Magnesium in PDB 1d2i: 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: 1d2i 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.800, 101.700, 116.900, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20

The binding sites of Magnesium atom in the Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer (pdb code 1d2i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Restriction Endonuclease Bglii Complexed with Dna 16-Mer, PDB code: 1d2i:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:22.6 occ:0.50 O A:VAL94 2.3 9.7 1.0 OP1 C:DG8 2.4 13.2 1.0 O A:HOH657 2.4 13.5 1.0 OD2 A:ASP84 2.4 13.6 1.0 O A:HOH729 2.4 25.2 1.0 O A:HOH625 2.7 15.2 1.0 P C:DG8 2.9 12.0 1.0 OP2 C:DG8 2.9 12.3 1.0 CG A:ASP84 3.3 13.8 1.0 C A:VAL94 3.4 9.3 1.0 O5' C:DG8 3.5 11.0 1.0 OD1 A:ASP84 3.6 14.5 1.0 N A:VAL94 4.0 10.1 1.0 O C:HOH195 4.0 10.6 1.0 O A:HOH670 4.1 21.9 1.0 NE2 A:GLN95 4.1 8.7 1.0 CA A:VAL94 4.2 9.6 1.0 CA A:GLN95 4.3 8.2 1.0 N A:GLN95 4.3 8.6 1.0 C5' C:DG8 4.4 9.1 1.0 O3' C:DA7 4.4 10.6 1.0 CB A:VAL94 4.5 9.2 1.0 CD A:GLN95 4.5 8.7 1.0 OE1 A:GLN95 4.5 8.9 1.0 O A:HOH710 4.6 23.1 1.0 OE1 A:GLU93 4.6 14.5 1.0 CB A:ASP84 4.7 13.9 1.0 OD1 A:ASN54 4.8 9.3 1.0 O C:HOH225 4.9 24.5 1.0 C A:GLU93 4.9 10.8 1.0 CB A:GLN95 5.0 8.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:26.9 occ:0.50 O B:VAL94 2.2 8.5 1.0 OP1 D:DG24 2.3 10.8 1.0 O D:HOH472 2.3 19.0 1.0 O B:HOH762 2.4 22.0 1.0 OD2 B:ASP84 2.5 10.9 1.0 O B:HOH653 2.8 19.5 1.0 P D:DG24 2.9 10.2 1.0 OP2 D:DG24 3.0 10.1 1.0 C B:VAL94 3.4 8.2 1.0 CG B:ASP84 3.4 10.2 1.0 O5' D:DG24 3.5 9.6 1.0 OD1 B:ASP84 3.5 11.7 1.0 O D:HOH463 3.8 8.1 1.0 N B:VAL94 4.0 8.6 1.0 NE2 B:GLN95 4.1 6.9 1.0 CA B:VAL94 4.2 8.1 1.0 CA B:GLN95 4.3 6.8 1.0 N B:GLN95 4.3 7.1 1.0 C5' D:DG24 4.3 8.3 1.0 O3' D:DA23 4.4 9.6 1.0 CD B:GLN95 4.5 7.3 1.0 O B:HOH695 4.5 18.9 1.0 CB B:VAL94 4.5 8.3 1.0 OE1 B:GLN95 4.5 7.4 1.0 OE1 B:GLU93 4.7 13.1 1.0 OD1 B:ASN54 4.7 7.7 1.0 O B:HOH741 4.8 21.6 1.0 CB B:ASP84 4.8 10.1 1.0 CB B:GLN95 4.9 6.7 1.0 O D:HOH466 5.0 14.8 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