Magnesium in PDB 5wu6: Crystal Structure of Apo Human TUT1, Form IV

Enzymatic activity of Crystal Structure of Apo Human TUT1, Form IV

All present enzymatic activity of Crystal Structure of Apo Human TUT1, Form IV:
2.7.7.19; 2.7.7.52;

Protein crystallography data

The structure of Crystal Structure of Apo Human TUT1, Form IV, PDB code: 5wu6 was solved by S.Yamashita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.21
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 142.530, 142.530, 282.690, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo Human TUT1, Form IV (pdb code 5wu6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Apo Human TUT1, Form IV, PDB code: 5wu6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5wu6

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Magnesium binding site 1 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:57.3
occ:1.00
 OD1 A:ASP216 2.4 78.2 1.0
OD1 A:ASP381 3.2 89.2 1.0
CG A:ASP216 3.4 84.4 1.0
CB A:ASP216 3.8 75.6 1.0
OD1 A:ASP218 3.9 56.1 1.0
OD2 A:ASP218 4.2 69.1 1.0
CG A:ASP381 4.2 87.1 1.0
OD2 A:ASP216 4.5 94.7 1.0
CG A:ASP218 4.5 63.5 1.0
OD2 A:ASP381 4.9 90.1 1.0

Magnesium binding site 2 out of 7 in 5wu6

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Magnesium binding site 2 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:94.4
occ:1.00
 OE2 A:GLU189 2.1 0.6 1.0
OE1 D:GLU193 2.2 0.5 1.0
CD A:GLU189 3.1 97.4 1.0
CD D:GLU193 3.2 0.6 1.0
OE1 B:GLU189 3.4 0.0 1.0
O D:GLU193 3.4 69.5 1.0
OE1 A:GLU189 3.6 96.1 1.0
CG D:GLU193 3.9 91.5 1.0
CD B:GLU189 4.0 0.4 1.0
OE2 D:GLU193 4.1 0.3 1.0
OE2 B:GLU189 4.2 0.7 1.0
CG A:GLU189 4.2 92.0 1.0
C D:GLU193 4.3 74.9 1.0
CA D:GLU193 4.4 76.8 1.0
OE1 C:GLU193 4.6 0.6 1.0
CB D:GLU193 4.7 82.3 1.0

Magnesium binding site 3 out of 7 in 5wu6

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Magnesium binding site 3 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:46.7
occ:1.00
 OD1 B:ASP216 2.4 91.4 1.0
CG B:ASP216 3.4 93.0 1.0
OD1 B:ASP381 3.5 87.6 1.0
CB B:ASP216 3.9 80.6 1.0
OD1 B:ASP218 4.1 78.2 1.0
OD2 B:ASP216 4.5 0.2 1.0
CG B:ASP381 4.7 80.8 1.0
OD2 B:ASP218 4.7 90.2 1.0
CG B:ASP218 4.8 80.6 1.0

Magnesium binding site 4 out of 7 in 5wu6

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Magnesium binding site 4 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:48.4
occ:1.00
 OE1 B:GLU193 3.4 72.1 1.0
O D:CYS351 3.9 68.0 1.0
OE1 C:GLU189 4.1 65.9 1.0
OE2 C:GLU189 4.3 68.6 1.0
CD B:GLU193 4.6 73.5 1.0
O B:GLU193 4.6 47.8 1.0
CD C:GLU189 4.6 65.6 1.0
C D:CYS351 4.9 59.6 1.0

Magnesium binding site 5 out of 7 in 5wu6

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Magnesium binding site 5 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:57.7
occ:1.00
 OD2 C:ASP216 2.7 94.5 1.0
OD1 C:ASP381 2.9 95.6 1.0
CG C:ASP216 3.6 92.6 1.0
CB C:ASP216 4.0 83.7 1.0
CG C:ASP381 4.1 85.8 1.0
OD1 C:ASP218 4.1 61.3 1.0
OD2 C:ASP218 4.5 79.3 1.0
OD2 C:ASP381 4.6 90.7 1.0
OD1 C:ASP216 4.6 95.9 1.0
CG C:ASP218 4.7 68.6 1.0

Magnesium binding site 6 out of 7 in 5wu6

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Magnesium binding site 6 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:40.8
occ:1.00
 OE2 C:GLU193 1.9 0.9 1.0
OE2 D:GLU193 2.9 0.3 1.0
CD C:GLU193 3.0 0.6 1.0
O D:GLU189 3.5 49.1 1.0
OE1 C:GLU193 3.7 0.6 1.0
OE2 C:GLU189 3.7 68.6 1.0
OE2 D:GLU189 3.8 81.7 1.0
CG C:GLU193 3.9 99.8 1.0
CB C:GLU193 4.0 91.3 1.0
CG C:GLU189 4.0 55.8 1.0
CD D:GLU193 4.1 0.6 1.0
CB D:GLU193 4.2 82.3 1.0
CG D:GLU189 4.3 67.6 1.0
O C:GLU189 4.3 41.9 1.0
CD C:GLU189 4.3 65.6 1.0
C D:GLU189 4.5 53.3 1.0
CD D:GLU189 4.5 80.7 1.0
CG D:GLU193 4.6 91.5 1.0
C C:GLU189 4.9 40.3 1.0
CA D:GLU193 5.0 76.8 1.0

Magnesium binding site 7 out of 7 in 5wu6

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Magnesium binding site 7 out of 7 in the Crystal Structure of Apo Human TUT1, Form IV


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 Apo Human TUT1, Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:34.4
occ:1.00
 OD1 D:ASP216 2.5 87.8 1.0
CG D:ASP216 3.3 81.1 1.0
OD1 D:ASP381 3.5 97.9 1.0
CB D:ASP216 3.6 63.3 1.0
OD2 D:ASP218 4.0 67.8 1.0
OD1 D:ASP218 4.1 62.0 1.0
OD2 D:ASP216 4.4 87.8 1.0
CG D:ASP381 4.5 93.2 1.0
CG D:ASP218 4.5 60.9 1.0
OD2 D:ASP381 4.9 98.4 1.0

Reference:

S.Yamashita, Y.Takagi, T.Nagaike, K.Tomita. Crystal Structures of U6 Snrna-Specific Terminal Uridylyltransferase Nat Commun V. 8 15788 2017.
ISSN: ESSN 2041-1723
PubMed: 28589955
DOI: 10.1038/NCOMMS15788
Page generated: Mon Dec 14 21:25:08 2020

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