Magnesium in PDB 4lyk: Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++

The structure of Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++, PDB code: 4lyk was solved by A.Sundriyal, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.850, 109.547, 81.750, 90.00, 99.39, 90.00
R / Rfree (%)	18.9 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++ (pdb code 4lyk). 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 the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++, PDB code: 4lyk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++


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 Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:24.4 occ:1.00 O A:HOH515 1.9 30.6 1.0 O A:HOH505 2.0 31.4 1.0 OD1 A:ASN200 2.2 26.4 1.0 OE2 A:GLU141 2.2 26.5 1.0 OE1 A:GLU232 2.2 26.9 1.0 OD2 A:ASP262 2.2 25.9 1.0 CG A:ASP262 3.0 25.8 1.0 CD A:GLU141 3.0 27.5 1.0 OD1 A:ASP262 3.2 26.0 1.0 CG A:ASN200 3.2 29.1 1.0 CD A:GLU232 3.4 27.7 1.0 OE1 A:GLU141 3.5 28.5 1.0 ND2 A:ASN200 3.6 28.1 1.0 NZ A:LYS283 4.0 25.2 1.0 CB A:GLU232 4.1 26.9 1.0 O A:HOH510 4.2 31.6 1.0 CG A:GLU141 4.2 28.6 1.0 O A:HOH521 4.2 30.0 1.0 OE2 A:GLU232 4.3 29.0 1.0 CG A:GLU232 4.4 27.7 1.0 CB A:ASP262 4.4 26.7 1.0 O A:HOH533 4.4 42.3 1.0 CB A:ASN200 4.6 29.0 1.0 CD A:LYS283 4.6 25.0 1.0 OE1 A:GLU319 4.7 46.9 1.0 CE A:LYS283 4.9 25.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++


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 Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:25.0 occ:1.00 O B:HOH503 2.0 23.8 1.0 OE2 B:GLU141 2.1 27.8 1.0 OE1 B:GLU232 2.1 25.8 1.0 OD2 B:ASP262 2.2 23.8 1.0 OD1 B:ASN200 2.2 26.5 1.0 O B:HOH532 2.2 27.4 1.0 CD B:GLU141 3.0 28.2 1.0 CG B:ASP262 3.0 23.4 1.0 OD1 B:ASP262 3.2 23.3 1.0 CG B:ASN200 3.2 28.7 1.0 CD B:GLU232 3.4 25.7 1.0 OE1 B:GLU141 3.4 28.0 1.0 ND2 B:ASN200 3.6 31.2 1.0 O B:HOH572 4.0 47.4 1.0 NZ B:LYS283 4.0 24.7 1.0 CB B:GLU232 4.0 25.0 1.0 O B:HOH510 4.1 31.6 1.0 CG B:GLU141 4.1 28.5 1.0 OE2 B:GLU232 4.2 26.3 1.0 CG B:GLU232 4.3 25.2 1.0 CB B:ASP262 4.4 23.2 1.0 O B:HOH556 4.4 45.7 1.0 CD B:LYS283 4.6 23.7 1.0 CB B:ASN200 4.6 28.5 1.0 OE1 B:GLU319 4.7 36.2 1.0 CE B:LYS283 4.9 24.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++


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 the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:37.2 occ:1.00 O C:HOH504 2.0 33.0 1.0 OE1 C:GLU232 2.1 38.9 1.0 OE2 C:GLU141 2.1 38.9 1.0 OD2 C:ASP262 2.1 38.1 1.0 OD1 C:ASN200 2.2 36.1 1.0 O C:HOH506 2.3 29.6 1.0 CG C:ASP262 3.0 37.3 1.0 CD C:GLU141 3.0 41.2 1.0 OD1 C:ASP262 3.2 36.9 1.0 CG C:ASN200 3.2 35.8 1.0 CD C:GLU232 3.4 40.4 1.0 OE1 C:GLU141 3.4 40.2 1.0 ND2 C:ASN200 3.6 37.4 1.0 CB C:GLU232 3.9 39.0 1.0 O C:HOH524 4.0 48.6 1.0 NZ C:LYS283 4.0 43.7 1.0 O C:HOH510 4.1 43.1 1.0 CG C:GLU141 4.1 40.3 1.0 OE2 C:GLU232 4.2 41.6 1.0 CG C:GLU232 4.3 39.8 1.0 CB C:ASP262 4.3 36.6 1.0 CD C:LYS283 4.6 43.9 1.0 CB C:ASN200 4.6 34.5 1.0 O C:HOH530 4.7 42.7 1.0 OE1 C:GLU319 4.7 55.6 1.0 CE C:LYS283 4.9 44.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++


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 the Eal Domain of C-Di-Gmp Specific Phosphodiesterase Yaha in Complex with Activating Cofactor Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:37.2 occ:1.00 O D:HOH503 2.0 36.5 1.0 O D:HOH504 2.1 38.7 1.0 OE2 D:GLU141 2.2 38.4 1.0 OD2 D:ASP262 2.2 36.7 1.0 OD1 D:ASN200 2.2 40.1 1.0 OE1 D:GLU232 2.2 34.4 1.0 CG D:ASP262 3.0 37.4 1.0 CD D:GLU141 3.0 37.5 1.0 OD1 D:ASP262 3.2 39.6 1.0 CG D:ASN200 3.2 39.6 1.0 CD D:GLU232 3.4 34.8 1.0 OE1 D:GLU141 3.5 38.0 1.0 ND2 D:ASN200 3.6 40.4 1.0 O D:HOH516 4.0 43.5 1.0 CB D:GLU232 4.1 33.5 1.0 NZ D:LYS283 4.1 38.8 1.0 O D:HOH502 4.1 35.2 1.0 CG D:GLU141 4.2 37.2 1.0 OE2 D:GLU232 4.2 35.5 1.0 CG D:GLU232 4.3 35.1 1.0 CB D:ASP262 4.4 36.4 1.0 CB D:ASN200 4.6 37.8 1.0 CD D:LYS283 4.6 37.5 1.0 OE1 D:GLU319 4.7 47.8 1.0 CE D:LYS283 5.0 38.3 1.0

A.Sundriyal, C.Massa, D.Samoray, F.Zehender, T.Sharpe, U.Jenal, T.Schirmer. Inherent Regulation of Eal Domain-Catalyzed Hydrolysis of Second Messenger Cyclic Di-Gmp. J.Biol.Chem. V. 289 6978 2014.
ISSN: ISSN 0021-9258
PubMed: 24451384
DOI: 10.1074/JBC.M113.516195