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Zinc in PDB 5w0m: Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna

Enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna

All present enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna:
2.7.7.52;

Protein crystallography data

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna, PDB code: 5w0m 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) 98.17 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 135.472, 135.472, 179.268, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.9

Other elements in 5w0m:

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna also contains other interesting chemical elements:

Iodine (I) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna (pdb code 5w0m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna, PDB code: 5w0m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5w0m

Go back to Zinc Binding Sites List in 5w0m
Zinc binding site 1 out of 2 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1403

b:0.5
occ:1.00
NE2 A:HIS1355 2.0 53.6 1.0
SG A:CYS1360 2.3 61.8 1.0
SG A:CYS1350 2.3 53.0 1.0
SG A:CYS1347 2.5 56.8 1.0
CE1 A:HIS1355 2.8 67.1 1.0
HE1 A:HIS1355 2.8 80.5 1.0
HB2 A:CYS1360 2.9 65.6 1.0
HB3 A:CYS1347 2.9 68.4 1.0
H A:CYS1350 2.9 62.7 1.0
HB3 A:CYS1350 3.0 60.0 1.0
CB A:CYS1360 3.1 54.7 1.0
CB A:CYS1347 3.1 57.0 1.0
CD2 A:HIS1355 3.2 55.3 1.0
CB A:CYS1350 3.2 50.0 1.0
HB2 A:CYS1347 3.3 68.4 1.0
HB A:ILE1349 3.4 64.0 1.0
HA A:CYS1360 3.5 69.5 1.0
HD2 A:HIS1355 3.5 66.3 1.0
N A:CYS1350 3.6 52.3 1.0
HD2 A:PRO1361 3.8 77.0 1.0
CA A:CYS1360 3.9 58.0 1.0
HB3 A:CYS1360 3.9 65.6 1.0
CA A:CYS1350 4.0 52.6 1.0
ND1 A:HIS1355 4.0 52.3 1.0
HB2 A:CYS1350 4.0 60.0 1.0
CG A:HIS1355 4.2 54.4 1.0
H A:ILE1349 4.2 64.7 1.0
H A:LYS1352 4.2 58.7 1.0
CB A:ILE1349 4.3 53.3 1.0
H A:GLY1351 4.4 70.8 1.0
CD A:PRO1361 4.5 64.2 1.0
HD3 A:PRO1361 4.5 77.0 1.0
HB2 A:LYS1352 4.6 55.1 1.0
CA A:CYS1347 4.6 64.4 1.0
HG22 A:ILE1349 4.6 68.7 1.0
C A:ILE1349 4.6 58.2 1.0
H A:MET1362 4.7 58.8 1.0
HD12 A:ILE1349 4.7 66.4 1.0
C A:CYS1350 4.7 64.4 1.0
HD1 A:HIS1355 4.7 62.8 1.0
C A:CYS1360 4.7 70.1 1.0
N A:GLY1351 4.8 59.0 1.0
HA A:MET1357 4.8 72.9 1.0
HA A:CYS1350 4.8 63.1 1.0
CA A:ILE1349 4.8 55.5 1.0
N A:ILE1349 4.9 53.9 1.0
N A:PRO1361 4.9 71.8 1.0
HB2 A:MET1362 4.9 69.3 1.0
CG2 A:ILE1349 4.9 57.2 1.0
HG21 A:ILE1349 4.9 68.7 1.0
O A:LYS1352 4.9 55.5 1.0
N A:CYS1360 5.0 55.4 1.0
C A:CYS1347 5.0 57.6 1.0

Zinc binding site 2 out of 2 in 5w0m

Go back to Zinc Binding Sites List in 5w0m
Zinc binding site 2 out of 2 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1402

b:56.9
occ:1.00
NE2 C:HIS1355 2.0 54.4 1.0
SG C:CYS1360 2.3 81.8 1.0
SG C:CYS1350 2.4 55.5 1.0
SG C:CYS1347 2.5 64.7 1.0
CE1 C:HIS1355 2.8 47.7 1.0
HE1 C:HIS1355 2.8 57.2 1.0
HB3 C:CYS1347 2.9 65.9 1.0
HB2 C:CYS1360 2.9 71.3 1.0
CB C:CYS1347 3.1 54.9 1.0
H C:CYS1350 3.1 98.0 1.0
HB3 C:CYS1350 3.1 77.3 1.0
CB C:CYS1360 3.2 59.4 1.0
CD2 C:HIS1355 3.2 57.5 1.0
HB2 C:CYS1347 3.3 65.9 1.0
CB C:CYS1350 3.4 64.4 1.0
HB C:ILE1349 3.5 93.1 1.0
HD2 C:HIS1355 3.6 69.0 1.0
HA C:CYS1360 3.6 0.4 1.0
N C:CYS1350 3.8 81.7 1.0
HD2 C:PRO1361 3.9 0.3 1.0
HB3 C:CYS1360 4.0 71.3 1.0
CA C:CYS1360 4.0 83.7 1.0
ND1 C:HIS1355 4.0 46.5 1.0
HB2 C:CYS1350 4.1 77.3 1.0
CA C:CYS1350 4.2 69.9 1.0
CG C:HIS1355 4.2 47.4 1.0
H C:LYS1352 4.4 62.4 1.0
H C:ILE1349 4.4 87.3 1.0
CB C:ILE1349 4.5 77.6 1.0
H C:MET1362 4.5 92.2 1.0
HB2 C:MET1362 4.6 1.0 1.0
CA C:CYS1347 4.6 55.6 1.0
H C:GLY1351 4.6 77.5 1.0
HB2 C:LYS1352 4.6 55.0 1.0
CD C:PRO1361 4.7 83.6 1.0
HD12 C:ILE1349 4.7 0.9 1.0
HD1 C:HIS1355 4.7 55.8 1.0
HD3 C:PRO1361 4.8 0.3 1.0
C C:CYS1360 4.8 84.7 1.0
HA C:MET1357 4.8 0.7 1.0
HG22 C:ILE1349 4.9 0.7 1.0
C C:ILE1349 4.9 74.6 1.0
C C:CYS1350 4.9 67.2 1.0
N C:PRO1361 5.0 0.7 1.0
HA C:CYS1350 5.0 83.8 1.0
N C:GLY1351 5.0 64.6 1.0
O C:LYS1352 5.0 48.3 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: Wed Dec 16 11:13:50 2020

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