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Magnesium in PDB 4cyu: Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp

Enzymatic activity of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp

All present enzymatic activity of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp:
2.7.6.3;

Protein crystallography data

The structure of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp, PDB code: 4cyu was solved by M.L.Dennis, J.D.Swarbrick, T.S.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.53 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.002, 94.263, 62.989, 90.00, 112.44, 90.00
R / Rfree (%) 19.217 / 24.223

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp (pdb code 4cyu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp, PDB code: 4cyu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4cyu

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Magnesium binding site 1 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg170

b:36.4
occ:1.00
 O1A A:APC1158 2.0 44.3 1.0
OD1 A:ASP97 2.0 45.1 1.0
O1B A:APC1158 2.2 41.8 1.0
O A:HOH2002 2.3 28.0 1.0
OD1 A:ASP95 2.5 36.9 1.0
PA A:APC1158 3.0 41.6 1.0
CG A:ASP97 3.0 40.8 1.0
PB A:APC1158 3.1 43.5 1.0
C3A A:APC1158 3.1 40.1 1.0
CG A:ASP95 3.3 42.8 1.0
OD2 A:ASP97 3.4 44.6 1.0
OD2 A:ASP95 3.4 43.5 1.0
O5' A:APC1158 3.7 36.8 1.0
O2B A:APC1158 4.0 44.1 1.0
MG A:MG171 4.2 46.2 1.0
O3G A:APC1158 4.2 41.8 1.0
O A:VAL96 4.2 40.0 1.0
N3 A:APC1158 4.3 49.8 1.0
O2A A:APC1158 4.3 43.9 1.0
OE2 A:GLU78 4.3 60.7 1.0
CB A:ASP97 4.3 41.1 1.0
O3B A:APC1158 4.3 43.1 1.0
C2 A:APC1158 4.3 48.5 1.0
O1G A:APC1158 4.4 48.1 1.0
NH2 A:ARG92 4.4 65.3 1.0
NH1 A:ARG92 4.5 66.3 1.0
C5' A:APC1158 4.5 39.6 1.0
PG A:APC1158 4.6 47.3 1.0
CA A:ASP97 4.6 41.6 1.0
C A:VAL96 4.7 38.8 1.0
CB A:ASP95 4.8 42.1 1.0
N A:ASP97 4.9 40.2 1.0
CZ A:ARG92 4.9 65.6 1.0

Magnesium binding site 2 out of 8 in 4cyu

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Magnesium binding site 2 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg171

b:46.2
occ:1.00
 OD2 A:ASP95 2.1 43.5 1.0
O1G A:APC1158 2.1 48.1 1.0
OD2 A:ASP97 2.4 44.6 1.0
O1B A:APC1158 2.5 41.8 1.0
CG A:ASP95 3.3 42.8 1.0
PG A:APC1158 3.4 47.3 1.0
PB A:APC1158 3.4 43.5 1.0
CG A:ASP97 3.5 40.8 1.0
O3B A:APC1158 3.5 43.1 1.0
O A:HOH2001 3.8 46.1 1.0
OD1 A:ASP97 3.9 45.1 1.0
O2B A:APC1158 4.0 44.1 1.0
OD1 A:ASP95 4.0 36.9 1.0
NH1 A:ARG121 4.0 49.9 1.0
MG A:MG170 4.2 36.4 1.0
CB A:ASP95 4.3 42.1 1.0
O3G A:APC1158 4.3 41.8 1.0
O2G A:APC1158 4.4 45.6 1.0
CB A:ASP97 4.7 41.1 1.0
CZ A:ARG121 4.8 49.0 1.0
NH2 A:ARG121 4.9 47.6 1.0
NE2 A:HIS115 5.0 47.3 1.0

