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

Go back to Magnesium Binding Sites List in 7rf0
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

Go back to Magnesium Binding Sites List in 7rf0
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

Go back to Magnesium Binding Sites List in 7rf0
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

Go back to Magnesium Binding Sites List in 7rf0
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 Oct 3 07:51:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy