Magnesium in PDB 7rcl: Crystal Structure of Adp-Bound Galactokinase

All present enzymatic activity of Crystal Structure of Adp-Bound Galactokinase:
2.7.1.6;

The structure of Crystal Structure of Adp-Bound Galactokinase, PDB code: 7rcl was solved by F.G.Whitby, M.D.Hall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.63 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.901, 114.126, 206.705, 90, 90, 90
R / Rfree (%)	17.3 / 22.8

The structure of Crystal Structure of Adp-Bound Galactokinase also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Adp-Bound Galactokinase (pdb code 7rcl). 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 Adp-Bound Galactokinase, PDB code: 7rcl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:60.2 occ:1.00 O2A A:ADP402 2.4 52.0 1.0 O2B A:ADP402 2.5 50.4 1.0 OG A:SER142 2.5 53.3 1.0 O A:HOH553 2.6 52.4 1.0 O A:HOH520 2.7 44.5 1.0 PB A:ADP402 3.3 49.1 1.0 O3B A:ADP402 3.4 52.4 1.0 CB A:SER142 3.4 41.5 1.0 PA A:ADP402 3.5 48.9 1.0 O3A A:ADP402 3.6 50.6 1.0 OE2 A:GLU174 4.0 57.6 1.0 O5' A:ADP402 4.1 49.4 1.0 O A:HOH554 4.1 71.8 1.0 CA A:SER140 4.3 40.7 1.0 O A:HOH586 4.3 59.8 1.0 O A:HOH511 4.3 54.5 1.0 OD2 A:ASP186 4.3 40.7 1.0 N A:SER142 4.4 42.7 1.0 CA A:SER142 4.4 41.9 1.0 CD1 A:LEU231 4.5 76.5 1.0 O1B A:ADP402 4.6 46.4 1.0 O2 A:GLA401 4.7 46.4 1.0 O1 A:GLA401 4.7 43.6 1.0 O1A A:ADP402 4.8 52.5 1.0 N A:ALA143 4.8 37.3 1.0 CD A:GLU174 4.8 53.2 1.0 OE1 A:GLU174 4.9 58.0 1.0 C A:SER140 4.9 39.6 1.0 OG A:SER140 4.9 44.5 1.0 CB A:SER140 4.9 43.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:72.8 occ:1.00 O B:HOH505 2.3 56.9 1.0 O B:HOH564 2.6 53.9 1.0 O2B B:ADP402 2.6 48.1 1.0 O1A B:ADP402 2.6 48.2 1.0 OG B:SER142 2.7 51.4 1.0 O B:HOH522 2.9 73.0 1.0 O B:HOH566 3.4 51.0 1.0 PB B:ADP402 3.7 47.5 1.0 CB B:SER142 3.8 43.8 1.0 PA B:ADP402 3.8 48.9 1.0 O B:HOH511 3.9 49.1 1.0 OE2 B:GLU174 3.9 56.4 1.0 O1B B:ADP402 3.9 51.5 1.0 OD2 B:ASP186 3.9 45.2 1.0 O3A B:ADP402 4.0 44.8 1.0 O2 B:GLA401 4.1 47.3 1.0 CD1 B:LEU231 4.3 60.0 0.5 CA B:SER140 4.3 44.9 1.0 O5' B:ADP402 4.5 48.9 1.0 O B:HOH590 4.6 57.8 1.0 OG B:SER140 4.6 48.0 1.0 N B:SER142 4.6 43.0 1.0 O1 B:GLA401 4.6 43.4 1.0 CA B:SER142 4.7 43.4 1.0 CD B:GLU174 4.7 52.9 1.0 OE1 B:GLU174 4.8 53.4 1.0 NH2 B:ARG228 4.8 60.4 0.5 N B:ALA143 4.8 41.1 1.0 CB B:SER140 4.8 46.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg405 b:96.8 occ:1.00 O C:HOH564 1.7 105.5 1.0 O C:HOH503 2.4 73.2 1.0 O2A C:ADP402 2.6 56.6 1.0 OG C:SER142 2.9 57.9 1.0 O2B C:ADP402 2.9 47.1 1.0 O C:HOH534 3.3 77.1 1.0 OE2 C:GLU174 3.5 66.6 1.0 O C:HOH501 3.5 66.0 1.0 O C:HOH530 3.7 48.5 1.0 O C:HOH574 3.9 74.2 1.0 PA C:ADP402 3.9 57.2 1.0 PB C:ADP402 3.9 53.8 1.0 CB C:SER142 4.0 52.3 1.0 O3A C:ADP402 4.1 49.4 1.0 O3B C:ADP402 4.2 61.6 1.0 O2 C:GLA401 4.3 60.4 1.0 OD2 C:ASP186 4.4 56.3 1.0 CD C:GLU174 4.5 63.3 1.0 CE C:MET180 4.6 87.0 1.0 O5' C:ADP402 4.7 58.0 1.0 OE1 C:GLU174 4.8 64.4 1.0 CA C:SER140 4.8 57.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


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 Adp-Bound Galactokinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg406 b:94.8 occ:1.00 O D:HOH537 2.6 55.0 1.0 OG D:SER142 2.6 71.5 1.0 O D:HOH540 2.8 63.4 1.0 O D:HOH508 2.9 73.4 1.0 OD2 D:ASP186 2.9 61.1 1.0 O2B D:ADP402 3.0 64.2 1.0 O2 D:GLA401 3.7 61.6 1.0 O2A D:ADP402 3.8 76.7 1.0 CB D:SER142 3.9 65.0 1.0 OE2 D:GLU174 4.0 84.6 1.0 CA D:SER140 4.1 56.4 1.0 CG D:ASP186 4.1 57.5 1.0 CB D:SER140 4.1 56.9 1.0 OG D:SER140 4.3 61.2 1.0 PB D:ADP402 4.3 67.7 1.0 OE1 D:GLU174 4.4 81.2 1.0 O1 D:GLA401 4.4 58.7 1.0 CB D:ASP186 4.5 56.1 1.0 N D:ALA143 4.5 57.4 1.0 CD D:GLU174 4.6 78.4 1.0 O1B D:ADP402 4.6 71.9 1.0 O D:HOH566 4.7 67.2 1.0 O D:HOH551 4.8 55.5 1.0 CA D:SER142 4.9 63.2 1.0 PA D:ADP402 4.9 73.7 1.0 C D:SER140 5.0 56.9 1.0 C2 D:GLA401 5.0 58.4 1.0 N D:SER140 5.0 54.0 1.0 O3A D:ADP402 5.0 70.9 1.0 N D:SER142 5.0 64.4 1.0

L.Liu, M.Tang, R.Pragani, F.G.Whitby, Y.Q.Zhang, B.Balakrishnan, Y.Fang, S.Karavadhi, D.Tao, C.A.Leclair, M.D.Hall, J.J.Marugan, M.Boxer, M.Shen, C.P.Hill, K.Lai, S.Patnaik. Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors Journal of Medicinal 2021CHEMISTRY.
DOI: 10.1021/ACS.JMEDCHEM.1C00945