Atomistry » Magnesium » PDB 4doa-4dv5 » 4dpg
Atomistry »
  Magnesium »
    PDB 4doa-4dv5 »
      4dpg »

Magnesium in PDB 4dpg: Crystal Structure of Human Lysrs: P38/AIMP2 Complex I

Enzymatic activity of Crystal Structure of Human Lysrs: P38/AIMP2 Complex I

All present enzymatic activity of Crystal Structure of Human Lysrs: P38/AIMP2 Complex I:
6.1.1.6;

Protein crystallography data

The structure of Crystal Structure of Human Lysrs: P38/AIMP2 Complex I, PDB code: 4dpg was solved by P.Fang, J.Wang, S.P.Bennett, M.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 2.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.200, 122.010, 149.200, 89.16, 85.58, 89.71
R / Rfree (%) 18.5 / 22.3

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I (pdb code 4dpg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I, PDB code: 4dpg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 1 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:53.4
occ:1.00
 OE1 A:GLU494 2.4 73.7 1.0
OE2 A:GLU487 3.0 68.2 1.0
CD A:GLU494 3.7 69.6 1.0
C3A A:APC602 3.7 0.3 1.0
CD A:GLU487 3.9 65.4 1.0
OE1 A:GLU487 4.1 71.9 1.0
OE2 A:GLU494 4.4 71.2 1.0
C5' A:APC602 4.5 0.5 1.0
CB A:GLU494 4.6 56.4 1.0
CG A:GLU494 4.6 61.3 1.0
O1A A:APC602 4.7 0.5 1.0
OD1 A:ASP445 4.7 79.4 1.0
PA A:APC602 4.8 0.2 1.0
CZ A:PHE489 4.8 35.1 1.0

Magnesium binding site 2 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 2 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:63.5
occ:1.00
 OE2 B:GLU487 2.0 26.8 1.0
OE1 B:GLU494 2.2 62.0 1.0
O1A B:APC602 2.3 0.3 1.0
CD B:GLU487 3.3 25.4 1.0
CD B:GLU494 3.3 54.7 1.0
PA B:APC602 3.4 0.7 1.0
O5' B:APC602 3.7 0.4 1.0
OE2 B:GLU494 3.8 62.4 1.0
O2A B:APC602 3.9 98.9 1.0
OE1 B:GLU487 4.0 24.1 1.0
NH2 B:ARG485 4.1 17.3 1.0
CG B:GLU487 4.4 25.8 1.0
CG B:GLU494 4.5 38.7 1.0
C5' B:APC602 4.6 0.3 1.0
CB B:GLU494 4.8 16.7 1.0
C3A B:APC602 5.0 86.8 1.0

Magnesium binding site 3 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 3 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:59.0
occ:1.00
 OE2 C:GLU487 1.9 51.7 1.0
OE1 C:GLU494 2.4 64.0 1.0
CD C:GLU487 3.2 46.1 1.0
CD C:GLU494 3.4 57.2 1.0
OE2 C:GLU494 3.8 61.4 1.0
NH2 C:ARG485 3.8 31.3 1.0
OE1 C:GLU487 3.9 44.7 1.0
CG C:GLU487 4.2 40.8 1.0
O1A C:APC602 4.6 0.1 1.0
C3A C:APC602 4.7 93.5 1.0
C5' C:APC602 4.7 0.5 1.0
CG C:GLU494 4.7 44.2 1.0
CZ C:ARG485 5.0 25.8 1.0

Magnesium binding site 4 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 4 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:68.2
occ:1.00
 OE2 D:GLU487 2.1 36.3 1.0
OE1 D:GLU494 2.4 45.2 1.0
O1A D:APC602 2.6 0.6 1.0
CD D:GLU487 3.4 32.9 1.0
CD D:GLU494 3.4 39.2 1.0
PA D:APC602 3.5 0.7 1.0
NH2 D:ARG485 3.6 38.1 1.0
O2A D:APC602 3.7 0.5 1.0
OE2 D:GLU494 3.7 42.7 1.0
O5' D:APC602 3.8 0.5 1.0
OE1 D:GLU487 4.2 42.8 1.0
CG D:GLU487 4.4 21.6 1.0
C5' D:APC602 4.5 0.4 1.0
CG D:GLU494 4.8 26.2 1.0
CG D:ASN497 4.9 30.9 1.0
CZ D:ARG485 4.9 31.6 1.0

Magnesium binding site 5 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 5 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:53.2
occ:1.00
 OE2 E:GLU487 2.6 48.4 1.0
OE1 E:GLU494 2.7 50.8 1.0
CD E:GLU487 3.5 46.1 1.0
O E:HOH741 3.7 41.5 1.0
OE1 E:GLU487 3.8 45.9 1.0
CD E:GLU494 3.9 46.0 1.0
C3A E:APC602 4.1 94.1 1.0
OD1 E:ASP445 4.4 56.9 1.0
OE2 E:GLU494 4.6 49.5 1.0
O1A E:APC602 4.8 0.1 1.0
CG E:GLU487 4.8 40.6 1.0
NH2 E:ARG485 4.9 38.5 1.0
CG E:GLU494 4.9 38.7 1.0
C5' E:APC602 4.9 0.9 1.0

Magnesium binding site 6 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 6 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:59.6
occ:1.00
 O1A F:APC602 2.0 0.9 1.0
OE2 F:GLU487 2.2 45.8 1.0
OE1 F:GLU494 2.4 53.7 1.0
PA F:APC602 3.2 0.7 1.0
CD F:GLU487 3.5 39.4 1.0
CD F:GLU494 3.6 50.4 1.0
O5' F:APC602 3.7 0.5 1.0
O2A F:APC602 3.7 94.7 1.0
OE1 F:GLU487 4.1 49.8 1.0
OE2 F:GLU494 4.1 53.6 1.0
NH2 F:ARG485 4.2 28.8 1.0
C5' F:APC602 4.6 0.2 1.0
CG F:GLU487 4.6 19.3 1.0
C3A F:APC602 4.8 0.9 1.0
CG F:GLU494 4.8 39.6 1.0
OD2 F:ASP445 4.9 74.9 1.0

Magnesium binding site 7 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 7 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg604

b:13.0
occ:1.00
 NE2 F:HIS215 2.0 59.9 1.0
NE2 C:HIS100 2.2 32.7 1.0
NE2 F:HIS217 2.3 50.0 1.0
O K:PRO2 2.4 69.0 1.0
N K:PRO2 2.5 49.0 1.0
C K:PRO2 2.9 59.1 1.0
CE1 F:HIS215 2.9 58.1 1.0
CE1 C:HIS100 3.0 39.5 1.0
CD2 F:HIS215 3.0 59.1 1.0
CA K:PRO2 3.1 47.4 1.0
CE1 F:HIS217 3.2 54.9 1.0
CD2 F:HIS217 3.3 54.6 1.0
CD2 C:HIS100 3.3 36.2 1.0
CD K:PRO2 3.3 46.3 1.0
N K:MET3 3.9 48.4 1.0
ND1 F:HIS215 4.1 55.8 1.0
CG F:HIS215 4.2 56.7 1.0
ND1 C:HIS100 4.2 41.2 1.0
CG K:PRO2 4.3 39.5 1.0
ND1 F:HIS217 4.3 60.1 1.0
CB K:PRO2 4.4 43.2 1.0
CG C:HIS100 4.4 31.5 1.0
CG F:HIS217 4.4 57.6 1.0
O C:HOH707 4.6 29.3 1.0
CA K:MET3 4.6 41.5 1.0

