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Magnesium in PDB 3e9i: Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp

Enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp

All present enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp:
6.1.1.6;

Protein crystallography data

The structure of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp, PDB code: 3e9i 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) 14.98 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.143, 82.483, 149.779, 90.00, 89.99, 90.00
R / Rfree (%) 18.2 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp (pdb code 3e9i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp, PDB code: 3e9i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3e9i

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Magnesium binding site 1 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp


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 L-Lysine Hydroxamate-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:17.6
occ:1.00
 O14 A:XAH1001 2.8 15.3 1.0
O20 A:XAH1001 2.8 13.8 1.0
OE2 A:GLU411 2.8 33.9 1.0
OE2 A:GLU404 3.0 13.5 1.0
CD A:GLU411 3.5 30.5 1.0
CG A:GLU411 3.6 26.3 1.0
C19 A:XAH1001 3.6 16.9 1.0
CB A:GLU411 3.6 19.4 1.0
CB A:ASN414 3.7 9.9 1.0
O A:ALA413 3.7 17.1 1.0
P12 A:XAH1001 3.8 15.2 1.0
CD A:GLU404 3.9 14.3 1.0
C A:ALA413 4.1 15.7 1.0
CG A:GLU404 4.1 11.2 1.0
C16 A:XAH1001 4.1 15.4 1.0
O15 A:XAH1001 4.1 18.0 1.0
O13 A:XAH1001 4.2 15.7 1.0
N A:ASN414 4.4 14.7 1.0
CA A:ASN414 4.4 12.1 1.0
C17 A:XAH1001 4.4 17.2 1.0
CG A:ASN414 4.5 10.6 1.0
OE1 A:GLU411 4.6 33.0 1.0
N A:ALA413 4.8 15.4 1.0
CA A:ALA413 4.8 16.1 1.0
CA A:GLU411 4.9 18.0 1.0
CB A:GLU404 4.9 9.3 1.0
C A:GLU411 4.9 15.8 1.0
C21 A:XAH1001 5.0 16.1 1.0
ND2 A:ASN414 5.0 5.8 1.0

Magnesium binding site 2 out of 4 in 3e9i

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Magnesium binding site 2 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp


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 L-Lysine Hydroxamate-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1100

b:21.9
occ:1.00
 O20 B:XAH1101 2.6 15.8 1.0
O14 B:XAH1101 2.9 15.5 1.0
OE2 B:GLU404 3.0 21.7 1.0
C19 B:XAH1101 3.4 13.3 1.0
CB B:ASN414 3.6 13.0 1.0
CG B:GLU411 3.6 30.4 1.0
CB B:GLU411 3.6 23.1 1.0
O B:ALA413 3.8 12.9 1.0
P12 B:XAH1101 3.8 13.9 1.0
CD B:GLU404 3.9 20.7 1.0
C16 B:XAH1101 3.9 14.1 1.0
C B:ALA413 4.0 13.6 1.0
O15 B:XAH1101 4.1 17.0 1.0
CG B:GLU404 4.1 20.7 1.0
C17 B:XAH1101 4.2 13.9 1.0
O13 B:XAH1101 4.2 14.4 1.0
N B:ASN414 4.3 13.4 1.0
CA B:ASN414 4.3 12.4 1.0
CG B:ASN414 4.3 12.1 1.0
OE1 B:GLU411 4.7 37.1 1.0
CD B:GLU411 4.7 35.5 1.0
C21 B:XAH1101 4.7 15.8 1.0
N B:ALA413 4.8 13.6 1.0
CA B:ALA413 4.8 12.1 1.0
ND2 B:ASN414 4.8 12.7 1.0
CB B:GLU404 4.9 18.7 1.0
CA B:GLU411 4.9 19.6 1.0
OD1 B:ASN414 4.9 12.7 1.0

Magnesium binding site 3 out of 4 in 3e9i

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Magnesium binding site 3 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp


