Magnesium in PDB 4qh0: Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound

The structure of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound, PDB code: 4qh0 was solved by A.F.Moon, P.Gaudu, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.85 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	123.721, 123.721, 157.403, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 19

The structure of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound (pdb code 4qh0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound, PDB code: 4qh0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:35.4 occ:1.00 O A:HOH401 2.1 21.9 1.0 O A:HOH403 2.1 23.6 1.0 O A:HOH593 2.1 26.3 1.0 O A:HOH404 2.1 30.5 1.0 O A:HOH402 2.1 24.9 1.0 OD1 A:ASN179 2.1 29.7 1.0 CG A:ASN179 3.3 25.1 1.0 OE1 A:GLU193 3.9 24.7 1.0 ND2 A:ASN179 3.9 22.8 1.0 OD1 A:ASN190 3.9 39.8 1.0 OE2 A:GLU193 4.0 21.0 1.0 O A:ASN179 4.1 25.6 1.0 N A:ALA148 4.2 22.8 1.0 O A:HOH460 4.3 43.0 1.0 OE1 A:GLN174 4.3 24.0 1.0 O A:ALA148 4.3 25.0 1.0 O A:HOH407 4.4 27.9 1.0 O A:HOH434 4.4 28.8 1.0 CD A:GLU193 4.4 20.4 1.0 CB A:ASN179 4.5 18.6 1.0 NE2 A:GLN189 4.6 23.1 1.0 O A:HOH482 4.6 38.5 1.0 CB A:ALA148 4.7 19.2 1.0 CA A:ASN179 4.7 24.0 1.0 C A:ASN179 4.7 24.9 1.0 CA A:GLY147 4.8 26.0 1.0 CA A:ALA148 4.9 21.6 1.0 CD A:GLN189 4.9 19.7 1.0 O A:LYS146 4.9 28.4 1.0 C A:GLY147 4.9 23.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


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 Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:35.0 occ:1.00 O B:HOH409 2.1 22.0 1.0 O B:HOH591 2.1 24.2 1.0 O B:HOH531 2.1 35.0 1.0 O B:HOH402 2.1 24.9 1.0 O B:HOH412 2.1 26.7 1.0 OD1 B:ASN179 2.1 27.8 1.0 CG B:ASN179 3.3 26.1 1.0 OE2 B:GLU193 4.0 23.5 1.0 OE1 B:GLU193 4.0 26.0 1.0 N B:ALA148 4.0 22.3 1.0 ND2 B:ASN179 4.0 27.6 1.0 OE1 B:GLN174 4.1 24.1 1.0 O3 B:SO4306 4.1 40.4 0.8 O B:ASN179 4.2 22.9 1.0 O B:ALA148 4.2 23.0 1.0 O B:HOH440 4.4 32.9 1.0 O B:HOH537 4.4 31.4 1.0 CD B:GLU193 4.4 25.1 1.0 NE2 B:GLN189 4.4 18.2 1.0 CB B:ASN179 4.5 23.0 1.0 CB B:ALA148 4.6 20.1 1.0 CA B:GLY147 4.6 21.7 1.0 O1 B:SO4306 4.6 25.5 0.8 CD B:GLN189 4.7 21.8 1.0 CA B:ASN179 4.7 21.1 1.0 CA B:ALA148 4.7 22.3 1.0 C B:GLY147 4.8 22.9 1.0 C B:ASN179 4.8 26.0 1.0 S B:SO4306 4.9 47.9 0.8 CG B:GLN189 4.9 20.8 1.0 O B:LYS146 4.9 28.4 1.0 C B:ALA148 5.0 18.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:32.3 occ:1.00 OD1 C:ASN179 2.0 27.0 1.0 O C:HOH405 2.1 23.8 1.0 O C:HOH431 2.1 35.3 1.0 O C:HOH518 2.1 35.1 1.0 O C:HOH436 2.1 28.6 1.0 O C:HOH410 2.1 28.5 1.0 CG C:ASN179 3.2 24.1 1.0 ND2 C:ASN179 3.8 24.7 1.0 OE1 C:GLU193 4.0 23.6 1.0 OE2 C:GLU193 4.0 27.1 1.0 O C:ASN179 4.1 25.7 1.0 O4 C:SO4306 4.1 38.8 0.9 OE1 C:GLN174 4.2 23.0 1.0 N C:ALA148 4.2 24.9 1.0 O C:ALA148 4.3 24.8 1.0 O3 C:SO4306 4.3 55.3 0.9 CD C:GLU193 4.4 23.0 1.0 CB C:ASN179 4.4 20.6 1.0 CA C:ASN179 4.6 24.0 1.0 O1 C:SO4306 4.6 40.8 0.9 S C:SO4306 4.6 59.8 0.9 C C:ASN179 4.6 26.4 1.0 NE2 C:GLN189 4.7 23.1 1.0 CA C:GLY147 4.8 24.6 1.0 CB C:ALA148 4.8 24.7 1.0 CD C:GLN189 4.8 22.9 1.0 O C:LYS146 4.9 27.9 1.0 CA C:ALA148 5.0 24.1 1.0 C C:GLY147 5.0 23.8 1.0 CG C:GLN189 5.0 21.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Nuca From Streptococcus Agalactiae with Magnesium Ion Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:39.5 occ:1.00 O D:HOH581 1.9 41.3 1.0 O D:HOH570 2.1 27.5 1.0 O D:HOH416 2.1 30.0 1.0 O D:HOH407 2.1 24.2 1.0 O D:HOH414 2.1 27.8 1.0 OD1 D:ASN179 2.1 28.0 1.0 CG D:ASN179 3.3 26.5 1.0 O2 D:SO4306 3.5 47.5 0.9 ND2 D:ASN179 3.9 23.2 1.0 OE1 D:GLU193 3.9 26.5 1.0 O D:HOH461 4.0 36.0 1.0 OE2 D:GLU193 4.0 26.7 1.0 OE1 D:GLN174 4.2 22.2 1.0 N D:ALA148 4.2 24.5 1.0 O D:ALA148 4.2 22.4 1.0 O D:ASN179 4.2 26.9 1.0 CD D:GLU193 4.4 27.1 1.0 O4 D:SO4306 4.5 36.2 0.9 CB D:ASN179 4.5 22.8 1.0 NE2 D:GLN189 4.6 22.6 1.0 S D:SO4306 4.6 48.1 0.9 CA D:ASN179 4.7 23.2 1.0 CB D:ALA148 4.7 18.7 1.0 C D:ASN179 4.8 27.6 1.0 CA D:GLY147 4.8 19.5 1.0 CA D:ALA148 4.9 20.0 1.0 CD D:GLN189 4.9 23.6 1.0 C D:GLY147 5.0 25.3 1.0

A.F.Moon, P.Gaudu, L.C.Pedersen. Structural Characterization of the Virulence Factor Nuclease A From Streptococcus Agalactiae. Acta Crystallogr.,Sect.D V. 70 2937 2014.
ISSN: ISSN 0907-4449
PubMed: 25372684
DOI: 10.1107/S1399004714019725