Magnesium in PDB 5cge: Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol

Enzymatic activity of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol

All present enzymatic activity of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol:
2.7.1.50;

Protein crystallography data

The structure of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol, PDB code: 5cge was solved by M.Kuenz, J.Drebes, B.Windshuegel, H.Cang, C.Wrenger, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.345, 62.483, 109.167, 92.64, 92.05, 101.46
R / Rfree (%) 18.2 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol (pdb code 5cge). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol, PDB code: 5cge:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5cge

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Magnesium binding site 1 out of 5 in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:53.0
occ:1.00
 O A:HOH426 2.2 41.1 1.0
O A:HOH459 2.2 27.3 1.0
O A:HOH402 2.7 32.5 1.0
NZ A:LYS115 3.9 42.1 1.0
O A:HOH484 4.0 35.0 1.0
CA A:GLY189 4.1 20.9 1.0
C A:GLY189 4.3 19.9 1.0
OE1 A:GLU120 4.4 22.5 1.0
N A:CYS190 4.5 19.9 1.0
OE2 A:GLU120 4.5 21.5 1.0
OD2 A:ASP88 4.6 26.4 1.0
OD1 A:ASP88 4.6 27.1 1.0
SG A:CYS190 4.8 24.1 1.0
N A:GLY189 4.8 19.9 1.0
O A:GLY189 4.9 21.1 1.0
CE A:LYS115 4.9 38.3 1.0
CD A:GLU120 5.0 21.9 1.0

Magnesium binding site 2 out of 5 in 5cge

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Magnesium binding site 2 out of 5 in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:45.6
occ:1.00
 O B:HOH484 2.0 23.9 1.0
O B:HOH406 2.4 26.2 1.0
NZ B:LYS115 4.0 31.7 1.0
OE1 B:GLU120 4.2 18.4 1.0
O B:HOH496 4.2 28.5 1.0
OE2 B:GLU120 4.3 19.0 1.0
OD2 B:ASP88 4.3 20.5 1.0
OD1 B:ASP88 4.4 19.9 1.0
CA B:GLY189 4.5 21.8 1.0
C B:GLY189 4.6 20.7 1.0
CG2 B:VAL90 4.7 15.9 1.0
CD B:GLU120 4.7 19.1 1.0
N B:CYS190 4.7 19.2 1.0
SG B:CYS190 4.7 21.5 1.0
CE B:LYS115 4.8 30.3 1.0
CG B:ASP88 4.8 18.3 1.0

Magnesium binding site 3 out of 5 in 5cge

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Magnesium binding site 3 out of 5 in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:45.3
occ:1.00
 OD1 C:ASP88 2.4 22.7 1.0
OE1 C:GLU120 2.6 20.9 1.0
O C:HOH446 3.1 38.8 1.0
CG C:ASP88 3.4 20.4 1.0
O C:HOH403 3.4 31.8 1.0
OD2 C:ASP88 3.5 25.3 1.0
CD C:GLU120 3.5 19.8 1.0
CA C:GLY116 3.7 16.1 1.0
OE2 C:GLU120 3.7 19.9 1.0
NZ C:LYS115 3.7 33.7 1.0
CE C:LYS115 3.8 31.8 1.0
N C:ASN117 4.1 16.4 1.0
O C:LYS115 4.2 16.8 1.0
CG2 C:VAL90 4.2 17.5 1.0
C C:GLY116 4.3 16.1 1.0
CA C:VAL90 4.4 17.3 1.0
N C:GLY116 4.6 15.8 1.0
N C:VAL90 4.7 17.1 1.0
C C:LYS115 4.8 16.2 1.0
CB C:ASP88 4.8 17.9 1.0
CB C:VAL90 4.8 17.7 1.0
CG C:GLU120 4.9 20.3 1.0

Magnesium binding site 4 out of 5 in 5cge

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Magnesium binding site 4 out of 5 in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:27.6
occ:1.00
 OD2 C:ASP88 2.7 25.3 1.0
ND2 C:ASN59 2.9 14.5 1.0
O C:CYS190 2.9 15.3 1.0
CB C:ASP88 3.3 17.9 1.0
CG C:ASP88 3.4 20.4 1.0
CD1 C:LEU57 3.5 14.5 1.0
CA C:CYS190 3.5 18.0 1.0
CA C:GLY193 3.6 14.4 1.0
C C:CYS190 3.7 16.3 1.0
CD2 C:LEU57 3.8 14.4 1.0
CB C:ASN59 3.8 14.6 1.0
CG C:ASN59 3.8 14.6 1.0
O C:HOH429 4.0 12.5 1.0
N C:GLY193 4.0 14.3 1.0
O C:GLY189 4.1 21.8 1.0
CB C:CYS190 4.1 19.1 1.0
CG C:LEU57 4.2 14.5 1.0
C C:GLY193 4.3 14.4 1.0
O C:HOH446 4.4 38.8 1.0
N C:GLY194 4.4 14.3 1.0
N C:CYS190 4.6 19.8 1.0
OD1 C:ASP88 4.7 22.7 1.0
NZ C:LYS115 4.7 33.7 1.0
C C:GLY189 4.8 20.5 1.0
CE C:LYS115 4.8 31.8 1.0
CA C:ASP88 4.8 16.3 1.0
CA C:ASN59 4.9 14.7 1.0
SG C:CYS190 4.9 22.4 1.0
OG1 C:THR18 5.0 14.5 1.0
N C:LEU191 5.0 15.2 1.0
OD1 C:ASN59 5.0 14.7 1.0

Magnesium binding site 5 out of 5 in 5cge

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Magnesium binding site 5 out of 5 in the Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Hydroxyethylthiazole Kinase Thim From Staphylococcus Aureus in Complex with Substrate Analog 2-(2-Methyl-1H-Imidazole-1- Yl)Ethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:46.4
occ:1.00
 OE1 E:GLU120 2.6 30.7 1.0
OD1 E:ASP88 2.7 33.0 1.0
O E:HOH452 2.9 42.8 1.0
O E:HOH402 3.3 32.4 1.0
CD E:GLU120 3.5 29.4 1.0
CG E:ASP88 3.6 31.1 1.0
OE2 E:GLU120 3.6 30.4 1.0
OD2 E:ASP88 3.7 33.3 1.0
CA E:GLY116 3.7 23.2 1.0
NZ E:LYS115 3.8 44.1 1.0
CE E:LYS115 3.9 42.2 1.0
N E:ASN117 4.0 22.4 1.0
C E:GLY116 4.2 23.6 1.0
CG2 E:VAL90 4.4 27.3 1.0
O E:LYS115 4.4 26.1 1.0
CA E:VAL90 4.6 27.1 1.0
N E:GLY116 4.7 23.7 1.0
C E:LYS115 4.9 26.0 1.0
CG E:GLU120 4.9 28.5 1.0
ND2 E:ASN117 5.0 27.7 1.0
N E:VAL90 5.0 26.8 1.0
CB E:VAL90 5.0 27.2 1.0

Reference:

J.Drebes, M.Kunz, B.Windshugel, A.G.Kikhney, I.B.Muller, R.J.Eberle, D.Oberthur, H.Cang, D.I.Svergun, M.Perbandt, C.Betzel, C.Wrenger. Structure of Thim From Vitamin B1 Biosynthetic Pathway of Staphylococcus Aureus - Insights Into A Novel Pro-Drug Approach Addressing Mrsa Infections. Sci Rep V. 6 22871 2016.
ISSN: ESSN 2045-2322
PubMed: 26960569
DOI: 10.1038/SREP22871
Page generated: Mon Dec 14 20:06:46 2020

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