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Magnesium in PDB 4gyz: Mus Musculus TDP2 Bound to Damp and MG2+

Protein crystallography data

The structure of Mus Musculus TDP2 Bound to Damp and MG2+, PDB code: 4gyz was solved by M.J.Schellenberg, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.98 / 2.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.347, 169.326, 184.959, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22

Other elements in 4gyz:

The structure of Mus Musculus TDP2 Bound to Damp and MG2+ also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mus Musculus TDP2 Bound to Damp and MG2+ (pdb code 4gyz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Mus Musculus TDP2 Bound to Damp and MG2+, PDB code: 4gyz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4gyz

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Magnesium binding site 1 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.3
occ:1.00
 O A:HOH554 2.1 33.8 1.0
O A:HOH516 2.1 28.8 1.0
O A:HOH531 2.1 30.6 1.0
OE2 A:GLU162 2.1 33.5 1.0
O A:HOH521 2.1 34.4 1.0
O1P A:D5M401 2.3 36.6 1.0
CD A:GLU162 2.9 31.9 1.0
OE1 A:GLU162 3.0 32.1 1.0
P A:D5M401 3.6 36.7 1.0
OD1 A:ASP132 3.8 45.3 1.0
OD2 A:ASP358 3.9 37.5 1.0
O3P A:D5M401 3.9 34.6 1.0
OD1 A:ASN130 4.1 24.6 1.0
O5' A:D5M401 4.2 77.8 1.0
ND2 A:ASN130 4.2 24.1 1.0
CG A:GLU162 4.3 29.8 1.0
NE2 A:HIS359 4.4 38.1 1.0
OD1 A:ASP358 4.5 35.6 1.0
CG A:ASN130 4.5 24.8 1.0
CG A:ASP358 4.6 37.2 1.0
CG A:ASP132 4.7 44.4 1.0
CD2 A:HIS359 4.7 37.2 1.0
C5' A:D5M401 4.7 79.6 1.0
CD1 A:LEU134 4.7 34.9 1.0
O2P A:D5M401 4.8 37.5 1.0
CA A:ASP132 4.9 35.8 1.0

Magnesium binding site 2 out of 9 in 4gyz

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Magnesium binding site 2 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:47.5
occ:1.00
 OE2 B:GLU162 2.1 53.4 1.0
O B:HOH512 2.1 36.1 1.0
O B:HOH510 2.1 26.9 1.0
O B:HOH511 2.1 48.0 1.0
O B:HOH516 2.1 43.9 1.0
O3P B:D5M401 2.1 46.5 1.0
CD B:GLU162 3.0 50.9 1.0
OE1 B:GLU162 3.2 51.0 1.0
P B:D5M401 3.3 46.5 1.0
O2P B:D5M401 3.4 45.9 1.0
OD1 B:ASP132 4.0 59.8 1.0
ND2 B:ASN130 4.0 38.2 1.0
OD2 B:ASP358 4.0 41.0 1.0
O5' B:D5M401 4.1 88.8 1.0
OD1 B:ASN130 4.2 34.4 1.0
CG B:GLU162 4.4 47.6 1.0
NE2 B:HIS359 4.4 41.7 1.0
O1P B:D5M401 4.4 45.3 1.0
CG B:ASN130 4.5 35.8 1.0
OD1 B:ASP358 4.5 37.1 1.0
C8 B:D5M401 4.6 0.8 1.0
CD2 B:HIS359 4.7 40.6 1.0
CG B:ASP358 4.7 40.0 1.0
CD1 B:LEU134 4.8 41.9 1.0
N7 B:D5M401 4.8 1.0 1.0
CG B:ASP132 4.9 58.1 1.0
CA B:ASP132 4.9 48.5 1.0
C5' B:D5M401 4.9 89.4 1.0
NE2 B:HIS236 5.0 38.5 1.0

Magnesium binding site 3 out of 9 in 4gyz

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Magnesium binding site 3 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:32.9
occ:1.00
 O C:HOH548 2.0 32.1 1.0
O C:HOH546 2.1 32.3 1.0
O C:HOH547 2.1 33.6 1.0
O C:HOH536 2.1 20.8 1.0
OE1 C:GLU162 2.1 30.4 1.0
O3P C:D5M402 2.3 30.0 1.0
CD C:GLU162 2.9 30.1 1.0
OE2 C:GLU162 3.1 32.2 1.0
P C:D5M402 3.4 31.7 1.0
O2P C:D5M402 3.6 32.7 1.0
ND2 C:ASN130 4.1 27.4 1.0
OD1 C:ASP132 4.1 46.4 1.0
O5' C:D5M402 4.1 51.1 1.0
C8 C:D5M402 4.2 57.0 1.0
N7 C:D5M402 4.2 57.2 1.0
OD2 C:ASP358 4.3 37.9 1.0
CG C:GLU162 4.4 27.6 1.0
OD1 C:ASN130 4.4 25.0 1.0
NE2 C:HIS359 4.6 31.0 1.0
CG C:ASN130 4.6 26.0 1.0
O1P C:D5M402 4.6 31.8 1.0
OD1 C:ASP358 4.7 37.0 1.0
CG C:ASP132 4.8 44.4 1.0
CD1 C:LEU134 4.8 32.2 1.0
CD2 C:HIS359 4.9 30.6 1.0
C5' C:D5M402 4.9 51.8 1.0
CE1 C:HIS236 4.9 32.9 1.0
CG C:ASP358 4.9 36.5 1.0

Magnesium binding site 4 out of 9 in 4gyz

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Magnesium binding site 4 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:48.0
occ:1.00
 O D:HOH538 2.1 66.3 1.0
O D:HOH528 2.1 49.7 1.0
O D:HOH529 2.1 60.6 1.0
O D:HOH531 2.1 45.7 1.0
OE1 D:GLU162 2.1 46.3 1.0
O3P D:D5M402 2.3 43.4 1.0
CD D:GLU162 2.9 46.0 1.0
OE2 D:GLU162 3.0 47.4 1.0
P D:D5M402 3.5 42.2 1.0
O2P D:D5M402 3.8 41.9 1.0
OD1 D:ASP132 3.9 46.8 1.0
ND2 D:ASN130 4.1 30.7 1.0
O5' D:D5M402 4.1 66.8 1.0
CG D:GLU162 4.3 43.4 1.0
OD1 D:ASN130 4.4 30.3 1.0
NE2 D:HIS359 4.4 41.8 1.0
C8 D:D5M402 4.4 66.5 1.0
OD2 D:ASP358 4.4 52.3 1.0
CG D:ASN130 4.6 29.8 1.0
O1P D:D5M402 4.7 41.1 1.0
C5' D:D5M402 4.7 67.2 1.0
OD1 D:ASP358 4.8 50.9 1.0
CG D:ASP132 4.8 46.4 1.0
N7 D:D5M402 4.8 66.2 1.0
CE1 D:HIS236 4.9 30.8 1.0
CD2 D:HIS359 4.9 42.2 1.0
CA D:ASP132 4.9 40.2 1.0
CD1 D:LEU134 5.0 44.3 1.0