Magnesium binding site 8 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 8 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:55.8
occ:1.00
 OE1 G:GLU494 2.7 67.0 1.0
OE2 G:GLU487 3.1 68.7 1.0
C3A G:APC602 3.7 0.7 1.0
CD G:GLU494 3.9 59.8 1.0
CD G:GLU487 4.0 64.8 1.0
OE1 G:GLU487 4.2 63.3 1.0
OD1 G:ASP445 4.4 85.1 1.0
C5' G:APC602 4.6 0.7 1.0
O1A G:APC602 4.7 0.8 1.0
OE2 G:GLU494 4.7 66.7 1.0
PA G:APC602 4.8 0.1 1.0
CB G:GLU494 4.8 44.0 1.0
CG G:GLU494 4.9 45.8 1.0
CZ G:PHE489 4.9 32.3 1.0

Magnesium binding site 9 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 9 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


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 Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:66.0
occ:1.00
 O1A H:APC603 2.2 0.0 1.0
OE2 H:GLU487 2.2 41.5 1.0
OE1 H:GLU494 2.5 63.1 1.0
PA H:APC603 3.3 0.7 1.0
CD H:GLU487 3.4 34.4 1.0
CD H:GLU494 3.6 55.7 1.0
O2A H:APC603 3.7 0.5 1.0
O5' H:APC603 3.8 0.8 1.0
OE1 H:GLU487 4.0 27.2 1.0
NH2 H:ARG485 4.0 26.3 1.0
OE2 H:GLU494 4.2 59.0 1.0
CG H:GLU487 4.6 17.4 1.0
C5' H:APC603 4.7 0.6 1.0
CG H:GLU494 4.8 46.3 1.0
C3A H:APC603 4.9 86.2 1.0
OD2 H:ASP445 4.9 73.0 1.0

Magnesium binding site 10 out of 12 in 4dpg

Go back to Magnesium Binding Sites List in 4dpg
Magnesium binding site 10 out of 12 in the Crystal Structure of Human Lysrs: P38/AIMP2 Complex I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Lysrs: P38/AIMP2 Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg605

b:13.5
occ:1.00
 NE2 A:HIS100 2.0 29.6 1.0
NE2 H:HIS215 2.2 70.7 1.0
O I:PRO2 2.3 61.2 1.0
N I:PRO2 2.6 42.6 1.0
NE2 H:HIS217 2.6 77.5 1.0
CE1 A:HIS100 2.8 29.9 1.0
CE1 H:HIS215 2.9 64.7 1.0
C I:PRO2 3.0 53.7 1.0
CD2 A:HIS100 3.1 35.4 1.0
CA I:PRO2 3.2 51.2 1.0
CD2 H:HIS215 3.3 75.4 1.0
CE1 H:HIS217 3.5 79.2 1.0
CD2 H:HIS217 3.6 77.7 1.0
CD I:PRO2 3.7 46.3 1.0
ND1 A:HIS100 4.0 25.6 1.0
ND1 H:HIS215 4.1 63.5 1.0
N I:MET3 4.1 44.7 1.0
CG A:HIS100 4.2 31.1 1.0
CG H:HIS215 4.3 68.4 1.0
O A:HOH710 4.4 44.4 1.0
ND1 H:HIS217 4.6 77.1 1.0
CB I:PRO2 4.6 48.2 1.0
CG I:PRO2 4.6 47.7 1.0
CG H:HIS217 4.7 76.8 1.0
CA I:MET3 4.7 31.0 1.0

Reference:

Y.Ofir-Birin, P.Fang, S.P.Bennett, H.M.Zhang, J.Wang, I.Rachmin, R.Shapiro, J.Song, A.Dagan, J.Pozo, S.Kim, A.G.Marshall, P.Schimmel, X.L.Yang, H.Nechushtan, E.Razin, M.Guo. Structural Switch of Lysyl-Trna Synthetase Between Translation and Transcription. Mol.Cell V. 49 30 2013.
ISSN: ISSN 1097-2765
PubMed: 23159739
DOI: 10.1016/J.MOLCEL.2012.10.010
Page generated: Thu Aug 15 17:19:16 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