Magnesium in PDB 7rf0: Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium

Enzymatic activity of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium

All present enzymatic activity of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium:
2.1.1.228;

Protein crystallography data

The structure of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium, PDB code: 7rf0 was solved by G.R.Prucha, M.Ismail, A.Suske, B.Das, M.Oz, A.Perez, R.Bolen, S.Jayaraman, V.Stojanoff, J.Halloran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.22 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.398, 78.835, 86.656, 90, 90, 90
R / Rfree (%) 18 / 21.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium (pdb code 7rf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium, PDB code: 7rf0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7rf0

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Magnesium binding site 1 out of 4 in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:29.8
occ:1.00
 O B:VAL137 2.8 21.5 1.0
O A:ALA151 2.8 21.1 1.0
NH1 A:ARG154 2.9 27.4 1.0
NE2 A:GLN92 3.0 25.1 1.0
CG A:ARG154 3.1 29.7 1.0
CD A:ARG154 3.1 29.9 1.0
OE1 A:GLN92 3.6 25.7 1.0
C A:ALA151 3.6 23.0 1.0
CA A:ALA151 3.6 17.5 1.0
CD A:GLN92 3.7 24.6 1.0
CD2 A:LEU155 3.7 23.0 1.0
CG A:LEU155 3.8 23.0 1.0
CZ A:ARG154 3.8 25.3 1.0
C B:VAL137 3.8 21.2 1.0
NE A:ARG154 3.9 25.7 1.0
CB B:VAL137 4.0 23.3 1.0
CB A:ALA151 4.0 20.1 1.0
CD1 A:LEU155 4.1 20.3 1.0
CA B:VAL137 4.2 21.8 1.0
N B:VAL137 4.2 20.2 1.0
CB A:ARG154 4.6 29.1 1.0
CG1 B:VAL137 4.7 24.3 1.0
O A:GLU150 4.8 20.9 1.0
CB A:ALA95 4.9 20.9 1.0
N A:VAL152 4.9 18.9 1.0
N B:LEU138 4.9 21.7 1.0
N A:ALA151 5.0 17.7 1.0

Magnesium binding site 2 out of 4 in 7rf0

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Magnesium binding site 2 out of 4 in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.0
occ:1.00
 O B:GLY87 2.7 19.7 1.0
O B:PRO85 2.9 20.5 1.0
NH1 A:ARG223 3.0 30.4 1.0
CG A:ARG223 3.5 26.6 1.0
O B:HOH440 3.5 30.8 1.0
CD A:ARG223 3.6 27.4 1.0
CB B:SER132 3.6 17.3 1.0
N B:GLY87 3.6 18.4 1.0
CD2 A:LEU179 3.7 27.1 1.0
C B:GLY87 3.8 19.1 1.0
C B:PRO85 3.8 19.0 1.0
C B:ALA86 3.8 18.7 1.0
CA B:ALA86 4.1 19.6 1.0
OG B:SER132 4.1 22.1 1.0
CZ A:ARG223 4.1 32.1 1.0
CD1 A:LEU179 4.2 22.6 1.0
NE A:ARG223 4.3 29.6 1.0
CA B:GLY87 4.3 18.5 1.0
N B:ALA86 4.3 19.5 1.0
O B:ALA86 4.4 21.1 1.0
CG A:LEU179 4.6 21.8 1.0
CB A:ARG223 4.9 24.8 1.0
CA B:PRO85 4.9 18.8 1.0
N B:TYR88 4.9 18.8 1.0

Magnesium binding site 3 out of 4 in 7rf0

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Magnesium binding site 3 out of 4 in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:46.2
occ:1.00
 O3' A:SAH301 2.6 26.7 0.5
O3' A:SAH301 2.8 26.9 0.5
O A:HOH436 2.8 37.9 1.0
CB A:SAH301 3.0 39.5 0.5
O A:HOH423 3.2 31.1 1.0
O A:HOH525 3.2 33.9 1.0
OG1 A:THR84 3.3 20.5 1.0
C3' A:SAH301 3.3 24.5 0.5
C3' A:SAH301 3.5 24.4 0.5
CA A:GLY113 3.5 27.1 1.0
CB A:THR84 3.6 21.6 1.0
CG A:SAH301 3.7 32.7 0.5
OXT A:SAH301 3.8 57.6 0.5
O A:GLU112 4.0 38.7 1.0
CD A:PRO85 4.1 18.7 1.0
CA A:THR84 4.1 19.1 1.0
C2' A:SAH301 4.2 20.1 0.5
N A:GLY113 4.2 23.5 1.0
CG A:SAH301 4.3 36.6 0.5
C2' A:SAH301 4.3 20.1 0.5
CA A:SAH301 4.3 45.6 0.5
C A:GLU112 4.4 31.9 1.0
C A:SAH301 4.5 51.4 0.5
O A:PRO83 4.5 20.4 1.0
C4' A:SAH301 4.6 22.6 0.5
SD A:SAH301 4.7 25.6 0.5
C A:GLY113 4.7 25.1 1.0
N A:ILE114 4.8 21.8 1.0
C4' A:SAH301 4.8 22.6 0.5
O2' A:SAH301 4.8 22.1 0.5
O2' A:SAH301 4.9 22.1 0.5
CG2 A:THR84 4.9 20.6 1.0
C5' A:SAH301 4.9 26.9 0.5
N A:PRO85 5.0 17.7 1.0
CG A:PRO85 5.0 19.3 1.0

Magnesium binding site 4 out of 4 in 7rf0

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Magnesium binding site 4 out of 4 in the Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycobacterium Abscessus Trna Methyltransferase in Complex with S- Adenosyl-L-Homocysteine and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.1
occ:1.00
 O B:PRO83 2.6 18.9 1.0
O B:ALA107 2.8 21.2 1.0
N B:GLY109 2.9 21.2 1.0
O2' B:SAH301 3.1 20.1 1.0
O B:HOH513 3.2 33.4 1.0
CA B:GLY109 3.5 18.8 1.0
C B:PRO83 3.7 18.0 1.0
CG1 B:VAL82 3.7 21.9 1.0
N B:PRO83 3.7 15.3 1.0
C B:CYS108 3.8 21.9 1.0
CD B:PRO83 3.8 19.8 1.0
CD1 B:ILE114 3.8 21.3 1.0
O3' B:SAH301 3.9 24.2 1.0
C B:ALA107 3.9 19.6 1.0
CA B:CYS108 4.1 18.1 1.0
C2' B:SAH301 4.1 20.7 1.0
CA B:PRO83 4.1 16.5 1.0
C B:VAL82 4.2 15.8 1.0
CB B:PRO83 4.3 18.0 1.0
CG B:PRO83 4.4 24.7 1.0
N B:CYS108 4.4 19.0 1.0
CA B:VAL82 4.5 18.1 1.0
CG1 B:ILE114 4.5 24.3 1.0
C3' B:SAH301 4.6 25.8 1.0
C B:GLY109 4.7 21.8 1.0
CB B:VAL82 4.8 18.6 1.0
O B:CYS108 4.8 23.1 1.0
N B:THR84 4.9 16.8 1.0
O B:VAL82 4.9 20.6 1.0

Reference:

G.R.Prucha, M.Ismail, A.Suske, A.Perez, R.Bolen, S.Jayaraman, V.Stojanoff, J.Halloran. Crystal Structure of Divalent Mg+2 Dependent Mycobacterium Abscessus Trna (M1 G37) Methyltransferase (Trmd) To Be Published.
Page generated: Thu Apr 6 21:51:55 2023

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