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Magnesium in PDB 3a74: Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)

Enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)

All present enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A):
6.1.1.6;

Protein crystallography data

The structure of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A), PDB code: 3a74 was solved by H.Sakurama, T.Takita, B.Mikami, T.Itoh, K.Yasukawa, K.Inouye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.96 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.176, 85.080, 151.764, 90.00, 90.01, 90.00
R / Rfree (%) 20.7 / 22.8

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) (pdb code 3a74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A), PDB code: 3a74:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3a74

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Magnesium binding site 1 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:21.9
occ:1.00
 O3F A:B4P494 2.6 17.5 1.0
OE1 A:GLU411 2.6 17.0 0.5
OE2 A:GLU404 2.9 26.5 1.0
O2D A:B4P494 3.0 14.8 1.0
O3G A:B4P494 3.3 15.4 1.0
C3F A:B4P494 3.4 15.8 1.0
CB A:ASN414 3.6 10.2 1.0
CD A:GLU411 3.6 18.4 0.5
O A:ALA413 3.6 9.4 1.0
O A:HOH1300 3.6 23.1 1.0
CB A:GLU411 3.7 14.3 0.5
CB A:GLU411 3.7 15.2 0.5
CG A:GLU411 3.8 16.0 0.5
PD A:B4P494 3.8 15.0 1.0
CD A:GLU404 3.9 19.7 1.0
CG A:GLU411 3.9 14.4 0.5
C5F A:B4P494 3.9 13.9 1.0
C A:ALA413 3.9 10.1 1.0
MG A:MG1002 4.1 40.0 1.0
C4F A:B4P494 4.2 14.1 1.0
CG A:GLU404 4.2 17.1 1.0
CG A:ASN414 4.3 12.4 1.0
N A:ASN414 4.3 10.3 1.0
O5F A:B4P494 4.3 12.8 1.0
CA A:ASN414 4.4 9.5 1.0
O2G A:B4P494 4.4 18.1 1.0
PG A:B4P494 4.5 17.7 1.0
ND2 A:ASN414 4.5 13.0 1.0
N A:ALA413 4.6 11.4 1.0
CA A:ALA413 4.7 10.1 1.0
OE2 A:GLU411 4.7 19.0 0.5
O3B A:B4P494 4.7 17.7 1.0
C2F A:B4P494 4.8 15.7 1.0
CA A:GLU411 4.9 12.7 0.5
C A:GLU411 4.9 12.9 0.5
CA A:GLU411 4.9 13.0 0.5
CB A:GLU404 4.9 12.5 1.0
C A:GLU411 4.9 12.8 0.5
OE1 A:GLU404 4.9 20.9 1.0

Magnesium binding site 2 out of 12 in 3a74

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Magnesium binding site 2 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:16.4
occ:1.00
 O A:HOH543 2.0 12.6 1.0
O A:HOH508 2.1 17.0 1.0
O2B A:B4P494 2.1 19.1 1.0
O A:HOH802 2.1 13.0 1.0
O A:HOH1291 2.1 16.8 1.0
O1G A:B4P494 2.3 16.5 1.0
PG A:B4P494 3.2 17.7 1.0
PB A:B4P494 3.3 18.1 1.0
O3B A:B4P494 3.4 17.7 1.0
O2A A:B4P494 3.6 23.9 1.0
NH2 A:ARG253 3.9 9.5 1.0
O2G A:B4P494 3.9 18.1 1.0
OE2 A:GLU255 4.1 22.9 1.0
O A:HOH911 4.1 27.8 1.0
NE2 A:HIS261 4.3 13.4 1.0
O3A A:B4P494 4.3 22.8 1.0
N7A A:B4P494 4.3 22.9 1.0
OE1 A:GLU255 4.3 17.8 1.0
O1B A:B4P494 4.4 18.2 1.0
N7B A:B4P494 4.5 13.0 1.0
CD2 A:HIS261 4.6 12.8 1.0
C8A A:B4P494 4.6 23.4 1.0
CD A:GLU255 4.6 17.9 1.0
O3G A:B4P494 4.6 15.4 1.0
PA A:B4P494 4.7 24.4 1.0
O A:ALA209 4.8 14.0 1.0
C8B A:B4P494 4.9 14.8 1.0

