Magnesium in PDB 3ck5: Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium

The structure of Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium, PDB code: 3ck5 was solved by K.N.Rao, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.26 / 2.30
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.603, 177.603, 112.060, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.4

The binding sites of Magnesium atom in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium (pdb code 3ck5). 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 A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium, PDB code: 3ck5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium


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 A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:31.4 occ:1.00 OE1 A:GLU249 2.0 27.2 1.0 OE2 A:GLU223 2.1 23.5 1.0 O A:HOH501 2.2 27.6 1.0 OD2 A:ASP197 2.3 27.8 1.0 O A:HOH499 2.4 34.2 1.0 O A:HOH500 2.5 42.2 1.0 CD A:GLU249 2.9 28.5 1.0 CD A:GLU223 3.2 25.2 1.0 OE2 A:GLU249 3.2 30.2 1.0 CG A:ASP197 3.4 23.8 1.0 NZ A:LYS166 3.7 27.1 1.0 OD1 A:ASP197 3.8 24.0 1.0 OD1 A:ASN199 3.8 30.5 1.0 ND1 A:HIS299 3.9 35.0 1.0 CE1 A:HIS299 3.9 36.0 1.0 OE1 A:GLU223 4.0 24.2 1.0 CG A:GLU223 4.0 21.7 1.0 OE1 A:GLU270 4.1 32.6 1.0 O A:HOH491 4.2 35.1 1.0 CG A:GLU249 4.3 26.1 1.0 NZ A:LYS168 4.4 37.5 1.0 OE2 A:GLU224 4.6 32.2 1.0 CB A:ASP197 4.6 23.2 1.0 CE A:LYS166 4.8 27.1 1.0 CG A:ASN199 4.8 27.4 1.0 CB A:GLU249 4.9 24.1 1.0 CD A:GLU270 5.0 34.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium


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 A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:31.9 occ:1.00 OE1 B:GLU249 1.9 28.6 1.0 O B:HOH566 2.0 25.1 1.0 OE2 B:GLU223 2.0 30.8 1.0 OD2 B:ASP197 2.1 25.0 1.0 O B:HOH567 2.4 41.5 1.0 O B:HOH565 2.4 45.0 1.0 CD B:GLU249 2.9 30.8 1.0 CG B:ASP197 3.1 24.5 1.0 CD B:GLU223 3.1 28.8 1.0 OE2 B:GLU249 3.3 32.0 1.0 OD1 B:ASP197 3.5 26.8 1.0 CG B:GLU223 3.9 27.5 1.0 NZ B:LYS166 4.0 28.8 1.0 OE2 B:GLU224 4.0 31.1 1.0 OD1 B:ASN199 4.0 23.5 1.0 O B:HOH552 4.0 27.6 1.0 OE1 B:GLU223 4.1 29.7 1.0 CD2 B:HIS299 4.2 37.7 1.0 OE1 B:GLU270 4.2 32.2 1.0 CG B:GLU249 4.3 29.8 1.0 NZ B:LYS168 4.3 31.7 1.0 CB B:ASP197 4.4 25.9 1.0 O B:HOH550 4.4 46.8 1.0 NE2 B:HIS299 4.5 40.0 1.0 CG B:ASN199 4.8 22.8 1.0 CD B:GLU224 4.8 29.5 1.0 CB B:GLU223 4.9 25.8 1.0 CE B:LYS166 4.9 30.1 1.0 CB B:GLU249 4.9 29.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium


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 A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:42.2 occ:1.00 OE2 C:GLU223 1.8 32.3 1.0 OD2 C:ASP197 1.9 31.4 1.0 O C:HOH468 2.3 27.1 1.0 O C:HOH409 2.3 43.1 1.0 OE1 C:GLU249 2.4 44.3 1.0 O C:HOH470 2.6 44.5 1.0 CD C:GLU223 2.7 33.3 1.0 CG C:ASP197 3.0 31.3 1.0 CG C:GLU223 3.4 31.8 1.0 CD C:GLU249 3.5 42.5 1.0 OD1 C:ASP197 3.6 32.1 1.0 OE1 C:GLU223 3.6 32.6 1.0 NZ C:LYS166 3.7 30.1 1.0 OE2 C:GLU249 3.9 44.3 1.0 OD1 C:ASN199 4.1 36.4 1.0 ND1 C:HIS299 4.2 42.7 1.0 OE2 C:GLU270 4.2 39.1 1.0 CB C:ASP197 4.3 32.3 1.0 CE1 C:HIS299 4.4 44.2 1.0 O C:HOH439 4.4 41.7 1.0 CB C:GLU223 4.5 32.6 1.0 OE2 C:GLU224 4.5 35.2 1.0 NZ C:LYS168 4.5 42.9 1.0 CE C:LYS166 4.7 30.7 1.0 CG C:GLU249 4.7 40.5 1.0 OE1 C:GLU270 4.7 36.6 1.0 CG C:ASN199 4.8 35.5 1.0 CD C:GLU270 4.9 37.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium


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 A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:40.9 occ:1.00 OE1 D:GLU249 1.9 39.4 1.0 O D:HOH449 2.1 35.5 1.0 OD2 D:ASP197 2.1 34.8 1.0 O D:HOH448 2.1 40.7 1.0 OE2 D:GLU223 2.2 32.6 1.0 CD D:GLU249 2.8 38.2 1.0 O D:HOH451 2.9 44.9 1.0 CD D:GLU223 3.2 31.4 1.0 CG D:ASP197 3.2 34.8 1.0 OE2 D:GLU249 3.2 39.2 1.0 OD1 D:ASP197 3.6 35.7 1.0 OD1 D:ASN199 3.7 37.4 1.0 CG D:GLU223 3.7 30.5 1.0 O D:HOH450 3.8 43.0 1.0 OE2 D:GLU224 3.8 38.0 1.0 CG D:GLU249 4.1 36.9 1.0 OE1 D:GLU223 4.2 31.6 1.0 CD2 D:HIS299 4.2 43.6 1.0 NZ D:LYS166 4.2 32.7 1.0 OE2 D:GLU270 4.3 41.9 1.0 CB D:ASP197 4.5 33.1 1.0 NE2 D:HIS299 4.6 45.6 1.0 CG D:ASN199 4.6 36.2 1.0 CB D:GLU223 4.7 31.5 1.0 CD D:GLU224 4.8 34.0 1.0 NZ D:LYS168 4.8 44.2 1.0 CB D:GLU249 4.8 34.4 1.0

K.N.Rao, S.K.Burley, S.Swaminathan. Crystal Structure of A Racemase From Streptomyces Coelicolor A3(2) with Bound Magnesium. To Be Published.