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Magnesium in PDB 8w8l: Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38

Protein crystallography data

The structure of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38, PDB code: 8w8l was solved by Z.Luo, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.05 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.484, 103.06, 194.095, 90, 90, 90
R / Rfree (%) 21.1 / 24.1

Other elements in 8w8l:

The structure of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 (pdb code 8w8l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38, PDB code: 8w8l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8w8l

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Magnesium binding site 1 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:30.6
occ:1.00
 O A:HIS284 2.7 18.9 1.0
O A:ALA314 2.9 21.4 1.0
N A:VAL318 3.2 22.0 1.0
CG1 A:VAL313 3.4 22.5 1.0
CD1 A:LEU317 3.4 21.5 1.0
CB A:ALA314 3.5 21.6 1.0
N A:ALA314 3.5 21.4 1.0
O A:VAL318 3.6 20.9 1.0
N A:HIS284 3.6 17.6 1.0
CA A:LEU317 3.6 22.9 1.0
C A:ALA314 3.6 22.4 1.0
C A:HIS284 3.7 19.4 1.0
CA A:ALA314 3.7 21.6 1.0
C A:LEU317 3.9 22.6 1.0
CA A:HIS284 3.9 18.4 1.0
CB A:VAL283 4.0 17.6 1.0
CB A:HIS284 4.0 19.2 1.0
O A:PRO316 4.1 25.3 1.0
CA A:VAL318 4.1 22.1 1.0
CG A:LEU317 4.1 21.8 1.0
CG2 A:VAL283 4.2 17.9 1.0
C A:VAL318 4.2 21.5 1.0
CB A:LEU317 4.4 21.9 1.0
C A:VAL313 4.4 22.0 1.0
C A:VAL283 4.4 17.6 1.0
CB A:VAL318 4.4 22.6 1.0
N A:LEU317 4.6 23.9 1.0
C A:PRO316 4.7 24.9 1.0
CB A:VAL313 4.7 22.3 1.0
CA A:VAL283 4.7 18.0 1.0
CA A:VAL313 4.8 21.9 1.0
N A:SER315 4.9 23.5 1.0
N A:GLY285 4.9 20.9 1.0
O A:HOH1067 4.9 38.9 1.0
CG1 A:VAL283 5.0 18.1 1.0

Magnesium binding site 2 out of 9 in 8w8l

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Magnesium binding site 2 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:34.1
occ:1.00
 OG A:SER22 2.8 22.6 1.0
O A:PHE147 2.9 19.9 1.0
N A:HIS23 3.2 20.2 1.0
N A:LEU149 3.4 22.2 1.0
CA A:HIS23 3.5 19.9 1.0
CB A:ALA451 3.5 19.6 1.0
CB A:SER22 3.5 22.4 1.0
C A:SER22 3.7 21.1 1.0
CB A:HIS23 3.7 19.6 1.0
C A:PHE147 3.8 22.0 1.0
CA A:GLY148 3.8 22.8 1.0
CG A:MET150 3.9 32.2 1.0
C A:GLY148 4.1 22.6 1.0
CD1 A:LEU26 4.1 19.2 1.0
N A:GLY148 4.1 22.7 1.0
CA A:SER22 4.2 22.7 1.0
N A:MET150 4.2 24.9 1.0
O A:SER22 4.2 20.1 1.0
CB A:LEU149 4.3 21.7 1.0
CA A:LEU149 4.3 22.1 1.0
CG2 A:VAL20 4.4 26.4 1.0
CG A:HIS23 4.6 19.4 1.0
CG A:LEU149 4.6 21.5 1.0
CA A:ALA451 4.7 19.9 1.0
C A:LEU149 4.8 23.5 1.0
CB A:MET150 4.9 29.0 1.0
SD A:MET150 4.9 36.0 1.0
N A:SER22 4.9 23.2 1.0
OE2 A:GLU455 4.9 25.2 1.0
CA A:PHE147 5.0 23.1 1.0
C A:HIS23 5.0 20.2 1.0

