Sodium in PDB 7rcl: 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: 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

Other elements in 7rcl:

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

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Adp-Bound Galactokinase (pdb code 7rcl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Adp-Bound Galactokinase, PDB code: 7rcl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7rcl

Go back to Sodium Binding Sites List in 7rcl
Sodium binding site 1 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Adp-Bound Galactokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:37.6
occ:1.00
 O A:GLY374 2.4 55.8 1.0
O A:TYR372 2.5 61.1 1.0
OE1 A:GLN369 2.5 58.6 1.0
O A:GLN369 2.7 65.7 1.0
CD A:GLN369 3.5 58.8 1.0
C A:TYR372 3.7 61.9 1.0
C A:GLY374 3.7 56.7 1.0
C A:GLN369 3.8 60.3 1.0
CG A:GLN369 3.9 56.2 1.0
CB A:TYR372 4.1 60.2 1.0
CA A:TYR372 4.3 61.2 1.0
CA A:GLN369 4.4 58.3 1.0
N A:THR375 4.5 56.8 1.0
N A:TYR372 4.5 60.3 1.0
CA A:THR375 4.5 58.0 1.0
CD2 A:TYR372 4.6 64.3 1.0
N A:GLY374 4.6 65.0 1.0
NE2 A:GLN369 4.7 49.5 1.0
C A:GLY373 4.7 67.0 1.0
CG A:TYR372 4.7 60.1 1.0
CA A:GLY374 4.7 60.0 1.0
N A:GLY373 4.7 62.0 1.0
CB A:GLN369 4.8 57.8 1.0
N A:GLU370 4.9 62.9 1.0
O A:GLY373 4.9 72.3 1.0
O A:GLU370 5.0 61.6 1.0

Sodium binding site 2 out of 4 in 7rcl

Go back to Sodium Binding Sites List in 7rcl
Sodium binding site 2 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Adp-Bound Galactokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:43.7
occ:1.00
 O B:GLN369 2.5 60.5 1.0
O B:TYR372 2.5 64.3 1.0
OE1 B:GLN369 2.5 61.4 1.0
O B:GLY374 2.5 59.7 1.0
CD B:GLN369 3.5 63.4 1.0
C B:GLN369 3.6 67.3 1.0
C B:TYR372 3.7 65.7 1.0
C B:GLY374 3.8 60.4 1.0
CG B:GLN369 3.8 63.8 1.0
CA B:GLN369 4.2 68.0 1.0
CB B:TYR372 4.2 58.7 1.0
CA B:TYR372 4.3 64.9 1.0
CA B:THR375 4.4 61.6 1.0
N B:TYR372 4.5 63.5 1.0
N B:THR375 4.5 56.7 1.0
CB B:GLN369 4.6 65.5 1.0
CD2 B:TYR372 4.7 54.9 1.0
O B:GLY373 4.7 73.7 1.0
NE2 B:GLN369 4.7 52.1 1.0
N B:GLU370 4.7 68.0 1.0
C B:GLY373 4.7 68.4 1.0
N B:GLY373 4.8 68.6 1.0
CG B:TYR372 4.8 56.5 1.0
N B:GLY374 4.8 67.7 1.0
CA B:GLY374 4.9 64.5 1.0
N B:ALA376 4.9 57.8 1.0
OG1 B:THR375 5.0 70.5 1.0

Sodium binding site 3 out of 4 in 7rcl

Go back to Sodium Binding Sites List in 7rcl
Sodium binding site 3 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Adp-Bound Galactokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na406

b:65.3
occ:1.00
 O C:GLN369 2.6 96.7 1.0
O C:GLY374 2.7 97.9 1.0
O C:TYR372 2.7 89.2 1.0
OE1 C:GLN369 3.0 90.6 1.0
C C:GLN369 3.6 95.2 1.0
CD C:GLN369 3.8 89.3 1.0
O C:GLY373 3.9 103.3 1.0
C C:GLY374 3.9 95.7 1.0
C C:TYR372 3.9 94.1 1.0
CG C:GLN369 4.0 88.7 1.0
CA C:GLN369 4.2 90.7 1.0
CB C:TYR372 4.4 93.5 1.0
C C:GLY373 4.5 97.4 1.0
CA C:THR375 4.6 98.5 1.0
CA C:TYR372 4.6 94.5 1.0
N C:THR375 4.6 99.3 1.0
CB C:GLN369 4.7 89.5 1.0
N C:GLU370 4.7 101.2 1.0
N C:TYR372 4.7 94.8 1.0
CD2 C:TYR372 4.8 90.3 1.0
N C:GLY374 5.0 93.1 1.0
N C:GLY373 5.0 95.4 1.0
CG C:TYR372 5.0 88.2 1.0

Sodium binding site 4 out of 4 in 7rcl

Go back to Sodium Binding Sites List in 7rcl
Sodium binding site 4 out of 4 in the Crystal Structure of Adp-Bound Galactokinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Adp-Bound Galactokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na407

b:51.4
occ:1.00
 O D:GLY374 2.3 58.7 1.0
O D:GLN369 2.7 72.5 1.0
OE1 D:GLN369 2.7 62.9 1.0
O D:TYR372 2.8 71.0 1.0
C D:GLY374 3.6 64.5 1.0
CD D:GLN369 3.6 64.1 1.0
C D:GLN369 3.8 66.2 1.0
CG D:GLN369 3.8 65.4 1.0
C D:TYR372 3.8 69.8 1.0
CB D:TYR372 4.2 63.1 1.0
CA D:GLN369 4.2 66.8 1.0
N D:GLY374 4.3 73.5 1.0
CA D:TYR372 4.5 64.9 1.0
N D:THR375 4.5 61.9 1.0
CA D:GLY374 4.6 67.2 1.0
CA D:THR375 4.6 67.8 1.0
CB D:GLN369 4.6 67.0 1.0
N D:TYR372 4.6 63.2 1.0
CD2 D:TYR372 4.7 61.7 1.0
C D:GLY373 4.8 79.0 1.0
NE2 D:GLN369 4.8 57.8 1.0
CG D:TYR372 4.8 62.9 1.0
N D:GLY373 4.8 72.2 1.0
N D:GLU370 4.9 66.2 1.0
N D:ALA376 4.9 65.7 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 16:05:17 2021

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