Magnesium binding site 3 out of 12 in 3a74

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Magnesium binding site 3 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:40.0
occ:1.00
 OE1 A:GLU411 2.4 17.0 0.5
O2G A:B4P494 2.4 18.1 1.0
O A:HOH1300 2.5 23.1 1.0
OE2 A:GLU404 2.8 26.5 1.0
O1A A:B4P494 3.0 27.1 1.0
OE2 A:GLU411 3.1 19.0 0.5
CD A:GLU411 3.1 18.4 0.5
O A:HOH913 3.4 23.3 1.0
O3A A:B4P494 3.5 22.8 1.0
O A:HOH914 3.5 28.4 1.0
CD A:GLU404 3.7 19.7 1.0
PA A:B4P494 3.8 24.4 1.0
OE1 A:GLU404 3.8 20.9 1.0
PG A:B4P494 3.9 17.7 1.0
MG A:MG1000 4.1 21.9 1.0
O3G A:B4P494 4.2 15.4 1.0
O A:HOH583 4.3 11.7 1.0
O A:HOH911 4.4 27.8 1.0
O2A A:B4P494 4.4 23.9 1.0
O3B A:B4P494 4.4 17.7 1.0
OE2 A:GLU366 4.5 26.0 1.0
NH2 A:ARG402 4.5 12.1 1.0
CG A:GLU411 4.5 16.0 0.5
OE1 A:GLU411 4.6 17.4 0.5
CG A:GLU411 4.7 14.4 0.5
PB A:B4P494 4.7 18.1 1.0
O2D A:B4P494 4.8 14.8 1.0
O1G A:B4P494 5.0 16.5 1.0

Magnesium binding site 4 out of 12 in 3a74

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Magnesium binding site 4 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1100

b:22.5
occ:1.00
 O3E B:B4P494 2.4 14.4 1.0
OE1 B:GLU411 2.5 19.3 0.5
O2A B:B4P494 2.8 13.0 1.0
O B:HOH1206 3.0 24.1 1.0
OE2 B:GLU404 3.1 23.9 1.0
C3E B:B4P494 3.2 12.4 1.0
O3A B:B4P494 3.4 15.7 1.0
CD B:GLU411 3.5 20.3 0.5
CB B:ASN414 3.6 12.3 1.0
PA B:B4P494 3.7 15.5 1.0
CB B:GLU411 3.8 15.9 0.5
CB B:GLU411 3.8 16.1 0.5
O B:ALA413 3.8 11.5 1.0
CG B:GLU411 3.8 19.1 0.5
C5E B:B4P494 3.9 14.8 1.0
O1B B:B4P494 4.0 17.8 1.0
PB B:B4P494 4.1 15.0 1.0
C B:ALA413 4.1 10.8 1.0
C4E B:B4P494 4.1 12.4 1.0
O3B B:B4P494 4.1 16.6 1.0
CG B:GLU411 4.1 19.4 0.5
CD B:GLU404 4.1 18.5 1.0
MG B:MG1102 4.3 31.6 1.0
O5E B:B4P494 4.3 13.4 1.0
N B:ASN414 4.3 11.1 1.0
CG B:ASN414 4.4 14.2 1.0
CA B:ASN414 4.4 11.7 1.0
CG B:GLU404 4.4 16.6 1.0
C2E B:B4P494 4.5 11.3 1.0
OE2 B:GLU411 4.7 21.7 0.5
ND2 B:ASN414 4.7 12.8 1.0
N B:ALA413 4.7 10.6 1.0
CA B:ALA413 4.8 11.7 1.0
C B:GLU411 4.9 14.2 0.5
CA B:GLU411 5.0 14.3 0.5
C B:GLU411 5.0 14.3 0.5
O1A B:B4P494 5.0 14.3 1.0
O2E B:B4P494 5.0 12.3 1.0
CA B:GLU411 5.0 14.1 0.5

Magnesium binding site 5 out of 12 in 3a74

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Magnesium binding site 5 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1101

b:12.7
occ:1.00
 O2B B:B4P494 2.0 16.5 1.0
O1G B:B4P494 2.0 17.0 1.0
O B:HOH580 2.1 12.2 1.0
O B:HOH864 2.1 13.6 1.0
O B:HOH868 2.1 17.3 1.0
O B:HOH865 2.3 13.8 1.0
PG B:B4P494 3.3 16.6 1.0
PB B:B4P494 3.3 15.0 1.0
O2D B:B4P494 3.6 23.1 1.0
O3B B:B4P494 3.6 16.6 1.0
NH2 B:ARG253 3.9 11.3 1.0
O1B B:B4P494 4.1 17.8 1.0
OE2 B:GLU255 4.1 20.4 1.0
O B:HOH869 4.2 26.5 1.0
NE2 B:HIS261 4.2 15.1 1.0
O B:HOH867 4.3 24.1 1.0
OE1 B:GLU255 4.3 15.8 1.0
O2G B:B4P494 4.4 19.4 1.0
N7B B:B4P494 4.4 22.9 1.0
O3G B:B4P494 4.4 20.3 1.0
O3A B:B4P494 4.5 15.7 1.0
N7A B:B4P494 4.5 12.0 1.0
CD B:GLU255 4.6 17.6 1.0
CD2 B:HIS261 4.6 15.3 1.0
C8B B:B4P494 4.7 23.3 1.0
PD B:B4P494 4.7 23.4 1.0
O B:ALA209 4.8 13.2 1.0
C8A B:B4P494 4.9 12.0 1.0

