Magnesium in PDB 5w0n: Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna

Enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna

All present enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna:
2.7.7.52;

Protein crystallography data

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna, PDB code: 5w0n was solved by C.R.Faehnle, J.Walleshauser, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.88 / 2.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 135.972, 135.972, 181.574, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 21.5

Other elements in 5w0n:

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iodine (I) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna (pdb code 5w0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna, PDB code: 5w0n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5w0n

Go back to Magnesium Binding Sites List in 5w0n
Magnesium binding site 1 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:78.4
occ:1.00
O2A A:2KH1402 2.0 82.8 1.0
O A:HOH1512 2.0 83.3 1.0
OD1 A:ASP1058 2.1 51.7 1.0
O1B A:2KH1402 2.1 87.4 1.0
OD2 A:ASP1060 2.1 47.1 1.0
O3G A:2KH1402 2.2 87.0 1.0
CG A:ASP1060 3.1 39.0 1.0
CG A:ASP1058 3.1 42.4 1.0
H7 A:2KH1402 3.1 92.3 1.0
PB A:2KH1402 3.3 79.0 0.9
PA A:2KH1402 3.3 73.2 1.0
OD1 A:ASP1060 3.4 40.8 1.0
H A:SER1047 3.5 50.0 1.0
OD2 A:ASP1058 3.5 40.7 1.0
PG A:2KH1402 3.5 80.5 0.9
N3A A:2KH1402 3.7 79.9 0.9
O3B A:2KH1402 3.8 84.5 1.0
C5' A:2KH1402 3.8 77.0 1.0
O A:HOH1520 3.8 39.0 1.0
H6 A:2KH1402 3.8 92.3 1.0
O A:ASP1058 3.9 37.2 1.0
OG A:SER1047 4.0 37.5 1.0
O A:HOH1526 4.0 36.1 1.0
HG A:SER1047 4.0 45.0 1.0
H A:ASP1058 4.1 49.2 1.0
HB3 A:SER1057 4.1 46.6 1.0
HA3 A:GLY1046 4.1 54.7 1.0
O5' A:2KH1402 4.1 75.5 1.0
H3AO A:UPU1403 4.2 51.6 1.0
N A:SER1047 4.3 41.7 1.0
HB3 A:SER1047 4.4 39.9 1.0
O1G A:2KH1402 4.4 84.7 0.9
C A:ASP1058 4.4 42.2 1.0
O1A A:2KH1402 4.4 75.3 1.0
CB A:ASP1058 4.4 44.7 1.0
CB A:ASP1060 4.4 41.4 1.0
O2G A:2KH1402 4.5 84.0 1.0
N A:ASP1058 4.5 41.0 1.0
O2B A:2KH1402 4.5 82.8 1.0
H2 A:2KH1402 4.5 95.8 0.9
HB2 A:ASP1060 4.5 49.6 1.0
H A:ASP1060 4.6 49.0 1.0
CA A:ASP1058 4.7 44.3 1.0
CB A:SER1047 4.7 33.2 1.0
O3'A A:UPU1403 4.8 43.0 1.0
HB3 A:ASP1058 4.9 53.6 1.0
CA A:GLY1046 4.9 45.6 1.0
N A:ASP1060 5.0 40.8 1.0

Magnesium binding site 2 out of 3 in 5w0n

Go back to Magnesium Binding Sites List in 5w0n
Magnesium binding site 2 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1401

b:37.8
occ:1.00
OD1 B:ASP1058 2.0 43.3 1.0
O2B B:2KH1402 2.0 28.7 1.0
O B:HOH1502 2.1 42.4 1.0
OD2 B:ASP1060 2.1 38.9 1.0
O3G B:2KH1402 2.2 27.3 1.0
O1A B:2KH1402 2.2 32.5 1.0
CG B:ASP1058 3.1 41.8 1.0
CG B:ASP1060 3.2 39.5 1.0
PB B:2KH1402 3.2 34.1 0.9
H6 B:2KH1402 3.2 42.6 1.0
H B:SER1047 3.3 46.7 1.0
PG B:2KH1402 3.4 28.6 0.9
PA B:2KH1402 3.5 35.0 1.0
OD1 B:ASP1060 3.5 38.0 1.0
OD2 B:ASP1058 3.5 43.9 1.0
OG B:SER1047 3.7 40.6 1.0
O3B B:2KH1402 3.7 36.4 1.0
HG B:SER1047 3.7 48.8 1.0
N3A B:2KH1402 3.8 39.5 0.9
O B:ASP1058 3.8 37.9 1.0
HB3 B:SER1057 3.9 51.9 1.0
H B:ASP1058 4.0 40.8 1.0
C5' B:2KH1402 4.0 35.5 1.0
O B:HOH1506 4.0 35.5 1.0
O B:HOH1524 4.0 40.1 1.0
H7 B:2KH1402 4.0 42.6 1.0
HA3 B:GLY1046 4.1 50.1 1.0
N B:SER1047 4.1 38.9 1.0
HB3 B:SER1047 4.2 45.9 1.0
O2G B:2KH1402 4.2 32.3 1.0
O5' B:2KH1402 4.3 35.6 1.0
C B:ASP1058 4.3 40.2 1.0
N B:ASP1058 4.4 34.0 1.0
CB B:ASP1058 4.4 38.7 1.0
H3AO B:UPU1403 4.4 56.9 1.0
CB B:SER1047 4.4 38.2 1.0
O1B B:2KH1402 4.4 38.2 1.0
H B:ASP1060 4.5 50.2 1.0
CB B:ASP1060 4.5 40.6 1.0
O1G B:2KH1402 4.5 33.3 0.9
HB2 B:ASP1060 4.5 48.7 1.0
H2 B:2KH1402 4.5 47.4 0.9
O2A B:2KH1402 4.6 39.3 1.0
CA B:ASP1058 4.6 38.8 1.0
H B:SER1048 4.8 53.2 1.0
CB B:SER1057 4.9 43.2 1.0
CA B:GLY1046 4.9 41.8 1.0
CA B:SER1047 4.9 44.4 1.0
N B:ASP1060 4.9 41.8 1.0
HB3 B:ASP1058 4.9 46.4 1.0
HB2 B:ASP1058 5.0 46.4 1.0

Magnesium binding site 3 out of 3 in 5w0n

Go back to Magnesium Binding Sites List in 5w0n
Magnesium binding site 3 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1401

b:45.9
occ:1.00
O C:HOH1504 2.0 47.0 1.0
O1A C:2KH1402 2.1 41.7 1.0
OD1 C:ASP1058 2.1 47.6 1.0
OD2 C:ASP1060 2.1 44.7 1.0
O1G C:2KH1402 2.1 42.0 1.0
O1B C:2KH1402 2.2 43.2 1.0
CG C:ASP1060 3.1 44.5 1.0
H6 C:2KH1402 3.1 57.7 1.0
CG C:ASP1058 3.1 47.5 1.0
PB C:2KH1402 3.3 44.1 0.9
PA C:2KH1402 3.3 43.5 1.0
H C:SER1047 3.3 47.8 1.0
OD1 C:ASP1060 3.4 42.0 1.0
PG C:2KH1402 3.4 38.3 0.9
OD2 C:ASP1058 3.5 47.8 1.0
N3A C:2KH1402 3.7 41.1 0.9
OG C:SER1047 3.7 47.6 1.0
HG C:SER1047 3.7 57.2 1.0
O3B C:2KH1402 3.8 41.2 1.0
O C:ASP1058 3.8 48.1 1.0
C5' C:2KH1402 3.9 48.1 1.0
O C:HOH1520 3.9 54.6 1.0
HB3 C:SER1057 4.0 48.5 1.0
H7 C:2KH1402 4.0 57.7 1.0
H C:ASP1058 4.1 57.7 1.0
O C:HOH1505 4.1 37.1 1.0
HA3 C:GLY1046 4.1 47.5 1.0
O5' C:2KH1402 4.2 50.0 1.0
HB3 C:SER1047 4.2 53.9 1.0
N C:SER1047 4.2 39.9 1.0
H3AO C:UPU1403 4.2 60.0 1.0
O2G C:2KH1402 4.2 39.5 0.9
C C:ASP1058 4.4 45.9 1.0
CB C:ASP1060 4.4 43.3 1.0
CB C:SER1047 4.4 44.9 1.0
CB C:ASP1058 4.4 47.6 1.0
N C:ASP1058 4.5 48.1 1.0
O3G C:2KH1402 4.5 40.6 1.0
H2 C:2KH1402 4.5 49.4 0.9
O2A C:2KH1402 4.5 47.9 1.0
HB2 C:ASP1060 4.5 52.0 1.0
H C:ASP1060 4.5 51.9 1.0
O2B C:2KH1402 4.6 41.4 1.0
CA C:ASP1058 4.7 49.1 1.0
O3'A C:UPU1403 4.9 50.0 1.0
CA C:GLY1046 4.9 39.6 1.0
CB C:SER1057 4.9 40.5 1.0
N C:ASP1060 4.9 43.2 1.0
H C:SER1048 4.9 50.0 1.0
CA C:SER1047 4.9 42.1 1.0
HB3 C:ASP1058 5.0 57.1 1.0

Reference:

C.R.Faehnle, J.Walleshauser, L.Joshua-Tor. Multi-Domain Utilization By TUT4 and TUT7 in Control of Let-7 Biogenesis. Nat. Struct. Mol. Biol. V. 24 658 2017.
ISSN: ESSN 1545-9985
PubMed: 28671666
DOI: 10.1038/NSMB.3428
Page generated: Mon Dec 14 21:19:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy