Atomistry » Magnesium » PDB 3e3z-3ef8 » 3e9h
Atomistry »
  Magnesium »
    PDB 3e3z-3ef8 »
      3e9h »

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

Go back to Magnesium Binding Sites List in 3e9h
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

Go back to Magnesium Binding Sites List in 3e9h
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

Go back to Magnesium Binding Sites List in 3e9h
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy