Magnesium in PDB 4oe7: Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal

The structure of Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal, PDB code: 4oe7 was solved by P.Manoj Kumar, V.Baskar, S.Manicka, S.Krishnaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.240, 155.140, 55.580, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal (pdb code 4oe7). 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 Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal, PDB code: 4oe7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal


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 Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:27.9 occ:1.00 O1 A:PYR410 2.1 27.8 1.0 O A:GXT409 2.2 29.9 0.5 C A:GXT409 2.9 27.4 0.5 C3 A:PYR410 3.0 24.7 1.0 C1 A:PYR410 3.1 23.7 1.0 O A:HOH519 3.1 19.2 1.0 C2 A:PYR410 3.4 26.8 1.0 CA A:GLY57 3.5 16.8 1.0 N A:GLY57 3.5 15.0 1.0 C1 A:GXT409 3.7 29.0 0.5 CG A:PRO20 3.8 13.8 1.0 O1 A:GXT409 3.9 30.7 0.5 CB A:PRO20 4.0 14.1 1.0 CB A:ALA221 4.1 16.5 1.0 O2 A:PYR410 4.2 22.4 1.0 O A:HOH530 4.3 21.0 1.0 CA A:ALA221 4.4 18.2 1.0 N A:ALA221 4.6 17.2 1.0 C A:SER56 4.7 14.6 1.0 NZ A:LYS174 4.7 24.2 1.0 CD1 A:ILE269 4.8 19.4 1.0 CB A:SER56 4.8 14.8 1.0 C A:GLY57 4.9 16.6 1.0 O A:HOH529 5.0 52.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal


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 Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:26.9 occ:1.00 O3 B:GXP410 2.2 27.5 0.8 O3 B:GXS411 2.2 25.0 0.2 O B:HOH512 2.3 15.5 1.0 CA B:GLY57 3.2 13.9 1.0 C4 B:GXP410 3.3 28.8 0.8 C4 B:GXS411 3.3 24.5 0.2 C1 B:GXS411 3.3 25.3 0.2 O B:GXS411 3.3 23.3 0.2 C2 B:GXP410 3.4 34.3 0.8 C2 B:GXS411 3.4 24.7 0.2 N B:GLY57 3.4 12.8 1.0 O B:GXP410 3.5 44.2 0.8 C B:GXP410 3.6 46.4 0.8 CG B:PRO20 3.7 13.4 1.0 C B:GXS411 3.8 25.0 0.2 C3 B:GXP410 3.9 32.9 0.8 CB B:ALA221 3.9 14.5 1.0 C3 B:GXS411 3.9 25.2 0.2 CB B:PRO20 3.9 13.4 1.0 C1 B:GXP410 4.0 43.4 0.8 CA B:ALA221 4.3 13.6 1.0 O4 B:GXS411 4.4 22.8 0.2 O4 B:GXP410 4.4 22.6 0.8 CD1 B:ILE269 4.4 19.4 1.0 N B:ALA221 4.5 13.3 1.0 C B:SER56 4.6 13.3 1.0 C B:GLY57 4.6 13.2 1.0 O1 B:GXS411 4.6 26.7 0.2 O B:PRO20 4.6 10.1 1.0 O B:HOH523 4.7 16.6 1.0 O1 B:GXP410 4.8 46.4 0.8 CB B:SER56 4.9 14.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal


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 Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:29.4 occ:1.00 O1 C:PYR412 2.1 28.8 1.0 C3 C:PYR412 3.0 24.2 1.0 C1 C:PYR412 3.1 24.9 1.0 O C:HOH524 3.2 21.5 1.0 C2 C:PYR412 3.5 28.0 1.0 CA C:GLY57 3.5 16.5 1.0 N C:GLY57 3.6 14.3 1.0 CG C:PRO20 3.8 13.8 1.0 CB C:PRO20 4.0 14.1 1.0 CB C:ALA221 4.1 18.6 1.0 O2 C:PYR412 4.2 20.4 1.0 O C:HOH523 4.3 17.4 1.0 CA C:ALA221 4.5 17.8 1.0 N C:ALA221 4.6 16.8 1.0 C C:SER56 4.7 14.7 1.0 NZ C:LYS174 4.7 24.6 1.0 CD1 C:ILE269 4.8 17.4 1.0 CB C:SER56 4.8 14.1 1.0 C C:GLY57 4.9 16.7 1.0 O C:HOH527 4.9 42.2 1.0 O C:PRO20 5.0 15.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal


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 Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg406 b:25.4 occ:1.00 O3 D:GXS409 2.2 26.6 0.5 O3 D:GXP408 2.2 29.2 0.5 O D:HOH524 2.3 18.3 1.0 CA D:GLY57 3.2 14.2 1.0 C2 D:GXP408 3.2 35.8 0.5 C4 D:GXS409 3.2 28.0 0.5 C4 D:GXP408 3.3 31.8 0.5 N D:GLY57 3.4 13.2 1.0 C2 D:GXS409 3.5 29.5 0.5 C D:GXP408 3.5 42.6 0.5 CG D:PRO20 3.5 15.0 1.0 O D:GXP408 3.7 41.7 0.5 C1 D:GXS409 3.8 32.0 0.5 C3 D:GXP408 3.8 34.2 0.5 O D:GXS409 3.8 34.3 0.5 CB D:PRO20 3.8 15.3 1.0 C3 D:GXS409 3.8 30.0 0.5 C1 D:GXP408 3.8 38.7 0.5 CB D:ALA221 4.0 17.9 1.0 C D:GXS409 4.2 33.4 0.5 CA D:ALA221 4.3 16.4 1.0 O1 D:GXP408 4.3 41.5 0.5 O4 D:GXS409 4.3 24.4 0.5 O4 D:GXP408 4.3 28.1 0.5 O D:PRO20 4.5 12.6 1.0 N D:ALA221 4.5 15.4 1.0 CD1 D:ILE269 4.6 16.4 1.0 C D:SER56 4.6 13.5 1.0 C D:GLY57 4.6 13.7 1.0 O D:HOH537 4.8 19.2 1.0 CB D:SER56 4.9 14.6 1.0 CD D:PRO20 5.0 14.6 1.0

P.Manoj Kumar, V.Baskar, S.Manicka, S.Krishnaswamy. Crystal Structure of Yage, A Kdg Aldolase Protein, in Complex with Aldol Condensed Product of Pyruvate and Glyoxal To Be Published.