Magnesium binding site 3 out of 8 in 4cyu

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Magnesium binding site 3 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg170

b:46.2
occ:1.00
 O B:HOH2001 2.1 39.9 1.0
OD1 B:ASP95 2.2 42.9 1.0
O1A B:APC1159 2.3 42.5 0.4
OD1 B:ASP97 2.4 49.7 1.0
O1A B:APC1159 2.6 31.7 0.6
OE2 B:GLU78 2.8 66.3 1.0
O B:VAL96 3.1 38.9 1.0
O1B B:APC1159 3.1 29.7 0.6
O2B B:APC1159 3.2 41.9 0.4
CG B:ASP95 3.4 41.2 1.0
PA B:APC1159 3.6 44.1 0.4
O5' B:APC1159 3.6 32.6 0.6
CG B:ASP97 3.7 41.1 1.0
PA B:APC1159 3.7 32.6 0.6
C B:VAL96 3.8 37.3 1.0
O5' B:APC1159 3.8 43.8 0.4
CD B:GLU78 3.9 61.5 1.0
OD2 B:ASP95 3.9 48.0 1.0
NH1 B:ARG92 4.0 50.2 1.0
N B:VAL96 4.0 36.5 1.0
OE1 B:GLU78 4.2 75.7 1.0
C2 B:APC1159 4.3 48.8 0.4
C2 B:APC1159 4.3 41.5 0.6
PB B:APC1159 4.3 31.4 0.6
OD2 B:ASP97 4.3 42.3 1.0
N3 B:APC1159 4.4 50.3 0.4
N B:ASP97 4.4 38.8 1.0
N3 B:APC1159 4.4 43.5 0.6
CA B:ASP97 4.5 39.3 1.0
C3A B:APC1159 4.5 30.0 0.6
CA B:VAL96 4.6 37.1 1.0
CB B:ASP95 4.6 39.0 1.0
O2A B:APC1159 4.6 45.1 0.4
PB B:APC1159 4.6 42.9 0.4
CA B:ASP95 4.6 39.2 1.0
CB B:ASP97 4.7 37.3 1.0
C B:ASP95 4.7 37.8 1.0
C3A B:APC1159 4.7 41.8 0.4
NH2 B:ARG92 4.7 43.7 1.0
CZ B:ARG92 4.8 45.5 1.0
CD2 B:LEU75 4.9 57.2 1.0
C5' B:APC1159 4.9 33.6 0.6

Magnesium binding site 4 out of 8 in 4cyu

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Magnesium binding site 4 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg171

b:45.4
occ:1.00
 O1G B:APC1159 1.9 27.3 0.6
OD2 B:ASP95 2.1 48.0 1.0
OD2 B:ASP97 2.4 42.3 1.0
O1B B:APC1159 2.5 29.7 0.6
O2B B:APC1159 2.6 41.9 0.4
O1B B:APC1159 2.8 42.7 0.4
PG B:APC1159 3.0 25.1 0.6
PB B:APC1159 3.0 31.4 0.6
O3B B:APC1159 3.1 28.6 0.6
PB B:APC1159 3.2 42.9 0.4
CG B:ASP95 3.2 41.2 1.0
O2B B:APC1159 3.4 31.5 0.6
CG B:ASP97 3.5 41.1 1.0
O3B B:APC1159 3.7 40.6 0.4
OD1 B:ASP97 3.8 49.7 1.0
O2G B:APC1159 3.8 24.3 0.6
OD1 B:ASP95 3.8 42.9 1.0
O3G B:APC1159 4.1 25.0 0.6
NH1 B:ARG121 4.2 40.3 1.0
CB B:ASP95 4.3 39.0 1.0
O1A B:APC1159 4.5 42.5 0.4
O B:HOH2001 4.5 39.9 1.0
CB B:ASP97 4.8 37.3 1.0
C3A B:APC1159 4.8 30.0 0.6
C3A B:APC1159 4.8 41.8 0.4
NH2 B:ARG121 4.8 44.0 1.0
NH2 B:ARG92 4.9 43.7 1.0
CZ B:ARG121 4.9 41.8 1.0
NE2 B:HIS115 4.9 46.1 1.0
O1A B:APC1159 5.0 31.7 0.6