Magnesium binding site 6 out of 12 in 3a74

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Magnesium binding site 6 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1102

b:31.6
occ:1.00
 O B:HOH1206 2.3 24.1 1.0
O1B B:B4P494 2.6 17.8 1.0
OE1 B:GLU411 2.6 19.3 0.5
O1D B:B4P494 2.7 24.4 1.0
OE2 B:GLU404 2.8 23.9 1.0
OE2 B:GLU411 3.2 21.7 0.5
CD B:GLU411 3.3 20.3 0.5
O B:HOH1148 3.3 19.3 1.0
PD B:B4P494 3.6 23.4 1.0
CD B:GLU404 3.7 18.5 1.0
O3G B:B4P494 3.8 20.3 1.0
PB B:B4P494 3.8 15.0 1.0
OE1 B:GLU404 3.9 20.0 1.0
O3B B:B4P494 4.1 16.6 1.0
OE2 B:GLU366 4.2 21.6 1.0
O B:HOH1147 4.2 17.1 1.0
O2D B:B4P494 4.2 23.1 1.0
MG B:MG1100 4.3 22.5 1.0
O B:HOH867 4.4 24.1 1.0
NH2 B:ARG402 4.5 13.1 1.0
OE1 B:GLU411 4.5 21.5 0.5
PG B:B4P494 4.7 16.6 1.0
CG B:GLU411 4.8 19.1 0.5
O3A B:B4P494 4.8 15.7 1.0
O2A B:B4P494 4.8 13.0 1.0
CG B:GLU411 4.9 19.4 0.5

Magnesium binding site 7 out of 12 in 3a74

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Magnesium binding site 7 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1200

b:23.7
occ:1.00
 O3F C:B4P494 2.5 15.7 1.0
OE1 C:GLU411 2.5 18.4 0.5
OE2 C:GLU404 2.9 25.9 1.0
O2D C:B4P494 3.0 14.5 1.0
O3G C:B4P494 3.3 14.9 1.0
C3F C:B4P494 3.4 16.3 1.0
CD C:GLU411 3.5 18.4 0.5
CB C:ASN414 3.6 10.4 1.0
O C:HOH1302 3.6 26.6 1.0
O C:ALA413 3.6 9.3 1.0
CB C:GLU411 3.6 15.0 0.5
CB C:GLU411 3.7 15.1 0.5
CG C:GLU411 3.7 16.3 0.5
CG C:GLU411 3.8 15.9 0.5
PD C:B4P494 3.8 15.0 1.0
CD C:GLU404 3.9 20.0 1.0
C C:ALA413 4.0 9.4 1.0
C5F C:B4P494 4.0 16.0 1.0
C4F C:B4P494 4.2 15.5 1.0
MG C:MG1202 4.2 51.8 1.0
CG C:GLU404 4.2 17.2 1.0
CG C:ASN414 4.3 12.6 1.0
N C:ASN414 4.3 9.6 1.0
CA C:ASN414 4.4 9.9 1.0
O5F C:B4P494 4.4 14.0 1.0
O2G C:B4P494 4.4 17.1 1.0
PG C:B4P494 4.5 16.7 1.0
ND2 C:ASN414 4.6 13.6 1.0
OE2 C:GLU411 4.6 19.4 0.5
N C:ALA413 4.6 11.6 1.0
O3B C:B4P494 4.7 17.6 1.0
CA C:ALA413 4.7 9.4 1.0
C2F C:B4P494 4.7 15.7 1.0
CA C:GLU411 4.9 13.4 0.5
C C:GLU411 4.9 13.0 0.5
CA C:GLU411 4.9 13.3 0.5
C C:GLU411 4.9 13.2 0.5
CB C:GLU404 4.9 12.8 1.0
OE1 C:GLU404 4.9 20.7 1.0

Magnesium binding site 8 out of 12 in 3a74

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Magnesium binding site 8 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1201

b:14.9
occ:1.00
 O C:HOH509 2.0 14.8 1.0
O2B C:B4P494 2.0 20.3 1.0
O C:HOH917 2.1 11.2 1.0
O C:HOH819 2.1 12.5 1.0
O C:HOH915 2.2 13.7 1.0
O1G C:B4P494 2.3 15.9 1.0
PG C:B4P494 3.2 16.7 1.0
PB C:B4P494 3.4 18.7 1.0
O3B C:B4P494 3.5 17.6 1.0
O2A C:B4P494 3.7 23.7 1.0
NH2 C:ARG253 3.9 10.3 1.0
O2G C:B4P494 3.9 17.1 1.0
O C:HOH916 4.0 24.5 1.0
OE2 C:GLU255 4.0 21.9 1.0
NE2 C:HIS261 4.3 14.7 1.0
N7A C:B4P494 4.3 23.2 1.0
OE1 C:GLU255 4.3 17.5 1.0
O3A C:B4P494 4.3 22.2 1.0
O1B C:B4P494 4.4 20.2 1.0
N7B C:B4P494 4.5 14.4 1.0
CD C:GLU255 4.6 17.7 1.0
CD2 C:HIS261 4.6 12.2 1.0
C8A C:B4P494 4.6 23.1 1.0
O3G C:B4P494 4.7 14.9 1.0
PA C:B4P494 4.7 23.4 1.0
O C:ALA209 4.8 13.3 1.0
C8B C:B4P494 5.0 17.1 1.0

