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

Enzymatic activity of Crystal Structure of Adp-Bound Galactokinase

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

Protein crystallography data

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

Resolution Low / High (Å) 39.82 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 128.793, 128.793, 240.652, 90, 90, 120
R / Rfree (%) 19.6 / 23.6

Other elements in 7rcm:

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

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adp-Bound Galactokinase (pdb code 7rcm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Adp-Bound Galactokinase, PDB code: 7rcm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7rcm

Go back to Magnesium Binding Sites List in 7rcm
Magnesium binding site 1 out of 2 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:65.9
occ:1.00
O A:HOH501 2.4 50.1 1.0
O2B A:ADP401 2.4 40.8 1.0
O A:HOH545 2.6 49.5 1.0
OG A:SER142 2.6 42.8 1.0
O2A A:ADP401 2.7 42.4 1.0
O A:HOH536 2.8 52.4 1.0
PB A:ADP401 3.4 43.3 1.0
O3B A:ADP401 3.5 42.8 1.0
O3A A:ADP401 3.7 43.6 1.0
PA A:ADP401 3.7 44.8 1.0
CB A:SER142 3.7 42.4 1.0
O A:HOH593 4.0 57.5 1.0
OD2 A:ASP186 4.1 42.6 1.0
O A:HOH524 4.2 37.1 1.0
OE2 A:GLU174 4.2 51.1 1.0
CA A:SER140 4.2 38.2 0.5
CA A:SER140 4.3 37.7 0.5
O2 A:GLA402 4.3 44.0 1.0
OG A:SER140 4.4 37.9 0.5
O5' A:ADP401 4.5 42.6 1.0
O A:HOH592 4.5 47.0 1.0
O1 A:GLA402 4.7 44.6 1.0
CB A:SER140 4.7 38.0 0.5
N A:SER142 4.7 41.1 1.0
CA A:SER142 4.8 41.2 1.0
O1B A:ADP401 4.8 43.6 1.0
CB A:SER140 4.9 37.1 0.5
OG A:SER140 5.0 37.0 0.5
N A:SER140 5.0 39.2 0.5
N A:SER140 5.0 38.9 0.5

Magnesium binding site 2 out of 2 in 7rcm

Go back to Magnesium Binding Sites List in 7rcm
Magnesium binding site 2 out of 2 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:48.2
occ:1.00
O1A B:ADP401 2.4 33.9 1.0
O1B B:ADP401 2.4 34.3 1.0
OG B:SER142 2.4 32.6 1.0
O B:HOH579 2.5 50.3 1.0
O B:HOH511 2.6 38.2 1.0
CB B:SER142 3.3 32.4 1.0
O B:HOH598 3.4 51.7 1.0
PB B:ADP401 3.4 34.8 1.0
PA B:ADP401 3.5 37.1 1.0
O B:HOH507 3.5 71.5 1.0
O3A B:ADP401 3.6 34.3 1.0
O3B B:ADP401 3.7 36.7 1.0
O B:HOH575 3.7 59.1 1.0
O B:HOH540 3.7 37.4 1.0
O5' B:ADP401 3.9 33.3 1.0
OE2 B:GLU174 4.1 43.1 1.0
N B:SER142 4.2 33.0 1.0
CA B:SER140 4.2 35.0 1.0
CA B:SER142 4.2 31.9 1.0
OD2 B:ASP186 4.3 32.6 1.0
O2 B:GLA402 4.6 33.6 1.0
N B:ALA143 4.6 31.5 1.0
OE1 B:GLU174 4.7 39.7 1.0
O2B B:ADP401 4.7 34.7 1.0
CD B:GLU174 4.8 38.0 1.0
C B:SER140 4.8 34.5 1.0
O2A B:ADP401 4.8 35.3 1.0
CB B:SER140 4.9 35.8 1.0
C B:SER142 4.9 31.7 1.0
OG B:SER140 4.9 36.9 1.0
N B:SER141 5.0 35.1 1.0

Reference:

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
Page generated: Fri Nov 5 15:34:30 2021

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