Calcium in PDB 1dfm: Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer

The structure of Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer, PDB code: 1dfm was solved by C.M.Lukacs, R.Kucera, I.Schildkraut, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.700, 101.800, 116.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.4

The binding sites of Calcium atom in the Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer (pdb code 1dfm). 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 Restriction Endonuclease Bglii Complexed with Dna 16-Mer, PDB code: 1dfm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer


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 Restriction Endonuclease Bglii Complexed with Dna 16-Mer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:24.4 occ:0.59 OP1 C:DG8 2.2 14.0 1.0 O A:VAL94 2.3 9.6 1.0 O A:HOH841 2.3 24.7 1.0 OD2 A:ASP84 2.3 13.6 1.0 O C:HOH30 2.3 11.5 1.0 O A:HOH722 2.7 14.8 1.0 P C:DG8 3.0 13.3 1.0 OP2 C:DG8 3.0 13.5 1.0 CG A:ASP84 3.3 13.7 1.0 C A:VAL94 3.4 8.8 1.0 OD1 A:ASP84 3.5 14.1 1.0 O5' C:DG8 3.6 11.5 1.0 N A:VAL94 3.9 9.4 1.0 O C:HOH22 4.1 7.7 1.0 NE2 A:GLN95 4.1 7.8 1.0 O A:HOH782 4.1 24.5 1.0 CA A:VAL94 4.2 9.3 1.0 N A:GLN95 4.3 8.0 1.0 CA A:GLN95 4.3 7.4 1.0 C5' C:DG8 4.3 9.3 1.0 O3' C:DA7 4.4 11.5 1.0 CD A:GLN95 4.5 7.2 1.0 CB A:VAL94 4.5 9.4 1.0 O A:HOH807 4.5 22.9 1.0 OE1 A:GLN95 4.6 7.2 1.0 OE1 A:GLU93 4.6 12.9 1.0 CB A:ASP84 4.7 13.9 1.0 OD1 A:ASN54 4.8 8.0 1.0 O C:HOH39 4.8 20.2 1.0 C A:GLU93 4.9 10.2 1.0 CB A:GLN95 5.0 7.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer


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 Restriction Endonuclease Bglii Complexed with Dna 16-Mer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:30.9 occ:0.55 O B:VAL94 2.2 9.2 1.0 OP1 D:DG24 2.2 10.5 1.0 O D:HOH48 2.2 15.3 1.0 OD2 B:ASP84 2.5 10.7 1.0 O B:HOH856 2.5 21.5 1.0 O B:HOH768 2.9 16.6 1.0 P D:DG24 2.9 9.6 1.0 OP2 D:DG24 3.1 9.4 1.0 C B:VAL94 3.3 8.2 1.0 CG B:ASP84 3.4 10.1 1.0 OD1 B:ASP84 3.5 11.1 1.0 O5' D:DG24 3.5 8.5 1.0 O D:HOH41 3.8 7.1 1.0 N B:VAL94 4.0 7.6 1.0 CA B:VAL94 4.2 7.9 1.0 NE2 B:GLN95 4.2 7.9 1.0 C5' D:DG24 4.2 7.6 1.0 N B:GLN95 4.3 7.5 1.0 CA B:GLN95 4.3 6.8 1.0 CB B:VAL94 4.4 7.8 1.0 O3' D:DA23 4.4 9.0 1.0 O B:HOH806 4.5 20.1 1.0 CD B:GLN95 4.6 7.5 1.0 OD1 B:ASN54 4.6 6.9 1.0 OE1 B:GLN95 4.7 7.4 1.0 O B:HOH848 4.7 25.4 1.0 OE1 B:GLU93 4.8 11.9 1.0 CB B:ASP84 4.8 9.2 1.0 C B:GLU93 5.0 8.0 1.0 CB B:GLN95 5.0 7.2 1.0

C.M.Lukacs, R.Kucera, I.Schildkraut, A.K.Aggarwal. Understanding the Immutability of Restriction Enzymes: Crystal Structure of Bglii and Its Dna Substrate at 1.5 A Resolution. Nat.Struct.Biol. V. 7 134 2000.
ISSN: ISSN 1072-8368
PubMed: 10655616
DOI: 10.1038/72405