Magnesium binding site 5 out of 9 in 4gyz

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Magnesium binding site 5 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:38.6
occ:1.00
 O3P E:D5M401 2.0 41.6 1.0
O E:HOH532 2.1 38.2 1.0
O E:HOH533 2.1 25.2 1.0
OE2 E:GLU162 2.1 36.0 1.0
O E:HOH521 2.1 24.0 1.0
O E:HOH534 2.1 38.7 1.0
CD E:GLU162 3.1 36.6 1.0
P E:D5M401 3.2 40.9 1.0
OE1 E:GLU162 3.4 37.9 1.0
O2P E:D5M401 3.5 39.1 1.0
O5' E:D5M401 3.8 68.7 1.0
ND2 E:ASN130 3.9 35.5 1.0
NE2 E:HIS359 4.0 41.6 1.0
OD1 E:ASP132 4.1 46.2 1.0
OD1 E:ASN130 4.1 36.0 1.0
OD2 E:ASP358 4.1 43.7 1.0
CG E:ASN130 4.4 35.4 1.0
O1P E:D5M401 4.4 40.9 1.0
CG E:GLU162 4.4 34.8 1.0
OD1 E:ASP358 4.4 43.5 1.0
CD2 E:HIS359 4.4 41.4 1.0
C5' E:D5M401 4.5 68.5 1.0
CG E:ASP358 4.7 43.7 1.0
CG E:ASP132 4.8 44.7 1.0
O E:HOH540 4.8 59.4 1.0
CE1 E:HIS236 4.9 30.9 1.0
CA E:ASP132 4.9 35.4 1.0
C8 E:D5M401 5.0 76.6 1.0

Magnesium binding site 6 out of 9 in 4gyz

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Magnesium binding site 6 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:69.2
occ:1.00
 O F:HOH523 2.1 62.2 1.0
O F:HOH510 2.1 51.7 1.0
O F:HOH511 2.1 53.0 1.0
O F:HOH518 2.1 63.8 1.0
OE1 F:GLU162 2.1 74.2 1.0
OE2 F:GLU162 2.2 70.3 1.0
O1 F:PO4401 2.3 67.3 1.0
CD F:GLU162 2.5 71.4 1.0
P F:PO4401 3.6 67.5 1.0
OD1 F:ASN130 3.7 49.9 1.0
OD1 F:ASP132 3.8 75.5 1.0
ND2 F:ASN130 3.8 48.0 1.0
CG F:GLU162 4.0 69.4 1.0
O2 F:PO4401 4.0 67.3 1.0
CG F:ASN130 4.2 49.6 1.0
NE2 F:HIS359 4.2 66.5 1.0
O4 F:PO4401 4.3 68.2 1.0
OD2 F:ASP358 4.3 71.7 1.0
OD1 F:ASP358 4.4 70.3 1.0
CG F:ASP132 4.4 76.5 1.0
CD2 F:HIS359 4.5 67.2 1.0
CA F:ASP132 4.6 71.4 1.0
CB F:ASP132 4.7 74.2 1.0
CB F:GLU162 4.7 66.3 1.0
O3 F:PO4401 4.7 67.1 1.0
NE2 F:HIS236 4.7 69.5 1.0
CG F:ASP358 4.8 71.6 1.0
CD1 F:LEU134 5.0 77.3 1.0

Magnesium binding site 7 out of 9 in 4gyz

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Magnesium binding site 7 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:50.1
occ:1.00
 O G:HOH538 2.1 40.3 1.0
O G:HOH539 2.1 52.2 1.0
O G:HOH536 2.1 67.7 1.0
O G:HOH537 2.1 33.3 1.0
OD1 G:ASP132 2.1 36.2 1.0
OE2 G:GLU162 2.2 31.8 1.0
OE1 G:GLU162 2.3 33.5 1.0
CD G:GLU162 2.5 32.2 1.0
CG G:ASP132 3.2 36.4 1.0
CA G:ASP132 3.9 29.9 1.0
O G:HOH532 3.9 48.5 1.0
CB G:ASP132 4.0 32.9 1.0
OD2 G:ASP132 4.0 37.8 1.0
CG G:GLU162 4.0 31.3 1.0
OD1 G:ASP358 4.3 30.2 1.0
OD1 G:ASN130 4.4 31.8 1.0
N E:LEU370 4.4 38.3 1.0
OD2 G:ASP358 4.5 31.2 1.0
CB G:LEU134 4.6 34.0 1.0
O E:VAL368 4.7 50.0 1.0
C G:ASP132 4.7 29.4 1.0
CG G:ASP358 4.7 31.0 1.0
OXT E:LEU370 4.7 43.6 1.0
CB G:GLU162 4.8 30.3 1.0
CD1 G:LEU134 4.8 34.0 1.0
N G:ASP132 4.9 28.2 1.0
ND2 G:ASN130 4.9 33.5 1.0