Magnesium binding site 5 out of 8 in 4cyu

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Magnesium binding site 5 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg170

b:28.9
occ:1.00
 O1A C:APC1158 1.9 35.5 1.0
O C:HOH2002 2.1 44.7 1.0
OD1 C:ASP97 2.1 45.0 1.0
O C:HOH2001 2.1 38.9 1.0
O1B C:APC1158 2.2 40.1 1.0
OD1 C:ASP95 2.2 41.1 1.0
PA C:APC1158 2.9 40.2 1.0
PB C:APC1158 3.1 43.2 1.0
CG C:ASP95 3.2 43.3 1.0
CG C:ASP97 3.2 44.0 1.0
C3A C:APC1158 3.3 40.0 1.0
OD2 C:ASP95 3.4 47.8 1.0
O5' C:APC1158 3.4 43.8 1.0
OD2 C:ASP97 3.6 46.8 1.0
O2B C:APC1158 3.9 42.9 1.0
OE2 C:GLU78 4.0 57.0 1.0
O C:VAL96 4.1 41.8 1.0
NH1 C:ARG92 4.1 74.9 1.0
NH2 C:ARG92 4.1 71.3 1.0
MG C:MG171 4.2 38.0 1.0
O2A C:APC1158 4.4 42.9 1.0
O3B C:APC1158 4.5 45.3 1.0
CB C:ASP97 4.5 41.3 1.0
N3 C:APC1158 4.5 50.1 1.0
O1G C:APC1158 4.6 48.6 1.0
C2 C:APC1158 4.6 52.6 1.0
C C:VAL96 4.6 40.2 1.0
CZ C:ARG92 4.6 71.8 1.0
CB C:ASP95 4.6 41.3 1.0
CA C:ASP97 4.7 43.2 1.0
O3G C:APC1158 4.8 42.0 1.0
C5' C:APC1158 4.8 43.8 1.0
N C:VAL96 4.8 38.8 1.0
N C:ASP97 4.9 42.7 1.0
PG C:APC1158 5.0 44.6 1.0
CD C:GLU78 5.0 56.9 1.0

Magnesium binding site 6 out of 8 in 4cyu

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Magnesium binding site 6 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg171

b:38.0
occ:1.00
 O1G C:APC1158 2.0 48.6 1.0
OD2 C:ASP95 2.0 47.8 1.0
OD2 C:ASP97 2.3 46.8 1.0
O1B C:APC1158 2.5 40.1 1.0
CG C:ASP95 3.2 43.3 1.0
CG C:ASP97 3.3 44.0 1.0
PG C:APC1158 3.3 44.6 1.0
PB C:APC1158 3.5 43.2 1.0
O3B C:APC1158 3.5 45.3 1.0
OD1 C:ASP97 3.8 45.0 1.0
OD1 C:ASP95 3.9 41.1 1.0
NH1 C:ARG121 4.0 47.2 1.0
O2B C:APC1158 4.1 42.9 1.0
MG C:MG170 4.2 28.9 1.0
O2G C:APC1158 4.3 41.6 1.0
CB C:ASP95 4.3 41.3 1.0
O3G C:APC1158 4.4 42.0 1.0
CB C:ASP97 4.6 41.3 1.0
CZ C:ARG121 4.8 46.2 1.0
NE2 C:HIS115 4.9 48.0 1.0
NH2 C:ARG121 4.9 45.3 1.0
NH2 C:ARG92 5.0 71.3 1.0

Magnesium binding site 7 out of 8 in 4cyu

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Magnesium binding site 7 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg170

