S.Pellenz, U.Ulge, B.L.Stoddard, R.J.Monnat. Generation of Single-Chain Laglidadg Homing Endonucleases From Native Homodimeric Precursor Proteins. Nucleic Acids Res. V. 37 1650 2009.
ISSN: ISSN 0305-1048
PubMed: 19153140
DOI: 10.1093/NAR/GKP004