Magnesium in PDB 3saf: Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3saf was solved by K.Januszyk, Q.Liu, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.74 / 2.50
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	138.900, 138.900, 58.400, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site also contains other interesting chemical elements:

Yttrium

(Y)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site (pdb code 3saf). 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 the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3saf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


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 the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2 b:59.5 occ:1.00 O A:HOH38 2.5 54.6 1.0 O A:HOH31 2.6 54.9 1.0 O A:HOH74 2.6 63.8 1.0 OD1 A:ASN313 2.6 40.9 1.0 CG A:ASN313 3.7 41.4 1.0 OD2 A:ASP371 3.7 59.1 1.0 O A:HIS366 3.9 51.1 1.0 ND2 A:ASN313 4.2 41.4 1.0 O A:GLY367 4.2 51.0 1.0 OD1 A:ASP371 4.5 62.4 1.0 O A:HOH5 4.5 35.7 1.0 CG A:ASP371 4.6 58.8 1.0 O A:HOH36 4.6 45.5 1.0 O A:LEU314 4.9 43.0 1.0 CB A:ASN313 5.0 39.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


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 the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:74.0 occ:1.00 O B:HOH647 2.0 87.1 1.0 O B:HOH648 2.0 46.5 1.0 O B:HOH165 2.4 59.6 1.0 OD1 B:ASN313 2.8 35.9 1.0 O B:HIS366 3.5 40.1 1.0 OD1 B:ASP371 3.7 57.2 1.0 O B:HOH168 3.7 54.9 1.0 O B:GLY367 3.7 42.2 1.0 CG B:ASN313 4.0 35.1 1.0 OD2 B:ASP371 4.1 54.2 1.0 O B:HOH46 4.2 33.4 1.0 CG B:ASP371 4.3 52.1 1.0 O B:HOH9 4.6 42.1 1.0 C B:HIS366 4.6 40.9 1.0 ND2 B:ASN313 4.6 36.5 1.0 C B:GLY367 4.7 42.0 1.0 O B:LEU314 4.8 39.9 1.0

K.Januszyk, Q.Liu, C.D.Lima. Activities of Human RRP6 and Structure of the Human RRP6 Catalytic Domain. Rna V. 17 1566 2011.
ISSN: ISSN 1355-8382
PubMed: 21705430
DOI: 10.1261/RNA.2763111