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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Aug 11 07:37:30 2025

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