Magnesium in PDB 5jy6: Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States

The structure of Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States, PDB code: 5jy6 was solved by N.Schormann, D.Chattopadhyay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.60 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.578, 107.465, 89.273, 90.00, 104.07, 90.00
R / Rfree (%)	19.5 / 21.6

The binding sites of Magnesium atom in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States (pdb code 5jy6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States, PDB code: 5jy6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:29.1 occ:1.00 O A:VAL24 2.1 32.1 1.0 O A:VAL27 2.3 41.7 1.0 O A:HOH623 2.3 30.1 1.0 O A:ILE21 2.5 33.2 1.0 O A:HOH556 2.7 35.2 1.0 C A:VAL24 3.3 37.0 1.0 C A:VAL27 3.5 42.4 1.0 C A:ILE21 3.7 34.1 1.0 N A:VAL24 3.9 38.0 1.0 CA A:VAL24 4.1 37.2 1.0 CG2 A:ILE21 4.1 29.1 1.0 N A:GLU25 4.2 41.6 1.0 O A:GLN22 4.2 43.9 1.0 C A:GLN22 4.2 39.8 1.0 N A:VAL27 4.3 51.8 1.0 CA A:GLN22 4.3 39.5 1.0 CA A:GLU25 4.3 46.5 1.0 N A:GLU28 4.4 40.7 1.0 CA A:GLU28 4.4 39.5 1.0 N A:GLN22 4.4 36.4 1.0 CA A:VAL27 4.5 47.7 1.0 CB A:VAL24 4.5 38.2 1.0 C A:GLU25 4.7 46.7 1.0 CB A:GLU28 4.7 42.2 1.0 N A:GLY26 4.7 47.6 1.0 CA A:ILE21 4.8 30.7 1.0 N A:ASN23 4.8 39.5 1.0 O A:HOH577 4.8 29.3 1.0 CB A:VAL27 4.9 48.6 1.0

Magnesium binding site 2 out of 4 in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:29.7 occ:1.00 O B:VAL27 2.2 31.1 1.0 O B:VAL24 2.3 29.5 1.0 O B:HOH640 2.5 28.6 1.0 O B:ILE21 2.5 25.8 1.0 C B:VAL27 3.4 31.9 1.0 C B:VAL24 3.4 32.1 1.0 C B:ILE21 3.7 25.7 1.0 CG2 B:ILE21 4.0 24.7 1.0 N B:VAL24 4.0 31.4 1.0 CA B:GLU28 4.2 34.6 1.0 CA B:VAL24 4.2 32.2 1.0 N B:GLU28 4.3 32.3 1.0 C B:GLN22 4.3 29.9 1.0 O B:GLN22 4.3 29.2 1.0 CA B:GLN22 4.3 29.1 1.0 N B:VAL27 4.4 33.9 1.0 N B:GLU25 4.4 34.2 1.0 N B:GLN22 4.4 27.4 1.0 CA B:VAL27 4.4 33.7 1.0 O B:GLU25 4.5 35.1 1.0 CB B:GLU28 4.5 37.4 1.0 CB B:VAL24 4.6 32.1 1.0 CA B:GLU25 4.6 34.0 1.0 O B:HOH581 4.6 29.8 1.0 C B:GLU25 4.6 33.6 1.0 CG1 B:VAL27 4.7 38.4 1.0 CA B:ILE21 4.7 24.8 1.0 N B:ASN23 4.9 30.7 1.0 CB B:ILE21 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:40.1 occ:1.00 O C:HOH579 2.1 38.9 1.0 O C:VAL27 2.1 47.4 1.0 O C:VAL24 2.2 47.4 1.0 O C:ILE21 2.6 43.7 1.0 C C:VAL27 3.3 52.4 1.0 C C:VAL24 3.4 50.8 1.0 C C:ILE21 3.8 42.4 1.0 CG2 C:ILE21 4.0 41.3 1.0 N C:VAL24 4.0 46.8 1.0 N C:VAL27 4.1 59.4 1.0 CA C:VAL24 4.2 50.0 1.0 N C:GLU28 4.2 51.4 1.0 CA C:GLU28 4.2 53.4 1.0 CA C:VAL27 4.3 54.8 1.0 N C:GLU25 4.3 56.7 1.0 O C:GLN22 4.4 51.9 1.0 C C:GLN22 4.4 46.6 1.0 CA C:GLU25 4.4 59.4 1.0 CA C:GLN22 4.5 46.6 1.0 CB C:GLU28 4.5 58.1 1.0 CB C:VAL24 4.5 50.9 1.0 N C:GLN22 4.5 45.4 1.0 N C:GLY26 4.7 60.7 1.0 C C:GLU25 4.7 60.7 1.0 CB C:VAL27 4.8 55.3 1.0 CA C:ILE21 4.8 39.7 1.0 N C:ASN23 5.0 44.6 1.0

Magnesium binding site 4 out of 4 in the Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structures of Streptococcus Agalactiae Gbs Gapdh in Different Enzymatic States within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:31.9 occ:1.00 O D:VAL24 2.3 31.1 1.0 O D:HOH648 2.3 25.0 1.0 O D:VAL27 2.3 35.8 1.0 O D:ILE21 2.5 23.7 1.0 C D:VAL24 3.4 32.7 1.0 C D:VAL27 3.5 35.9 1.0 C D:ILE21 3.7 25.1 1.0 N D:VAL24 4.0 28.4 1.0 CG2 D:ILE21 4.1 24.1 1.0 C D:GLN22 4.2 25.9 1.0 O D:GLN22 4.2 25.5 1.0 CA D:VAL24 4.2 30.2 1.0 CA D:GLN22 4.2 27.0 1.0 CA D:GLU28 4.3 32.2 1.0 N D:GLU25 4.3 34.5 1.0 N D:GLU28 4.4 33.8 1.0 N D:VAL27 4.4 39.1 1.0 N D:GLN22 4.4 25.7 1.0 CA D:GLU25 4.5 39.1 1.0 CA D:VAL27 4.5 37.5 1.0 CB D:VAL24 4.5 30.9 1.0 CB D:GLU28 4.5 36.6 1.0 O D:HOH576 4.6 22.2 1.0 CA D:ILE21 4.7 23.5 1.0 N D:ASN23 4.7 26.9 1.0 CG1 D:VAL27 4.7 41.5 1.0 C D:GLU25 4.8 37.1 1.0 N D:GLY26 4.8 37.0 1.0

N.Schormann, C.A.Ayres, A.Fry, T.J.Green, S.Banerjee, G.C.Ulett, D.Chattopadhyay. Crystal Structures of Group B Streptococcus Glyceraldehyde-3-Phosphate Dehydrogenase: Apo-Form, Binary and Ternary Complexes. Plos One V. 11 65917 2016.
ISSN: ESSN 1932-6203
PubMed: 27875551
DOI: 10.1371/JOURNAL.PONE.0165917