Magnesium binding site 3 out of 9 in 8w8l

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Magnesium binding site 3 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:29.5
occ:1.00
 ND1 A:HIS300 2.7 24.1 1.0
OD2 A:ASP348 2.8 17.8 1.0
N A:ARG297 2.9 20.7 1.0
CB A:ARG297 3.4 22.4 1.0
CG A:ASP348 3.5 18.2 1.0
CD A:ARG386 3.6 19.9 1.0
CB A:ASP348 3.6 17.8 1.0
CG A:HIS300 3.6 23.8 1.0
CB A:SER350 3.7 18.7 1.0
CE1 A:HIS300 3.7 23.6 1.0
CA A:VAL296 3.7 19.2 1.0
CA A:ARG297 3.8 21.4 1.0
C A:VAL296 3.8 19.9 1.0
CB A:HIS300 3.8 24.3 1.0
CB A:VAL296 3.8 19.5 1.0
CG2 A:VAL351 3.9 20.0 1.0
CG A:ARG386 4.3 19.4 1.0
NE A:ARG386 4.4 20.2 1.0
OG A:SER350 4.4 18.6 1.0
CB A:ARG386 4.4 18.9 1.0
N A:VAL351 4.4 19.4 1.0
CA A:SER350 4.5 18.7 1.0
OD1 A:ASP348 4.6 18.4 1.0
CG1 A:VAL296 4.6 19.9 1.0
N A:SER350 4.7 18.6 1.0
C A:SER350 4.7 19.4 1.0
O A:ARG297 4.8 22.0 1.0
C A:ARG297 4.8 22.3 1.0
CD2 A:HIS300 4.8 24.1 1.0
NE2 A:HIS300 4.8 24.1 1.0
CG A:ARG297 4.8 23.0 1.0
CA A:ASP348 4.9 17.3 1.0
CG2 A:VAL296 5.0 19.8 1.0
O A:VAL296 5.0 18.9 1.0

Magnesium binding site 4 out of 9 in 8w8l

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Magnesium binding site 4 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:27.7
occ:1.00
 OE1 A:GLN75 2.9 21.7 1.0
N A:VAL113 3.1 20.8 1.0
OE1 A:GLU112 3.1 20.2 1.0
N A:GLU112 3.2 19.1 1.0
CB A:GLU112 3.3 20.4 1.0
CA A:HIS110 3.3 17.4 1.0
C A:HIS110 3.3 18.0 1.0
CG2 A:VAL113 3.5 18.8 1.0
CZ2 A:TRP80 3.5 18.5 1.0
CA A:GLU112 3.5 20.3 1.0
O A:THR109 3.6 16.2 1.0
NE1 A:TRP80 3.6 19.5 1.0
O A:HIS110 3.7 18.9 1.0
CE2 A:TRP80 3.7 18.9 1.0
N A:GLU111 3.7 18.5 1.0
C A:GLU112 3.7 20.7 1.0
CD A:GLN75 3.8 21.9 1.0
CB A:VAL113 3.9 19.2 1.0
CD A:GLU112 4.0 20.7 1.0
CA A:VAL113 4.0 20.0 1.0
C A:GLU111 4.1 18.9 1.0
NE2 A:GLN75 4.1 20.9 1.0
N A:HIS110 4.2 17.0 1.0
CG A:GLU112 4.2 20.5 1.0
C A:THR109 4.3 16.5 1.0
CB A:HIS110 4.3 17.5 1.0
CH2 A:TRP80 4.4 18.7 1.0
CA A:GLU111 4.5 18.0 1.0
CD1 A:TRP80 4.7 20.4 1.0
CD2 A:TRP80 4.8 19.0 1.0
CG A:HIS110 4.8 17.7 1.0
NH1 A:ARG85 4.9 22.4 1.0
O A:GLU112 4.9 21.3 1.0
CG A:GLN75 5.0 21.5 1.0

