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Magnesium in PDB 4m5n: 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: 4m5n 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) 35.12 / 2.00
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 107.305, 107.305, 41.795, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.2

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 4m5n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 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: 4m5n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4m5n

Go back to Magnesium Binding Sites List in 4m5n
Magnesium binding site 1 out of 4 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:Mg501

b:17.9
occ:1.00
 O A:HOH604 2.1 14.2 1.0
OD1 A:ASP95 2.1 18.3 1.0
OD1 A:ASP97 2.1 20.3 1.0
O1A A:APC503 2.1 19.2 1.0
O A:HOH603 2.1 14.4 1.0
O1B A:APC503 2.1 18.3 1.0
CG A:ASP95 3.0 13.8 1.0
CG A:ASP97 3.1 15.8 1.0
PA A:APC503 3.2 21.5 1.0
PB A:APC503 3.2 20.9 1.0
OD2 A:ASP95 3.3 16.0 1.0
MG A:MG502 3.4 18.6 1.0
OD2 A:ASP97 3.5 17.9 1.0
C3A A:APC503 3.6 19.2 1.0
O5' A:APC503 3.8 29.0 1.0
O2B A:APC503 3.9 18.4 1.0
OE2 A:GLU77 4.0 24.1 1.0
O A:LEU96 4.1 17.9 1.0
O A:HOH689 4.2 30.6 1.0
O A:HOH605 4.2 24.6 1.0
NH1 A:ARG82 4.4 17.8 1.0
CB A:ASP95 4.4 12.9 1.0
CB A:ASP97 4.5 13.4 1.0
NH2 A:ARG82 4.5 21.4 1.0
O A:HOH606 4.5 20.9 1.0
C A:LEU96 4.5 12.8 1.0
O3B A:APC503 4.6 19.3 1.0
O2A A:APC503 4.6 19.1 1.0
N A:LEU96 4.7 16.5 1.0
CA A:ASP97 4.7 19.1 1.0
O2G A:APC503 4.7 19.6 1.0
N3 A:APC503 4.8 18.8 1.0
N A:ASP97 4.8 16.3 1.0
C2 A:APC503 4.8 20.8 1.0
O3G A:APC503 4.8 23.6 1.0
O A:HOH602 4.8 17.8 1.0
CA A:ASP95 4.9 16.1 1.0
CZ A:ARG82 4.9 21.2 1.0

Magnesium binding site 2 out of 4 in 4m5n

Go back to Magnesium Binding Sites List in 4m5n
Magnesium binding site 2 out of 4 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:Mg502

b:18.6
occ:1.00
 OD2 A:ASP97 2.0 17.9 1.0
OD2 A:ASP95 2.1 16.0 1.0
O A:HOH602 2.1 17.8 1.0
O A:HOH601 2.1 24.1 1.0
O1B A:APC503 2.1 18.3 1.0
O2G A:APC503 2.2 19.6 1.0
CG A:ASP97 2.9 15.8 1.0
CG A:ASP95 3.1 13.8 1.0
OD1 A:ASP97 3.2 20.3 1.0
PB A:APC503 3.2 20.9 1.0
PG A:APC503 3.3 22.1 1.0
MG A:MG501 3.4 17.9 1.0
O3B A:APC503 3.4 19.3 1.0
OD1 A:ASP95 3.5 18.3 1.0
O2B A:APC503 3.9 18.4 1.0
O A:HOH612 3.9 18.0 1.0
O3G A:APC503 4.1 23.6 1.0
NE2 A:HIS115 4.2 23.6 1.0
CB A:ASP97 4.2 13.4 1.0
NH1 A:ARG121 4.2 19.3 1.0
O A:HOH614 4.3 33.2 1.0
S11 A:YH7504 4.3 20.3 1.0
NH1 A:ARG92 4.4 18.7 1.0
O A:HOH603 4.4 14.4 1.0
CB A:ASP95 4.4 12.9 1.0
O A:HOH689 4.5 30.6 1.0
O1G A:APC503 4.6 23.2 1.0
C3A A:APC503 4.7 19.2 1.0
O1A A:APC503 4.8 19.2 1.0
CD2 A:HIS115 4.9 23.6 1.0