Magnesium binding site 8 out of 9 in 4gyz

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Magnesium binding site 8 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg402

b:41.0
occ:1.00
 O H:HOH516 2.1 37.4 1.0
O H:HOH519 2.1 38.6 1.0
O H:HOH520 2.1 46.2 1.0
O H:HOH521 2.1 32.7 1.0
OE2 H:GLU162 2.1 33.3 1.0
O3P H:D5M401 2.1 41.1 1.0
CD H:GLU162 3.0 32.7 1.0
OE1 H:GLU162 3.2 33.3 1.0
P H:D5M401 3.4 41.4 1.0
O2P H:D5M401 3.8 41.1 1.0
O5' H:D5M401 4.1 67.4 1.0
OD2 H:ASP358 4.1 36.6 1.0
OD1 H:ASP132 4.1 54.9 1.0
ND2 H:ASN130 4.3 36.8 1.0
NE2 H:HIS359 4.3 41.5 1.0
OD1 H:ASN130 4.4 36.8 1.0
C8 H:D5M401 4.4 85.7 1.0
CG H:GLU162 4.4 31.4 1.0
OD1 H:ASP358 4.5 37.0 1.0
O1P H:D5M401 4.6 41.2 1.0
C5' H:D5M401 4.7 68.8 1.0
CG H:ASN130 4.7 35.9 1.0
CG H:ASP358 4.8 36.7 1.0
CD2 H:HIS359 4.8 41.8 1.0
O H:HOH530 4.9 63.6 1.0
N7 H:D5M401 4.9 87.4 1.0
CG H:ASP132 4.9 54.0 1.0

Magnesium binding site 9 out of 9 in 4gyz

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Magnesium binding site 9 out of 9 in the Mus Musculus TDP2 Bound to Damp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mus Musculus TDP2 Bound to Damp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg402

b:55.2
occ:1.00
 O I:HOH537 2.1 43.1 1.0
O I:HOH529 2.1 31.3 1.0
O I:HOH530 2.1 58.0 1.0
OD1 I:ASP132 2.2 42.0 1.0
OE2 I:GLU162 2.2 44.9 1.0
OE1 I:GLU162 2.2 44.3 1.0
CD I:GLU162 2.5 43.8 1.0
CG I:ASP132 3.2 40.6 1.0
CG I:GLU162 4.0 42.1 1.0
CB I:ASP132 4.0 35.9 1.0
OD2 I:ASP132 4.0 42.0 1.0
CA I:ASP132 4.0 33.7 1.0
OD1 I:ASN130 4.3 31.5 1.0
OD1 I:ASP358 4.5 36.2 1.0
CB I:GLU162 4.7 40.0 1.0
OD2 I:ASP358 4.7 35.2 1.0
ND2 I:ASN130 4.7 32.9 1.0
CB I:LEU134 4.8 42.2 1.0
C I:ASP132 4.9 33.5 1.0
CD1 I:LEU134 4.9 40.4 1.0
CG I:ASN130 4.9 31.4 1.0
N I:ASP132 5.0 31.7 1.0
CG I:ASP358 5.0 35.4 1.0

Reference:

M.J.Schellenberg, C.D.Appel, S.Adhikari, P.D.Robertson, D.A.Ramsden, R.S.Williams. Mechanism of Repair of 5'-Topoisomerase II-Dna Adducts By Mammalian Tyrosyl-Dna Phosphodiesterase 2. Nat.Struct.Mol.Biol. V. 19 1363 2012.
ISSN: ISSN 1545-9993
PubMed: 23104055
DOI: 10.1038/NSMB.2418
Page generated: Mon Aug 11 13:41:47 2025

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