Magnesium binding site 5 out of 9 in 8w8l

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Magnesium binding site 5 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:44.5
occ:1.00
 O A:GLY416 2.7 26.1 1.0
N A:TYR419 3.1 28.9 1.0
SD A:MET439 3.2 29.4 1.0
N A:LYS418 3.4 28.6 1.0
CB A:MET439 3.5 25.6 1.0
N A:SER420 3.5 29.3 1.0
C A:THR417 3.5 28.5 1.0
C A:GLY416 3.6 27.4 1.0
CA A:THR417 3.6 27.9 1.0
CG A:MET439 3.6 26.6 1.0
CB A:TYR419 3.7 26.3 1.0
CA A:TYR419 3.8 27.2 1.0
OG A:SER420 3.9 29.7 1.0
N A:THR417 4.0 27.8 1.0
C A:LYS418 4.0 30.9 1.0
CA A:LYS418 4.1 31.1 1.0
O A:LEU415 4.1 28.6 1.0
CB A:LEU415 4.1 27.9 1.0
O A:THR417 4.2 28.5 1.0
C A:TYR419 4.2 28.1 1.0
O A:LEU437 4.2 28.7 1.0
CE A:MET439 4.2 28.4 1.0
CB A:SER420 4.3 29.8 1.0
N A:MET439 4.3 24.2 1.0
CD2 A:TYR419 4.3 24.0 1.0
CB A:LYS418 4.3 33.9 1.0
C A:LEU415 4.4 27.6 1.0
CA A:MET439 4.5 23.9 1.0
CA A:SER420 4.5 29.4 1.0
CG A:TYR419 4.5 24.8 1.0
N A:GLY416 4.7 27.5 1.0
CA A:GLY416 4.8 27.9 1.0
CA A:LEU415 5.0 27.3 1.0

Magnesium binding site 6 out of 9 in 8w8l

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Magnesium binding site 6 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:29.9
occ:1.00
 O A:VAL313 2.3 21.4 1.0
O A:ALA308 2.4 23.9 1.0
O A:GLN310 2.5 26.6 1.0
O A:HOH803 2.7 33.1 1.0
C A:GLN310 3.4 26.6 1.0
C A:VAL313 3.5 22.0 1.0
C A:ALA308 3.5 23.0 1.0
C A:ASN309 3.8 26.8 1.0
N A:GLN310 3.8 26.2 1.0
O A:HOH1117 4.1 37.4 1.0
CA A:PRO311 4.1 26.6 1.0
O A:ASN309 4.1 28.0 1.0
N A:PRO311 4.1 26.4 1.0
N A:VAL313 4.1 22.0 1.0
O A:PRO311 4.1 25.8 1.0
CB A:SER315 4.1 26.1 1.0
C A:PRO311 4.2 25.7 1.0
CA A:ASN309 4.2 27.4 1.0
CA A:VAL313 4.2 21.9 1.0
CA A:GLN310 4.3 25.9 1.0
N A:ASN309 4.3 25.9 1.0
N A:SER315 4.4 23.5 1.0
CB A:VAL313 4.5 22.3 1.0
C A:ALA314 4.5 22.4 1.0
CA A:ALA308 4.6 21.3 1.0
N A:ALA314 4.6 21.4 1.0
CA A:ALA314 4.8 21.6 1.0
O A:ALA314 4.8 21.4 1.0
CA A:SER315 4.9 25.6 1.0
O A:HOH981 4.9 36.2 1.0
O A:HOH930 5.0 35.5 1.0
O A:ALA307 5.0 19.3 1.0

Magnesium binding site 7 out of 9 in 8w8l

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Magnesium binding site 7 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:34.5
occ:1.00
 OE2 A:GLU142 2.3 27.8 1.0
CD A:GLU142 2.9 26.5 1.0
NH1 A:ARG146 3.0 21.1 1.0
CG A:GLU142 3.1 24.3 1.0
N A:ARG144 3.1 17.7 1.0
CG2 A:ILE143 3.3 15.8 1.0
N A:ILE143 3.4 17.4 1.0
O A:HOH904 3.6 19.3 1.0
O A:ARG144 3.7 18.7 1.0
CA A:ARG144 3.8 18.3 1.0
C A:ARG144 3.9 18.6 1.0
C A:GLU142 3.9 18.2 1.0
OE1 A:GLU142 4.0 28.4 1.0
NH2 A:ARG151 4.0 27.3 1.0
C A:ILE143 4.1 17.1 1.0
CB A:ARG144 4.1 18.6 1.0
CZ A:ARG146 4.1 20.8 1.0
CA A:ILE143 4.1 16.7 1.0
CB A:GLU142 4.2 22.1 1.0
CA A:GLU142 4.2 19.7 1.0
CB A:ILE143 4.3 16.0 1.0
NH2 A:ARG146 4.3 21.1 1.0
O A:GLU142 4.7 17.9 1.0
N A:PRO145 4.7 19.2 1.0
CD A:ARG151 4.8 25.6 1.0

