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Magnesium in PDB 4m5j: The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

Enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

All present enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase:
2.7.6.3;

Protein crystallography data

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5j was solved by M.Yun, D.Hoagland, G.Kumar, B.Waddell, C.O.Rock, R.E.Lee, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.37 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.458, 58.264, 38.374, 90.00, 113.76, 90.00
R / Rfree (%) 16.8 / 21.3

Other elements in 4m5j:

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase (pdb code 4m5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4m5j

Go back to Magnesium Binding Sites List in 4m5j
Magnesium binding site 1 out of 2 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:24.5
occ:1.00
 O1B A:APC301 2.1 54.8 1.0
OD2 A:ASP97 2.2 30.2 1.0
OD2 A:ASP95 2.3 32.6 1.0
O2G A:APC301 2.5 35.4 1.0
MG A:MG304 2.9 25.1 1.0
CG A:ASP97 3.0 25.6 1.0
OD1 A:ASP97 3.1 25.6 1.0
CG A:ASP95 3.3 26.8 1.0
PB A:APC301 3.4 47.6 1.0
OD1 A:ASP95 3.5 27.2 1.0
PG A:APC301 3.7 36.9 1.0
O3B A:APC301 3.8 31.6 1.0
O A:HOH460 3.9 27.8 1.0
O A:HOH431 4.1 29.2 1.0
O2B A:APC301 4.2 45.7 1.0
NH1 A:ARG121 4.2 27.8 1.0
O3G A:APC301 4.2 49.3 1.0
NH1 A:ARG92 4.3 43.8 1.0
O A:HOH427 4.4 32.5 1.0
NE2 A:HIS115 4.4 32.5 1.0
CB A:ASP97 4.5 19.1 1.0
CB A:ASP95 4.6 16.5 1.0
O A:HOH459 4.7 27.2 1.0
CE1 A:HIS115 4.7 27.2 1.0
C6 A:YH5302 4.7 58.6 1.0
O1A A:APC301 4.7 38.2 1.0
CE A:MET124 4.7 42.3 1.0
C3A A:APC301 4.8 66.8 1.0
O2 A:YH5302 4.8 60.2 1.0
N1 A:YH5302 4.8 31.4 1.0
O1G A:APC301 5.0 39.7 1.0

Magnesium binding site 2 out of 2 in 4m5j

Go back to Magnesium Binding Sites List in 4m5j
Magnesium binding site 2 out of 2 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:25.1
occ:1.00
 O A:HOH460 2.1 27.8 1.0
O A:HOH459 2.1 27.2 1.0
O1B A:APC301 2.2 54.8 1.0
OD1 A:ASP97 2.3 25.6 1.0
OD1 A:ASP95 2.3 27.2 1.0
O1A A:APC301 2.3 38.2 1.0
MG A:MG303 2.9 24.5 1.0
CG A:ASP95 3.1 26.8 1.0
OD2 A:ASP95 3.3 32.6 1.0
PA A:APC301 3.3 44.8 1.0
CG A:ASP97 3.3 25.6 1.0
PB A:APC301 3.4 47.6 1.0
C3A A:APC301 3.6 66.8 1.0
OD2 A:ASP97 3.7 30.2 1.0
O5' A:APC301 3.8 33.8 1.0
O2G A:APC301 4.1 35.4 1.0
O3G A:APC301 4.2 49.3 1.0
NH2 A:ARG82 4.4 41.3 1.0
O2B A:APC301 4.4 45.7 1.0
O3B A:APC301 4.4 31.6 1.0
PG A:APC301 4.5 36.9 1.0
OE2 A:GLU77 4.6 26.8 1.0
CB A:ASP95 4.6 16.5 1.0
O A:LEU96 4.6 21.2 1.0
CB A:ASP97 4.7 19.1 1.0
O2A A:APC301 4.7 50.3 1.0
NE2 A:HIS115 4.8 32.5 1.0
C2 A:APC301 4.9 24.3 1.0
CA A:ASP97 4.9 15.3 1.0
N3 A:APC301 5.0 25.7 1.0
C A:LEU96 5.0 17.5 1.0
O A:HOH417 5.0 30.1 1.0

Reference:

M.K.Yun, D.Hoagland, G.Kumar, M.B.Waddell, C.O.Rock, R.E.Lee, S.W.White. The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase. Bioorg.Med.Chem. V. 22 2157 2014.
ISSN: ISSN 0968-0896
PubMed: 24613625
DOI: 10.1016/J.BMC.2014.02.022
Page generated: Mon Aug 19 20:18:14 2024

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