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Magnesium in PDB 3e9h: Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine

Enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine

All present enzymatic activity of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine:
6.1.1.6;

Protein crystallography data

The structure of Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine, PDB code: 3e9h 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) 14.97 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.636, 83.209, 150.815, 90.00, 89.95, 90.00
R / Rfree (%) 19 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine (pdb code 3e9h). 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-Lysylsulfamoyl Adenosine, PDB code: 3e9h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3e9h

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Magnesium binding site 1 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine


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-Lysylsulfamoyl Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:40.2
occ:1.00
 OE2 A:GLU404 2.6 20.4 1.0
O2S A:KAA2002 2.8 15.9 1.0
OE2 A:GLU411 2.9 28.4 1.0
NH2 A:ARG402 3.2 9.2 1.0
CG A:ASN414 3.2 17.3 1.0
ND2 A:ASN414 3.4 11.4 1.0
CB A:ASN414 3.5 17.8 1.0
CD A:GLU411 3.5 28.5 1.0
OD1 A:ASN414 3.5 21.0 1.0
CD A:GLU404 3.6 20.3 1.0
OE1 A:GLU411 3.8 21.8 1.0
CG A:GLU404 3.9 22.0 1.0
O A:HOH845 3.9 34.1 1.0
S1 A:KAA2002 4.0 15.9 1.0
O A:HOH846 4.2 23.2 1.0
O1S A:KAA2002 4.4 18.5 1.0
CZ A:ARG402 4.4 18.8 1.0
N8 A:KAA2002 4.4 19.9 1.0
O A:HOH632 4.6 18.6 1.0
CG A:GLU411 4.6 28.4 1.0
CA A:ASN414 4.6 19.6 1.0
OE1 A:GLU404 4.8 15.7 1.0
NE A:ARG402 4.8 13.4 1.0
O3' A:KAA2002 4.9 16.3 1.0

Magnesium binding site 2 out of 4 in 3e9h

Go back to Magnesium Binding Sites List in 3e9h
Magnesium binding site 2 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine


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-Lysylsulfamoyl Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:34.3
occ:1.00
 OE2 B:GLU404 2.4 26.9 1.0
NH2 B:ARG402 3.0 12.2 1.0
O2S B:KAA2003 3.0 16.1 1.0
CG B:ASN414 3.0 22.1 1.0
OE2 B:GLU411 3.0 27.0 1.0
ND2 B:ASN414 3.2 16.9 1.0
CD B:GLU404 3.3 21.1 1.0
OD1 B:ASN414 3.4 16.9 1.0
CB B:ASN414 3.4 16.4 1.0
CG B:GLU404 3.5 8.8 1.0
CD B:GLU411 3.5 26.6 1.0
OE1 B:GLU411 3.7 25.9 1.0
CZ B:ARG402 4.3 14.4 1.0
S1 B:KAA2003 4.3 17.6 1.0
OE1 B:GLU404 4.5 15.3 1.0
CA B:ASN414 4.6 18.1 1.0
O1S B:KAA2003 4.7 21.0 1.0
CG B:GLU411 4.7 26.1 1.0
NE B:ARG402 4.7 12.1 1.0
N8 B:KAA2003 4.8 16.5 1.0
O B:HOH612 4.8 23.4 1.0
O B:HOH522 4.8 24.4 1.0
O3' B:KAA2003 4.9 13.9 1.0
CB B:GLU404 5.0 16.6 1.0

Magnesium binding site 3 out of 4 in 3e9h

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Magnesium binding site 3 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine


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-Lysylsulfamoyl Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:45.6
occ:1.00
 OE2 C:GLU404 2.6 20.4 1.0
OE2 C:GLU411 2.7 23.7 1.0
O2S C:KAA2004 2.8 10.8 1.0
CG C:ASN414 3.0 15.4 1.0
NH2 C:ARG402 3.3 12.6 1.0
CB C:ASN414 3.3 16.9 1.0
ND2 C:ASN414 3.3 8.1 1.0
OD1 C:ASN414 3.4 20.5 1.0
CD C:GLU411 3.4 26.0 1.0
CD C:GLU404 3.5 22.8 1.0
CG C:GLU404 3.7 22.5 1.0
OE1 C:GLU411 3.9 21.5 1.0
O C:HOH675 4.0 26.0 1.0
S1 C:KAA2004 4.0 11.5 1.0
O C:HOH677 4.2 24.3 1.0
CA C:ASN414 4.4 21.7 1.0
O1S C:KAA2004 4.4 13.7 1.0
CG C:GLU411 4.4 24.7 1.0
CZ C:ARG402 4.5 19.3 1.0
N8 C:KAA2004 4.5 14.3 1.0
O3' C:KAA2004 4.6 13.7 1.0
OE1 C:GLU404 4.7 16.6 1.0
O C:HOH676 4.7 16.1 1.0
NE C:ARG402 4.8 15.6 1.0
O C:ALA413 4.8 11.6 1.0

Magnesium binding site 4 out of 4 in 3e9h

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Magnesium binding site 4 out of 4 in the Lysyl-Trna Synthetase From Bacillus Stearothermophilus Complexed with L-Lysylsulfamoyl Adenosine


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-Lysylsulfamoyl Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:31.3
occ:1.00
 OE2 D:GLU404 2.5 27.4 1.0
O2S D:KAA2005 3.0 17.8 1.0
OE2 D:GLU411 3.0 26.1 1.0
NH2 D:ARG402 3.0 11.5 1.0
CG D:ASN414 3.0 19.0 1.0
ND2 D:ASN414 3.2 16.7 1.0
CB D:ASN414 3.4 16.3 1.0
CD D:GLU404 3.4 23.8 1.0
OD1 D:ASN414 3.4 20.5 1.0
CD D:GLU411 3.5 28.9 1.0
CG D:GLU404 3.6 11.7 1.0
OE1 D:GLU411 3.8 24.9 1.0
CZ D:ARG402 4.3 13.1 1.0
S1 D:KAA2005 4.3 18.0 1.0
CA D:ASN414 4.5 17.4 1.0
OE1 D:GLU404 4.6 13.8 1.0
CG D:GLU411 4.6 21.4 1.0
O1S D:KAA2005 4.7 20.4 1.0
N8 D:KAA2005 4.7 18.2 1.0
NE D:ARG402 4.7 16.9 1.0
O D:HOH663 4.7 20.4 1.0
O3' D:KAA2005 4.9 15.9 1.0
CB D:GLU404 4.9 15.4 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: Wed Aug 14 12:58:06 2024

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