Magnesium in PDB 6tep: Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp, PDB code: 6tep was solved by T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, C.Young, S.Charnock, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.58 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.272, 164.495, 115.873, 90.00, 95.80, 90.00
R / Rfree (%)	18.4 / 24.5

The structure of Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp (pdb code 6tep). 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 Galactokinase From Bifidobacterium Infantis in Complex with Adp, PDB code: 6tep:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp


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 Galactokinase From Bifidobacterium Infantis in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:17.3 occ:1.00 O A:HOH641 2.0 17.2 1.0 O A:HOH690 2.0 18.9 1.0 O A:HOH835 2.1 23.0 1.0 O2B A:ADP504 2.1 13.8 1.0 O1A A:ADP504 2.2 14.7 1.0 OG A:SER142 2.2 18.2 1.0 PB A:ADP504 3.2 16.1 1.0 PA A:ADP504 3.3 16.1 1.0 CB A:SER142 3.3 14.6 1.0 O3A A:ADP504 3.4 16.4 1.0 O A:HOH693 3.7 19.1 1.0 O A:HOH613 3.7 23.1 1.0 O3B A:ADP504 3.8 18.5 1.0 O A:HOH634 4.0 15.2 1.0 O5' A:ADP504 4.0 17.5 1.0 OE2 A:GLU179 4.1 8.4 0.5 OD2 A:ASP191 4.2 19.2 1.0 N A:SER142 4.3 11.8 1.0 OG A:SER140 4.3 10.5 0.5 CA A:SER140 4.4 11.1 0.5 CA A:SER142 4.4 12.9 1.0 O2A A:ADP504 4.5 17.7 1.0 CA A:SER140 4.5 12.2 0.5 O1B A:ADP504 4.5 16.0 1.0 CB A:SER140 4.9 11.3 0.5 CD A:GLU179 4.9 7.7 0.5

Magnesium binding site 2 out of 4 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp


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 Galactokinase From Bifidobacterium Infantis in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg507 b:24.0 occ:1.00 O D:HOH625 2.0 30.6 1.0 O1A D:ADP505 2.1 27.9 1.0 O1B D:ADP505 2.1 22.6 1.0 OG D:SER142 2.1 21.9 1.0 O D:HOH602 2.3 23.7 0.5 PB D:ADP505 3.2 20.3 1.0 PA D:ADP505 3.3 24.6 1.0 CB D:SER142 3.3 17.6 1.0 O3A D:ADP505 3.5 21.4 1.0 O D:HOH606 3.7 18.5 0.5 OE2 D:GLU179 3.7 36.7 1.0 OG D:SER140 3.8 23.5 0.5 O3B D:ADP505 3.8 26.3 1.0 O D:HOH637 3.9 20.9 0.5 O5' D:ADP505 3.9 24.3 1.0 O D:HOH638 3.9 24.6 1.0 OD2 D:ASP191 4.0 24.2 1.0 N D:SER142 4.2 17.6 1.0 CA D:SER142 4.3 16.6 1.0 CA D:SER140 4.3 15.8 0.5 C3 D:PEG503 4.3 27.5 0.5 C2 D:PEG503 4.3 27.4 0.5 CA D:SER140 4.4 12.8 0.5 CB D:SER140 4.5 18.0 0.5 O2B D:ADP505 4.5 20.9 1.0 O2A D:ADP505 4.5 33.3 1.0 CD D:GLU179 4.6 24.9 1.0 C1 D:PEG503 4.6 29.8 0.4 OE1 D:GLU179 4.7 29.6 1.0 C D:SER140 4.9 12.3 0.5 N D:ALA143 4.9 16.8 1.0 O2 D:PEG503 5.0 29.7 0.5 C D:SER140 5.0 14.1 0.5

Magnesium binding site 3 out of 4 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp


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 Galactokinase From Bifidobacterium Infantis in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg509 b:18.7 occ:1.00 O C:HOH658 2.0 29.7 1.0 O2A C:ADP507 2.0 20.8 1.0 O C:HOH609 2.1 21.6 1.0 O2B C:ADP507 2.1 14.1 1.0 OG C:SER142 2.2 17.3 1.0 O C:HOH603 2.4 16.9 0.5 O C:HOH713 2.4 26.8 1.0 PB C:ADP507 3.2 16.9 1.0 PA C:ADP507 3.2 18.4 1.0 CB C:SER142 3.4 16.0 1.0 O3A C:ADP507 3.4 18.5 1.0 O C:HOH605 3.6 29.6 1.0 O3B C:ADP507 3.6 19.4 1.0 OE2 C:GLU179 3.8 27.2 1.0 O C:HOH673 3.9 14.4 0.5 O5' C:ADP507 3.9 19.5 1.0 O C:HOH617 4.0 23.3 1.0 OG C:SER140 4.1 16.5 0.5 OD2 C:ASP191 4.2 25.2 1.0 N C:SER142 4.2 12.1 1.0 CA C:SER142 4.3 11.6 1.0 CA C:SER140 4.4 12.3 0.5 CA C:SER140 4.4 9.8 0.5 O C:HOH781 4.5 30.0 1.0 O1B C:ADP507 4.5 16.1 1.0 O1A C:ADP507 4.5 24.1 1.0 CD C:GLU179 4.7 27.3 1.0 CB C:SER140 4.7 14.6 0.5 OE1 C:GLU179 4.8 23.1 1.0 C C:SER140 5.0 9.6 0.5

Magnesium binding site 4 out of 4 in the Crystal Structure of A Galactokinase From Bifidobacterium Infantis in Complex with Adp


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 Galactokinase From Bifidobacterium Infantis in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg511 b:17.9 occ:1.00 O B:HOH700 1.9 21.5 1.0 O B:HOH730 2.0 28.8 1.0 OG B:SER142 2.1 18.8 1.0 O1A B:ADP509 2.1 19.4 1.0 O1B B:ADP509 2.1 17.8 1.0 PB B:ADP509 3.2 17.9 1.0 PA B:ADP509 3.2 19.2 1.0 CB B:SER142 3.2 16.7 1.0 O3A B:ADP509 3.4 17.2 1.0 O B:HOH643 3.6 24.4 1.0 O B:HOH665 3.6 25.7 1.0 O2B B:ADP509 3.8 18.5 1.0 O5' B:ADP509 3.9 19.3 1.0 O B:HOH625 3.9 18.3 1.0 OE2 B:GLU179 4.1 11.0 0.5 N B:SER142 4.2 11.1 1.0 OG B:SER140 4.2 14.2 0.5 CA B:SER142 4.3 13.7 1.0 CA B:SER140 4.3 13.1 0.5 OD2 B:ASP191 4.3 20.7 1.0 CA B:SER140 4.5 13.8 0.5 O3B B:ADP509 4.5 18.2 1.0 O2A B:ADP509 4.5 22.0 1.0 CB B:SER140 4.8 14.1 0.5 O B:HOH721 4.8 30.1 1.0 CD B:GLU179 4.9 10.6 0.5

T.Keenan, F.Parmeggiani, C.Q.Fontenelle, J.Malassis, J.Vendeville, W.A.Offen, P.Both, K.Huang, A.Marchesi, A.Heyam, G.J.Davies, B.Linclau, S.L.Flitsch, M.A.Fascione. Substrate Promiscuity of Wild-Type Sugar Kinases: Chemo-Enzymatic Synthesis of Multi-Fluorinated Monosaccharide-1-Phosphates. To Be Published.