Magnesium in PDB 3a52: Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp.

The structure of Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp., PDB code: 3a52 was solved by H.Tsuruta, B.Mikami, T.Higashi, Y.Aizono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.059, 95.863, 71.058, 90.00, 101.62, 90.00
R / Rfree (%)	18.3 / 24.4

The structure of Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. (pdb code 3a52). 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 Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp., PDB code: 3a52:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp.


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 Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:28.3 occ:1.00 ND1 A:HIS109 2.2 16.2 1.0 OE1 A:GLU222 2.9 8.5 1.0 CG A:HIS109 3.1 15.8 1.0 CB A:HIS109 3.3 11.9 1.0 CE1 A:HIS109 3.3 18.4 1.0 N A:THR111 3.5 8.1 1.0 OG1 A:THR111 3.5 8.4 1.0 OE2 A:GLU222 3.5 10.4 1.0 CD A:GLU222 3.6 10.6 1.0 CB A:THR111 3.7 8.8 1.0 CD A:PRO112 3.8 7.0 1.0 N A:ALA110 3.8 5.4 1.0 OD1 A:ASP9 3.8 21.0 1.0 C A:HIS109 4.0 7.7 1.0 CA A:THR111 4.2 8.4 1.0 CA A:HIS109 4.3 9.5 1.0 CD2 A:HIS109 4.3 17.6 1.0 CA A:ALA110 4.4 6.5 1.0 NE2 A:HIS109 4.4 18.8 1.0 C A:ALA110 4.4 6.5 1.0 CB A:ALA110 4.5 2.4 1.0 OG A:SER224 4.5 6.2 1.0 CB A:ALA105 4.5 3.6 1.0 O A:HIS109 4.6 8.2 1.0 CB A:SER224 4.7 2.4 1.0 CG A:PRO112 4.7 6.1 1.0 N A:PRO112 4.8 7.3 1.0 CG A:ASP9 5.0 17.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp.


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 Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:1.0 occ:1.00 N B:ILE277 3.0 7.3 1.0 OG1 A:THR363 3.2 5.5 1.0 O B:HOH2025 3.3 9.4 1.0 N A:VAL365 3.3 3.8 1.0 CB A:VAL365 3.4 5.1 1.0 CB A:THR363 3.4 5.1 1.0 CA B:SER276 3.4 6.1 1.0 CG1 A:VAL365 3.7 4.2 1.0 C B:SER276 3.7 7.7 1.0 CA A:VAL365 3.9 5.2 1.0 CB B:ILE277 3.9 7.7 1.0 CB B:SER276 3.9 8.6 1.0 N A:GLY364 4.0 6.0 1.0 CG1 B:ILE277 4.0 8.5 1.0 CA B:ILE277 4.0 7.6 1.0 CD1 B:ILE277 4.2 9.1 1.0 CB B:ALA14 4.2 5.4 1.0 O B:LEU275 4.3 7.5 1.0 C A:GLY364 4.3 4.5 1.0 C A:THR363 4.3 6.7 1.0 O B:ILE277 4.4 10.2 1.0 CG2 A:THR363 4.4 5.8 1.0 CA A:THR363 4.4 6.8 1.0 C B:ILE277 4.5 8.7 1.0 CA A:GLY364 4.6 5.3 1.0 N B:SER276 4.6 6.9 1.0 CG2 A:VAL365 4.6 6.1 1.0 OD1 A:ASN271 4.7 10.3 1.0 CA B:ALA14 4.8 7.0 1.0 C B:LEU275 4.9 8.3 1.0 O B:SER276 4.9 6.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp.


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 Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1006 b:29.5 occ:1.00 CD2 B:HIS109 2.3 22.3 1.0 CG B:HIS109 3.0 20.2 1.0 OE2 B:GLU222 3.1 11.3 1.0 CB B:HIS109 3.3 15.8 1.0 O B:HOH2786 3.4 29.6 1.0 OE1 B:GLU222 3.4 13.5 1.0 NE2 B:HIS109 3.4 24.5 1.0 OG1 B:THR111 3.6 8.6 1.0 N B:THR111 3.6 8.7 1.0 CD B:GLU222 3.7 11.2 1.0 OD1 B:ASP9 3.8 19.8 1.0 CB B:THR111 3.9 9.0 1.0 CD B:PRO112 3.9 9.1 1.0 N B:ALA110 3.9 8.7 1.0 C B:HIS109 4.1 10.9 1.0 ND1 B:HIS109 4.2 24.6 1.0 CA B:HIS109 4.3 13.3 1.0 CA B:THR111 4.4 9.1 1.0 CE1 B:HIS109 4.4 24.6 1.0 CA B:ALA110 4.5 8.8 1.0 C B:ALA110 4.5 8.4 1.0 OG B:SER224 4.5 3.9 1.0 CB B:ALA105 4.5 5.6 1.0 CB B:ALA110 4.5 5.9 1.0 CB B:SER224 4.6 1.0 1.0 O B:HIS109 4.7 11.4 1.0 CG B:PRO112 4.9 10.7 1.0 CG B:ASP9 5.0 15.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp.


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 Cold-Active Alkailne Phosphatase From Psychrophile Shewanella Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1008 b:1.0 occ:1.00 N A:ILE277 3.0 6.7 1.0 OG1 B:THR363 3.0 6.0 1.0 O A:HOH2021 3.1 9.7 1.0 CB B:VAL365 3.3 4.1 1.0 CB B:THR363 3.3 5.7 1.0 N B:VAL365 3.4 3.5 1.0 CA A:SER276 3.5 5.1 1.0 CG1 B:VAL365 3.6 3.5 1.0 C A:SER276 3.7 6.5 1.0 CA B:VAL365 3.8 3.7 1.0 CB A:ILE277 3.9 7.2 1.0 CB A:SER276 4.0 5.5 1.0 CA A:ILE277 4.0 7.2 1.0 N B:GLY364 4.0 5.1 1.0 CG1 A:ILE277 4.1 7.8 1.0 CB A:ALA14 4.1 5.7 1.0 O A:LEU275 4.3 5.2 1.0 C B:THR363 4.3 5.2 1.0 CG2 B:THR363 4.3 6.0 1.0 C B:GLY364 4.4 4.2 1.0 CA B:THR363 4.4 6.3 1.0 CG2 B:VAL365 4.5 5.2 1.0 O A:ILE277 4.5 10.7 1.0 CD1 A:ILE277 4.6 6.9 1.0 C A:ILE277 4.6 8.2 1.0 N A:SER276 4.6 5.6 1.0 CA B:GLY364 4.7 4.1 1.0 ND2 B:ASN271 4.7 2.3 1.0 CA A:ALA14 4.8 7.0 1.0 C A:LEU275 4.9 6.0 1.0 O A:SER276 5.0 6.3 1.0

H.Tsuruta, B.Mikami, T.Higashi, Y.Aizono. Crystal Structure of Cold-Active Alkaline Phosphatase From the Psychrophile Shewanella Sp. Biosci.Biotechnol.Biochem. V. 74 69 2010.
ISSN: ISSN 0916-8451
PubMed: 20057143
DOI: 10.1271/BBB.90563