Magnesium binding site 8 out of 9 in 8w8l

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Magnesium binding site 8 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:33.4
occ:1.00
 OG B:SER22 2.7 23.4 1.0
O B:PHE147 2.7 23.0 1.0
N B:LEU149 3.3 22.8 1.0
N B:HIS23 3.4 23.7 1.0
C B:PHE147 3.6 22.8 1.0
CB B:ALA451 3.6 22.3 1.0
CA B:HIS23 3.7 24.1 1.0
CB B:HIS23 3.7 24.4 1.0
CA B:GLY148 3.7 22.8 1.0
CG B:MET150 3.8 27.5 0.5
CB B:SER22 3.8 23.3 1.0
C B:SER22 3.9 23.6 1.0
C B:GLY148 3.9 23.2 1.0
CE B:MET150 4.0 28.1 0.5
N B:GLY148 4.0 22.5 1.0
CG2 B:VAL20 4.1 27.8 1.0
N B:MET150 4.2 22.9 1.0
CA B:LEU149 4.3 22.6 1.0
CB B:LEU149 4.3 22.8 1.0
CD1 B:LEU26 4.3 23.8 1.0
CA B:SER22 4.4 22.9 1.0
O B:SER22 4.5 24.6 1.0
CE B:MET150 4.5 31.4 0.5
CG B:HIS23 4.5 25.0 1.0
SD B:MET150 4.6 29.2 0.5
C B:LEU149 4.7 22.6 1.0
CB B:MET150 4.7 25.6 0.5
CB B:MET150 4.7 24.6 0.5
CG B:LEU149 4.7 23.3 1.0
CA B:ALA451 4.7 21.2 1.0
CA B:PHE147 4.8 24.1 1.0
SD B:MET150 4.9 32.1 0.5

Magnesium binding site 9 out of 9 in 8w8l

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Magnesium binding site 9 out of 9 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:30.4
occ:1.00
 O B:ALA308 2.2 19.4 1.0
O B:GLN310 2.3 24.2 1.0
O B:VAL313 2.4 22.1 1.0
C B:GLN310 3.3 24.0 1.0
C B:ALA308 3.4 20.7 1.0
C B:VAL313 3.5 22.7 1.0
N B:GLN310 3.9 22.2 1.0
C B:ASN309 3.9 22.4 1.0
CB B:SER315 3.9 27.9 1.0
N B:PRO311 4.1 25.5 1.0
CA B:PRO311 4.1 27.0 1.0
O B:PRO311 4.2 28.1 1.0
N B:VAL313 4.2 23.5 1.0
N B:ASN309 4.2 20.9 1.0
CA B:ASN309 4.2 22.0 1.0
CA B:VAL313 4.2 22.8 1.0
CA B:GLN310 4.2 22.8 1.0
N B:SER315 4.2 24.4 1.0
C B:PRO311 4.2 26.8 1.0
O B:ASN309 4.3 22.0 1.0
CA B:ALA308 4.3 20.6 1.0
CB B:VAL313 4.4 22.6 1.0
C B:ALA314 4.4 22.8 1.0
O B:HOH1073 4.5 36.8 1.0
N B:ALA314 4.5 22.2 1.0
O B:HOH919 4.5 34.4 1.0
O B:HOH775 4.6 37.1 1.0
CA B:SER315 4.7 27.3 1.0
CA B:ALA314 4.7 22.1 1.0
O B:ALA314 4.8 20.5 1.0
O B:ALA307 4.8 21.4 1.0
OG B:SER315 4.9 28.4 1.0
N B:LEU312 5.0 26.4 1.0
CG1 B:VAL313 5.0 22.8 1.0

Reference:

Z.Luo, H.Zhou. Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-Trna Synthetase To Be Published.
Page generated: Fri Aug 15 18:19:17 2025

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