Magnesium binding site 9 out of 12 in 3a74

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Magnesium binding site 9 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1202

b:51.8
occ:1.00
 OE1 C:GLU411 2.4 18.4 0.5
O2G C:B4P494 2.6 17.1 1.0
O C:HOH1302 2.7 26.6 1.0
OE2 C:GLU404 2.8 25.9 1.0
O1A C:B4P494 2.9 26.2 1.0
OE2 C:GLU411 3.0 19.4 0.5
CD C:GLU411 3.0 18.4 0.5
O C:HOH1301 3.3 23.4 1.0
O C:HOH1303 3.4 32.7 1.0
O3A C:B4P494 3.4 22.2 1.0
PA C:B4P494 3.7 23.4 1.0
CD C:GLU404 3.7 20.0 1.0
OE1 C:GLU404 3.8 20.7 1.0
O C:HOH1304 3.9 38.7 1.0
PG C:B4P494 4.0 16.7 1.0
OE2 C:GLU411 4.2 17.6 0.5
MG C:MG1200 4.2 23.7 1.0
OE2 C:GLU366 4.3 26.5 1.0
O2A C:B4P494 4.4 23.7 1.0
O C:HOH597 4.4 10.0 1.0
O3G C:B4P494 4.4 14.9 1.0
O3B C:B4P494 4.5 17.6 1.0
CG C:GLU411 4.5 16.3 0.5
CG C:GLU411 4.6 15.9 0.5
NH2 C:ARG402 4.6 12.1 1.0
PB C:B4P494 4.7 18.7 1.0
CD C:GLU411 4.9 18.1 0.5
O2D C:B4P494 5.0 14.5 1.0

Magnesium binding site 10 out of 12 in 3a74

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Magnesium binding site 10 out of 12 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with Diadenosine Tetraphosphate (AP4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1300

b:66.5
occ:1.00
 OE2 D:GLU411 1.8 8.7 0.5
O D:HOH1305 2.3 58.0 1.0
CB D:ASN414 2.3 11.6 1.0
O2A D:B4P494 2.6 12.1 1.0
CD D:GLU411 2.6 14.9 0.5
OE2 D:GLU404 2.9 22.9 1.0
CG D:ASN414 2.9 12.7 1.0
CA D:ASN414 3.2 11.4 1.0
O D:ALA413 3.3 10.9 1.0
CG D:GLU411 3.4 14.2 0.5
OE1 D:GLU411 3.4 14.7 0.5
ND2 D:ASN414 3.4 13.1 1.0
N D:ASN414 3.5 11.0 1.0
O3E D:B4P494 3.5 14.1 1.0
C D:ALA413 3.5 10.6 1.0
CG D:GLU404 3.5 16.5 1.0
OD1 D:ASN414 3.6 11.9 1.0
CD D:GLU404 3.6 18.0 1.0
PA D:B4P494 4.1 14.6 1.0
C5E D:B4P494 4.3 15.1 1.0
O3A D:B4P494 4.3 16.2 1.0
C3E D:B4P494 4.3 13.1 1.0
CB D:GLU404 4.4 13.1 1.0
O1B D:B4P494 4.6 17.8 1.0
C D:ASN414 4.6 10.5 1.0
CA D:ALA413 4.6 11.3 1.0
MG D:MG1302 4.7 33.1 1.0
NH2 D:ARG402 4.7 12.4 1.0
O5E D:B4P494 4.7 14.9 1.0
C4E D:B4P494 4.8 13.0 1.0
CB D:GLU411 4.8 16.1 0.5
OE1 D:GLU404 4.9 19.6 1.0
CB D:GLU411 4.9 12.9 0.5
CA D:GLU404 4.9 13.3 1.0
N D:ALA413 4.9 10.8 1.0
PB D:B4P494 5.0 15.1 1.0

Reference:

H.Sakurama, T.Takita, B.Mikami, T.Itoh, K.Yasukawa, K.Inouye. Crystal Structure of Lysyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights Into AP4A Synthesis Mechanisms and Implication For Recognition of Discriminator Base of Trna^Lys To Be Published.
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