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 L-Lysine Hydroxamate-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1200

b:22.4
occ:1.00
 O14 C:XAH1201 2.6 15.6 1.0
O20 C:XAH1201 2.7 13.8 1.0
OE2 C:GLU411 3.1 34.1 1.0
O C:HOH925 3.1 28.8 1.0
OE2 C:GLU404 3.1 16.9 1.0
C19 C:XAH1201 3.5 16.3 1.0
CB C:ASN414 3.6 10.1 1.0
P12 C:XAH1201 3.7 14.6 1.0
CD C:GLU411 3.7 29.9 1.0
CG C:GLU411 3.7 26.1 1.0
CB C:GLU411 3.8 21.0 1.0
O C:ALA413 3.8 14.6 1.0
C16 C:XAH1201 3.9 14.5 1.0
CD C:GLU404 4.0 17.1 1.0
C C:ALA413 4.1 14.5 1.0
O13 C:XAH1201 4.1 13.9 1.0
CG C:GLU404 4.1 16.9 1.0
O15 C:XAH1201 4.2 17.5 1.0
C17 C:XAH1201 4.3 17.3 1.0
CA C:ASN414 4.3 13.4 1.0
N C:ASN414 4.3 14.0 1.0
CG C:ASN414 4.3 11.9 1.0
OD1 C:ASN414 4.7 13.9 1.0
N C:ALA413 4.8 12.2 1.0
OE1 C:GLU411 4.8 30.4 1.0
C21 C:XAH1201 4.8 18.6 1.0
CB C:GLU404 4.9 15.7 1.0
CA C:ALA413 4.9 14.8 1.0
ND2 C:ASN414 5.0 7.8 1.0

Magnesium binding site 4 out of 4 in 3e9i

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Magnesium binding site 4 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysine Hydroxamate-Amp


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 L-Lysine Hydroxamate-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1300

b:19.4
occ:1.00
 OE2 D:GLU404 2.6 16.4 1.0
O20 D:XAH1301 2.7 15.6 1.0
O14 D:XAH1301 2.9 13.1 1.0
CB D:GLU411 3.6 20.5 1.0
CB D:ASN414 3.6 14.4 1.0
C19 D:XAH1301 3.6 17.1 1.0
CD D:GLU404 3.6 14.9 1.0
CG D:GLU411 3.7 27.2 1.0
O D:ALA413 3.8 11.5 1.0
P12 D:XAH1301 3.9 17.2 1.0
CG D:GLU404 3.9 14.5 1.0
C16 D:XAH1301 4.0 16.7 1.0
C D:ALA413 4.1 12.5 1.0
O15 D:XAH1301 4.2 14.1 1.0
O13 D:XAH1301 4.3 13.8 1.0
CG D:ASN414 4.3 14.3 1.0
CA D:ASN414 4.3 12.7 1.0
N D:ASN414 4.3 14.9 1.0
C17 D:XAH1301 4.3 13.3 1.0
OE1 D:GLU411 4.6 30.5 1.0
CD D:GLU411 4.7 30.6 1.0
OE1 D:GLU404 4.7 11.6 1.0
CB D:GLU404 4.7 14.5 1.0
OD1 D:ASN414 4.8 15.2 1.0
N D:ALA413 4.8 12.0 1.0
ND2 D:ASN414 4.8 14.0 1.0
CA D:GLU411 4.8 17.9 1.0
CA D:ALA413 4.9 11.4 1.0
C21 D:XAH1301 4.9 21.2 1.0

Reference:

H.Sakurama, T.Takita, B.Mikami, T.Itoh, K.Yasukawa, K.Inouye. Two Crystal Structures of Lysyl-Trna Synthetase From Bacillus Stearothermophilus in Complex with Lysyladenylate-Like Compounds: Insights Into the Irreversible Formation of the Enzyme-Bound Adenylate of L-Lysine Hydroxamate J.Biochem. V. 145 555 2009.
ISSN: ISSN 0021-924X
PubMed: 19174549
DOI: 10.1093/JB/MVP014
Page generated: Mon Dec 14 08:05:55 2020

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