Magnesium in PDB 6ihl: Crystal Structure of Bacterial Serine Phosphatase

All present enzymatic activity of Crystal Structure of Bacterial Serine Phosphatase:
3.1.3.16;

The structure of Crystal Structure of Bacterial Serine Phosphatase, PDB code: 6ihl was solved by C.-G.Yang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.74 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.669, 38.160, 64.891, 90.00, 101.47, 90.00
R / Rfree (%)	17 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of Bacterial Serine Phosphatase (pdb code 6ihl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Bacterial Serine Phosphatase, PDB code: 6ihl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Bacterial Serine Phosphatase


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 Bacterial Serine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:47.6 occ:1.00 OE2 A:GLU16 2.0 35.5 1.0 O A:HOH456 2.2 42.9 1.0 O A:HOH506 2.2 44.0 1.0 O A:HOH480 2.2 40.4 1.0 O A:HOH407 2.2 33.3 1.0 CD A:GLU16 3.1 39.4 1.0 OE1 A:GLU16 3.6 37.1 1.0 O A:HIS40 4.0 43.6 1.0 OE1 A:GLU44 4.2 34.6 1.0 N A:GLY43 4.3 25.7 1.0 CG A:GLU16 4.3 26.4 1.0 N A:ALA42 4.4 28.2 1.0 O A:GLY38 4.5 37.7 1.0 CA A:GLY38 4.7 32.7 1.0 O A:MET37 4.7 35.1 1.0 NZ A:LYS14 4.8 68.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Bacterial Serine Phosphatase


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 Bacterial Serine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:22.5 occ:1.00 O A:HOH454 2.1 24.7 1.0 O A:HOH420 2.1 24.9 1.0 OD1 A:ASP192 2.1 24.7 1.0 OD2 A:ASP35 2.1 21.8 1.0 O A:HOH415 2.1 25.0 1.0 OD2 A:ASP231 2.1 26.3 1.0 CG A:ASP35 3.0 21.4 1.0 CG A:ASP231 3.1 29.5 1.0 CG A:ASP192 3.1 22.2 1.0 OD1 A:ASP35 3.3 21.4 1.0 OD1 A:ASP231 3.4 28.5 1.0 OD2 A:ASP192 3.5 24.4 1.0 MG A:MG303 3.7 23.7 1.0 N A:GLY193 4.2 24.1 1.0 O A:HOH458 4.2 21.6 1.0 O A:HOH449 4.2 24.7 1.0 O A:HOH427 4.3 23.6 1.0 CB A:ASP35 4.4 19.7 1.0 CB A:ASP231 4.4 27.2 1.0 OD1 A:ASP17 4.4 25.2 1.0 O A:HOH426 4.5 30.5 1.0 O A:ASN232 4.5 24.9 1.0 CB A:ASP192 4.5 21.4 1.0 N A:ASP192 4.5 22.1 1.0 C A:ASP192 4.7 26.1 1.0 CA A:ASP192 4.8 23.3 1.0 CB A:SER191 4.9 24.5 1.0 CA A:GLY193 4.9 24.5 1.0 OG A:SER191 5.0 24.5 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Bacterial Serine Phosphatase


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 Bacterial Serine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:23.7 occ:1.00 OD1 A:ASP35 2.0 21.4 1.0 O A:HOH427 2.1 23.6 1.0 O A:GLY36 2.1 23.2 1.0 O A:HOH445 2.1 25.5 1.0 O A:HOH420 2.2 24.9 1.0 CG A:ASP35 3.1 21.4 1.0 C A:GLY36 3.3 23.6 1.0 OD2 A:ASP35 3.7 21.8 1.0 MG A:MG302 3.7 22.5 1.0 N A:GLY36 3.9 19.6 1.0 N A:GLY38 3.9 30.5 1.0 O A:HOH479 4.0 24.4 1.0 C A:ASP35 4.0 18.9 1.0 OD1 A:ASP17 4.1 25.2 1.0 CA A:GLY36 4.1 18.7 1.0 O A:HOH415 4.2 25.0 1.0 N A:MET37 4.2 24.1 1.0 O A:HOH454 4.3 24.7 1.0 CA A:MET37 4.3 29.0 1.0 O A:ASP35 4.3 20.1 1.0 OE1 A:GLU16 4.4 37.1 1.0 CB A:GLU16 4.4 23.5 1.0 CB A:ASP35 4.4 19.7 1.0 C A:MET37 4.4 32.2 1.0 OD1 A:ASN232 4.4 27.2 1.0 OD1 A:ASP231 4.5 28.5 1.0 CA A:ASP35 4.5 20.5 1.0 NH2 A:ARG12 4.5 49.9 1.0 CA A:GLY38 4.7 32.7 1.0 O A:GLU16 4.9 23.5 1.0 C A:GLU16 4.9 22.2 1.0 OD2 A:ASP231 5.0 26.3 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Bacterial Serine Phosphatase


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 Bacterial Serine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:26.3 occ:1.00 OD2 A:ASP118 2.0 26.0 1.0 O A:HOH468 2.1 26.1 1.0 O A:HOH409 2.1 28.2 1.0 OD2 A:ASP192 2.1 24.4 1.0 O A:HOH437 2.2 24.9 1.0 O A:HOH421 2.2 27.9 1.0 CG A:ASP118 3.2 26.3 1.0 CG A:ASP192 3.2 22.2 1.0 CB A:ASP192 3.7 21.4 1.0 OD1 A:ASP118 3.8 22.1 1.0 OD2 A:ASP196 3.9 29.9 1.0 O A:HOH449 3.9 24.7 1.0 O A:HOH415 4.1 25.0 1.0 CB A:ASP118 4.3 22.6 1.0 OD1 A:ASP192 4.3 24.7 1.0 O A:HOH440 4.4 23.3 1.0 O A:ASN160 4.4 34.7 1.0 O A:ARG159 4.4 52.2 1.0 OD1 A:ASP196 4.4 28.6 1.0 OD1 A:ASN160 4.5 54.4 1.0 CA A:ASN160 4.5 35.7 1.0 CG A:ASP196 4.6 25.9 1.0 CG2 A:ILE162 4.7 29.4 1.0 C A:ASN160 4.8 38.2 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Bacterial Serine Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Bacterial Serine Phosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:58.8 occ:1.00 O A:HOH511 2.1 57.0 1.0 O A:HOH502 2.4 53.3 1.0 OD1 A:ASP185 2.5 34.3 1.0 O A:HOH405 2.7 51.0 1.0 CG A:ASP185 3.4 39.9 1.0 OD2 A:ASP185 3.6 37.1 1.0 O A:PHE183 4.4 36.6 1.0 O A:HOH486 4.6 48.9 1.0 C A:PHE183 4.6 34.0 1.0 O A:TYR184 4.8 30.7 1.0 C A:TYR184 4.8 27.5 1.0 CB A:ASP185 4.8 31.3 1.0 CA A:PHE183 4.9 42.8 1.0 CB A:ASN125 4.9 25.6 1.0 N A:ASP185 5.0 27.0 1.0

T.Yang, T.Liu, J.Gan, K.Yu, K.Chen, W.Xue, L.Lan, S.Yang, C.G.Yang. Structural Insight Into the Mechanism of Staphylococcus Aureus STP1 Phosphatase. Acs Infect Dis. V. 5 841 2019.
ISSN: ESSN 2373-8227
PubMed: 30868877
DOI: 10.1021/ACSINFECDIS.8B00316