Magnesium in PDB 1rvc: MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution

The structure of MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution, PDB code: 1rvc was solved by D.Kostrewa, F.K.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.290, 50.340, 63.880, 96.66, 108.76, 108.41
R / Rfree (%)	15.6 / n/a

The binding sites of Magnesium atom in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution (pdb code 1rvc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution, PDB code: 1rvc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:47.1 occ:1.00 OP1 D:DA7 1.8 36.4 1.0 O D:HOH184 2.1 31.3 1.0 O D:HOH299 2.1 45.5 1.0 O D:HOH240 2.2 28.3 1.0 O A:GLN69 2.4 33.4 1.0 O A:HOH486 2.4 21.5 1.0 P D:DA7 3.3 29.1 1.0 C A:GLN69 3.5 31.5 1.0 O A:HOH478 3.8 27.4 1.0 O B:HOH488 3.9 39.9 1.0 NZ B:LYS38 4.0 31.5 1.0 OP3 D:DA7 4.0 18.9 1.0 CA A:GLN69 4.0 31.6 1.0 O B:HOH482 4.0 63.9 1.0 OP2 D:DA7 4.2 40.7 1.0 O5' D:DA7 4.2 35.4 1.0 CE B:LYS38 4.5 29.3 1.0 O A:HIS71 4.5 25.4 1.0 CB A:GLN69 4.5 30.0 1.0 N A:ASN70 4.6 29.9 1.0 O D:HOH212 4.6 22.0 1.0 CD B:LYS38 4.6 32.5 1.0 C2' C:DT6 4.8 35.5 1.0 CA A:ASN70 4.9 34.1 1.0 N A:HIS71 4.9 27.1 1.0

Magnesium binding site 2 out of 4 in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:21.3 occ:1.00 OP1 F:DA7 1.9 19.5 1.0 O B:HOH476 1.9 19.0 1.0 O B:GLN69 2.1 23.9 1.0 O A:HOH483 2.2 18.7 1.0 O F:HOH126 2.3 22.2 1.0 O B:HOH460 2.3 19.8 1.0 P F:DA7 3.2 19.9 1.0 C B:GLN69 3.3 20.0 1.0 OP3 F:DA7 3.7 18.3 1.0 O5' F:DA7 3.9 17.6 1.0 O F:HOH275 4.0 21.0 1.0 CA B:ASN70 4.1 18.5 1.0 O B:HOH480 4.2 21.5 1.0 NZ A:LYS38 4.2 31.6 1.0 N B:ASN70 4.2 18.2 1.0 CA B:GLN69 4.2 20.1 1.0 OP2 F:DA7 4.4 13.6 1.0 C2' E:DT6 4.4 16.3 1.0 O A:HOH454 4.4 14.2 1.0 CE A:LYS38 4.6 25.2 1.0 CB B:GLN69 4.6 22.3 1.0 O B:HIS71 4.7 14.8 1.0 CD A:LYS38 4.7 33.4 1.0 N B:HIS71 4.7 19.8 1.0 OD2 A:ASP36 4.8 45.8 1.0 C1' E:DT6 4.8 15.5 1.0 C B:ASN70 4.9 19.3 1.0 O D:HOH82 5.0 25.2 1.0

Magnesium binding site 3 out of 4 in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:24.1 occ:1.00 OP2 D:DA7 1.9 40.7 1.0 O A:HOH487 2.0 23.9 1.0 O D:HOH153 2.1 23.9 1.0 OD1 A:ASP74 2.2 12.5 1.0 OE2 A:GLU45 2.3 33.5 1.0 OD2 A:ASP74 2.3 13.8 1.0 CG A:ASP74 2.6 13.5 1.0 CD A:GLU45 3.2 39.2 1.0 P D:DA7 3.2 29.1 1.0 OP3 D:DA7 3.5 18.9 1.0 OE1 A:GLU45 3.9 43.3 1.0 O A:ILE91 3.9 18.5 1.0 NZ B:LYS38 4.0 31.5 1.0 CG A:GLU45 4.0 35.8 1.0 O5' D:DA7 4.1 35.4 1.0 CB A:ASP74 4.1 11.8 1.0 O A:HOH484 4.1 37.3 1.0 C5' D:DA7 4.2 29.4 1.0 O B:HOH482 4.3 63.9 1.0 OP1 D:DA7 4.3 36.4 1.0 OD1 A:ASP90 4.3 18.5 1.0 O A:HOH478 4.5 27.4 1.0 O A:HOH443 4.6 19.6 1.0 N A:ILE91 4.6 15.4 1.0 C4' D:DA7 4.8 30.8 1.0 CB A:ILE91 4.8 19.8 1.0 C A:ILE91 4.9 17.1 1.0 NZ A:LYS92 4.9 38.4 1.0 CG A:ASP90 4.9 18.9 1.0 CA A:ASP74 4.9 15.0 1.0

Magnesium binding site 4 out of 4 in the MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of MG2+ Binding to the Active Site of Eco Rv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:14.8 occ:1.00 OE2 B:GLU45 2.0 26.3 1.0 O B:HOH481 2.0 15.2 1.0 OP2 F:DA7 2.0 13.6 1.0 O F:HOH291 2.1 12.2 1.0 OD1 B:ASP74 2.2 11.8 1.0 OD2 B:ASP74 2.2 11.5 1.0 CG B:ASP74 2.5 12.0 1.0 CD B:GLU45 3.2 33.8 1.0 P F:DA7 3.3 19.9 1.0 OP3 F:DA7 3.6 18.3 1.0 OE1 B:GLU45 3.9 41.6 1.0 O B:ILE91 4.0 15.5 1.0 O B:HOH442 4.0 33.0 1.0 CB B:ASP74 4.0 7.6 1.0 CG B:GLU45 4.2 29.6 1.0 O B:HOH484 4.2 35.3 1.0 NZ A:LYS38 4.2 31.6 1.0 OD1 B:ASP90 4.2 18.9 1.0 OP1 F:DA7 4.3 19.5 1.0 O B:HOH480 4.4 21.5 1.0 O5' F:DA7 4.4 17.6 1.0 C5' F:DA7 4.4 17.9 1.0 N B:ILE91 4.5 14.1 1.0 O B:HOH429 4.6 24.8 1.0 CB B:ILE91 4.8 19.7 1.0 CA B:ASP74 4.8 14.2 1.0 C B:ILE91 4.8 13.5 1.0 CG B:ASP90 4.9 20.1 1.0 CA B:ILE91 4.9 13.4 1.0

D.Kostrewa, F.K.Winkler. MG2+ Binding to the Active Site of Ecorv Endonuclease: A Crystallographic Study of Complexes with Substrate and Product Dna at 2 A Resolution. Biochemistry V. 34 683 1995.
ISSN: ISSN 0006-2960
PubMed: 7819264
DOI: 10.1021/BI00002A036