b:31.0
occ:1.00
 O1A D:APC1158 1.9 35.0 0.4
OD1 D:ASP97 2.0 52.5 1.0
O D:HOH2002 2.1 45.3 1.0
O1A D:APC1158 2.1 44.5 0.6
O1B D:APC1158 2.2 36.2 0.6
O2B D:APC1158 2.4 31.7 0.4
OD1 D:ASP95 2.5 43.2 1.0
PA D:APC1158 3.0 42.1 0.6
CG D:ASP97 3.1 45.5 1.0
PA D:APC1158 3.2 32.4 0.4
PB D:APC1158 3.3 39.4 0.6
C3A D:APC1158 3.4 40.4 0.6
O5' D:APC1158 3.4 47.5 0.6
CG D:ASP95 3.4 43.0 1.0
OD2 D:ASP97 3.5 49.3 1.0
OD2 D:ASP95 3.6 47.6 1.0
O5' D:APC1158 3.7 34.7 0.4
PB D:APC1158 3.8 33.3 0.4
O D:VAL96 3.9 39.0 1.0
C3A D:APC1158 3.9 33.0 0.4
OE2 D:GLU78 4.1 59.9 1.0
C5' D:APC1158 4.1 35.2 0.4
N3 D:APC1158 4.1 35.1 0.4
C2 D:APC1158 4.1 34.3 0.4
N3 D:APC1158 4.1 56.5 0.6
MG D:MG171 4.2 43.8 1.0
C2 D:APC1158 4.2 55.1 0.6
O2B D:APC1158 4.2 41.3 0.6
CB D:ASP97 4.3 42.9 1.0
O2A D:APC1158 4.4 34.5 0.4
C D:VAL96 4.4 42.3 1.0
O2A D:APC1158 4.5 44.5 0.6
CA D:ASP97 4.5 42.6 1.0
NH1 D:ARG92 4.5 59.0 1.0
O3B D:APC1158 4.6 31.4 0.6
O1B D:APC1158 4.6 33.4 0.4
O1G D:APC1158 4.7 24.9 0.6
NH2 D:ARG92 4.7 52.0 1.0
N D:ASP97 4.7 42.5 1.0
C5' D:APC1158 4.8 48.8 0.6
CB D:ASP95 4.9 39.2 1.0
N1 D:APC1158 4.9 33.6 0.4
C4 D:APC1158 4.9 33.8 0.4
N D:VAL96 4.9 41.8 1.0
O3B D:APC1158 4.9 30.9 0.4
C4 D:APC1158 4.9 52.8 0.6
O4' D:APC1158 4.9 35.1 0.4
O3G D:APC1158 5.0 24.9 0.6
N1 D:APC1158 5.0 53.6 0.6

Magnesium binding site 8 out of 8 in 4cyu

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Magnesium binding site 8 out of 8 in the Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Staphylococcus Aureus 7,8-Dihydro-6-Hydroxymethylpterin- Pyrophosphokinase in Complex with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg171

b:43.8
occ:1.00
 O1G D:APC1158 1.8 24.9 0.6
OD2 D:ASP95 2.1 47.6 1.0
OD2 D:ASP97 2.3 49.3 1.0
O2B D:APC1158 2.4 31.7 0.4
O1B D:APC1158 2.4 36.2 0.6
O1B D:APC1158 2.8 33.4 0.4
PB D:APC1158 3.1 33.3 0.4
PG D:APC1158 3.2 24.3 0.6
PB D:APC1158 3.2 39.4 0.6
CG D:ASP95 3.3 43.0 1.0
CG D:ASP97 3.3 45.5 1.0
O3B D:APC1158 3.4 31.4 0.6
O2B D:APC1158 3.7 41.3 0.6
OD1 D:ASP97 3.7 52.5 1.0
O3B D:APC1158 3.8 30.9 0.4
OD1 D:ASP95 3.9 43.2 1.0
NH1 D:ARG121 4.1 50.1 1.0
O2G D:APC1158 4.1 23.0 0.6
O3G D:APC1158 4.1 24.9 0.6
MG D:MG170 4.2 31.0 1.0
CB D:ASP95 4.4 39.2 1.0
O1A D:APC1158 4.6 35.0 0.4
CB D:ASP97 4.6 42.9 1.0
C3A D:APC1158 4.7 33.0 0.4
NE2 D:HIS115 4.8 42.5 1.0
CZ D:ARG121 4.8 47.4 1.0
NH2 D:ARG121 4.8 46.2 1.0
O1A D:APC1158 4.8 44.5 0.6
C3A D:APC1158 4.9 40.4 0.6

Reference:

M.L.Dennis, S.Chhabra, Z.Wang, A.Debono, O.Dolezal, J.Newman, N.P.Pitcher, R.Rahmani, B.Cleary, N.Barlow, M.Hattarki, B.Graham, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structure-Based Design and Development of Functionalized Mercaptoguanine Derivatives As Inhibitors of the Folate Biosynthesis Pathway Enzyme 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase From Staphylococcus Aureus. J.Med.Chem. V. 57 9612 2014.
ISSN: ISSN 0022-2623
PubMed: 25357262
DOI: 10.1021/JM501417F
Page generated: Thu Aug 15 16:56:11 2024

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