Magnesium binding site 3 out of 4 in 4m5n

Go back to Magnesium Binding Sites List in 4m5n
Magnesium binding site 3 out of 4 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 3 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
B:Mg201

b:19.2
occ:1.00
 OD2 B:ASP97 2.0 20.9 1.0
OD2 B:ASP95 2.1 17.1 1.0
O B:HOH341 2.1 23.7 1.0
O B:HOH342 2.1 18.7 1.0
O2G B:APC203 2.2 19.4 1.0
O1B B:APC203 2.2 17.4 1.0
CG B:ASP97 2.9 16.4 1.0
CG B:ASP95 3.1 15.1 1.0
PB B:APC203 3.2 21.8 1.0
OD1 B:ASP97 3.3 18.5 1.0
PG B:APC203 3.3 20.8 1.0
O3B B:APC203 3.4 20.6 1.0
MG B:MG202 3.5 18.4 1.0
OD1 B:ASP95 3.5 17.3 1.0
O2B B:APC203 3.9 18.2 1.0
O B:HOH338 4.0 18.1 1.0
O3G B:APC203 4.0 19.9 1.0
NH1 B:ARG121 4.1 17.4 1.0
NE2 B:HIS115 4.1 21.3 1.0
O B:HOH380 4.2 33.5 1.0
CB B:ASP97 4.3 14.6 1.0
NH1 B:ARG92 4.4 18.4 1.0
S11 B:YH7204 4.4 19.8 1.0
CB B:ASP95 4.4 12.5 1.0
O B:HOH373 4.4 15.8 1.0
O1G B:APC203 4.5 26.3 1.0
O B:HOH374 4.5 28.3 1.0
C3A B:APC203 4.8 18.9 1.0
O1A B:APC203 4.9 18.3 1.0
CD2 B:HIS115 4.9 23.2 1.0

Magnesium binding site 4 out of 4 in 4m5n

Go back to Magnesium Binding Sites List in 4m5n
Magnesium binding site 4 out of 4 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 4 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
B:Mg202

b:18.4
occ:1.00
 OD1 B:ASP95 2.0 17.3 1.0
O1A B:APC203 2.1 18.3 1.0
OD1 B:ASP97 2.1 18.5 1.0
O B:HOH309 2.1 13.7 1.0
O B:HOH373 2.1 15.8 1.0
O1B B:APC203 2.1 17.4 1.0
CG B:ASP95 3.0 15.1 1.0
CG B:ASP97 3.1 16.4 1.0
OD2 B:ASP95 3.2 17.1 1.0
PB B:APC203 3.2 21.8 1.0
PA B:APC203 3.2 19.1 1.0
MG B:MG201 3.5 19.2 1.0
OD2 B:ASP97 3.5 20.9 1.0
C3A B:APC203 3.6 18.9 1.0
O5' B:APC203 3.8 22.7 1.0
O2B B:APC203 4.0 18.2 1.0
OE2 B:GLU77 4.0 25.9 1.0
O B:LEU96 4.1 15.4 1.0
O B:HOH374 4.2 28.3 1.0
O B:HOH308 4.2 24.3 1.0
NH1 B:ARG82 4.3 19.1 1.0
CB B:ASP95 4.4 12.5 1.0
O B:HOH310 4.4 18.6 1.0
CB B:ASP97 4.5 14.6 1.0
C B:LEU96 4.5 12.7 1.0
NH2 B:ARG82 4.5 18.4 1.0
O3B B:APC203 4.5 20.6 1.0
O2A B:APC203 4.6 19.1 1.0
N B:LEU96 4.6 15.6 1.0
CA B:ASP97 4.7 19.7 1.0
C2 B:APC203 4.7 18.6 1.0
O2G B:APC203 4.7 19.4 1.0
N3 B:APC203 4.8 18.3 1.0
N B:ASP97 4.8 15.4 1.0
O3G B:APC203 4.8 19.9 1.0
CA B:ASP95 4.8 18.4 1.0
O B:HOH342 4.9 18.7 1.0
CZ B:ARG82 5.0 21.4 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 11 20:19:24 2025

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