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Zinc in PDB 9w4r: Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1

Enzymatic activity of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1

All present enzymatic activity of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1:
2.7.7.52;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1 (pdb code 9w4r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1, PDB code: 9w4r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 9w4r

Go back to Zinc Binding Sites List in 9w4r
Zinc binding site 1 out of 4 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:222.7
occ:1.00
 ND1 A:HIS328 2.0 164.8 1.0
NE2 A:HIS322 2.1 194.5 1.0
SG A:CYS306 2.3 181.3 1.0
SG A:CYS309 2.3 180.6 1.0
CB A:CYS309 2.6 180.6 1.0
CB A:CYS306 2.6 181.3 1.0
CE1 A:HIS328 2.7 164.8 1.0
CE1 A:HIS322 2.9 194.5 1.0
CD2 A:HIS322 3.2 194.5 1.0
CG A:HIS328 3.3 164.8 1.0
N A:CYS309 3.7 180.6 1.0
CA A:CYS309 3.7 180.6 1.0
CB A:HIS328 3.9 164.8 1.0
NE2 A:HIS328 3.9 164.8 1.0
ND1 A:HIS322 4.0 194.5 1.0
CA A:CYS306 4.1 181.3 1.0
CD2 A:HIS328 4.2 164.8 1.0
CG A:HIS322 4.2 194.5 1.0
CD1 A:ILE289 4.5 191.6 1.0
CA A:HIS328 4.6 164.8 1.0
C A:CYS306 4.8 181.3 1.0
C A:LEU308 4.8 170.9 1.0
C A:CYS309 4.8 180.6 1.0
OE1 A:GLU325 4.8 184.6 1.0
N A:CYS306 4.9 181.3 1.0

Zinc binding site 2 out of 4 in 9w4r

Go back to Zinc Binding Sites List in 9w4r
Zinc binding site 2 out of 4 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:284.2
occ:1.00
 NE2 A:HIS923 2.1 225.3 1.0
SG A:CYS915 2.3 238.6 1.0
SG A:CYS918 2.3 239.6 1.0
SG A:CYS928 2.3 258.9 1.0
CB A:CYS928 2.5 258.9 1.0
CD2 A:HIS923 2.7 225.3 1.0
CA A:CYS928 3.0 258.9 1.0
CB A:CYS915 3.1 238.6 1.0
CB A:CYS918 3.2 239.6 1.0
CE1 A:HIS923 3.3 225.3 1.0
N A:CYS918 3.8 239.6 1.0
N A:CYS928 3.9 258.9 1.0
CG A:HIS923 4.0 225.3 1.0
C A:CYS928 4.1 258.9 1.0
CD A:PRO929 4.1 263.0 1.0
CA A:CYS918 4.1 239.6 1.0
OE1 A:GLU930 4.1 264.6 1.0
O A:SER924 4.1 241.8 1.0
ND1 A:HIS923 4.2 225.3 1.0
N A:PRO929 4.4 263.0 1.0
CA A:CYS915 4.6 238.6 1.0
O A:ASP927 4.6 244.4 1.0
C A:ASP927 4.6 244.4 1.0
CB A:ILE917 4.8 240.4 1.0
C A:CYS918 4.9 239.6 1.0
C A:ILE917 5.0 240.4 1.0

Zinc binding site 3 out of 4 in 9w4r

Go back to Zinc Binding Sites List in 9w4r
Zinc binding site 3 out of 4 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:294.3
occ:1.00
 ND1 B:HIS147 2.1 221.5 1.0
SG B:CYS139 2.3 236.3 1.0
SG B:CYS152 2.3 232.2 1.0
SG B:CYS142 2.3 243.3 1.0
CE1 B:HIS147 2.7 221.5 1.0
CB B:CYS139 2.8 236.3 1.0
CB B:CYS152 3.1 232.2 1.0
CG B:HIS147 3.3 221.5 1.0
CB B:CYS142 3.6 243.3 1.0
CB B:HIS147 3.8 221.5 1.0
NE2 B:HIS147 4.0 221.5 1.0
O B:HIS147 4.0 221.5 1.0
C B:HIS147 4.1 221.5 1.0
N B:CYS142 4.1 243.3 1.0
CB B:ASN141 4.2 227.2 1.0
CA B:CYS152 4.2 232.2 1.0
CD2 B:HIS147 4.2 221.5 1.0
CA B:CYS139 4.3 236.3 1.0
O B:HIS148 4.3 226.0 1.0
CA B:HIS147 4.4 221.5 1.0
CA B:CYS142 4.4 243.3 1.0
N B:HIS148 4.5 226.0 1.0
C B:HIS148 4.5 226.0 1.0
CA B:HIS148 4.7 226.0 1.0
N B:HIS147 4.7 221.5 1.0
CD2 B:LEU154 4.9 234.4 1.0
C B:CYS139 4.9 236.3 1.0
C B:ASN141 4.9 227.2 1.0
N B:CYS152 4.9 232.2 1.0
CA B:ASN141 5.0 227.2 1.0
O B:GLY144 5.0 247.5 1.0
CG B:ASN141 5.0 227.2 1.0

Zinc binding site 4 out of 4 in 9w4r

Go back to Zinc Binding Sites List in 9w4r
Zinc binding site 4 out of 4 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:345.4
occ:1.00
 NE2 B:HIS169 2.1 311.7 1.0
SG B:CYS161 2.3 289.8 1.0
SG B:CYS164 2.3 313.3 1.0
SG B:CYS174 2.3 298.2 1.0
CD2 B:HIS169 2.9 311.7 1.0
CB B:CYS174 3.1 298.2 1.0
CE1 B:HIS169 3.1 311.7 1.0
CB B:CYS161 3.1 289.8 1.0
CB B:CYS164 3.3 313.3 1.0
N B:CYS164 3.5 313.3 1.0
CA B:CYS174 3.7 298.2 1.0
CA B:CYS164 4.0 313.3 1.0
CG B:HIS169 4.1 311.7 1.0
OG B:SER166 4.1 318.7 1.0
ND1 B:HIS169 4.2 311.7 1.0
CB B:PHE163 4.4 289.9 1.0
CD B:PRO175 4.4 316.4 1.0
CA B:CYS161 4.6 289.8 1.0
C B:PHE163 4.6 289.9 1.0
O B:MET170 4.7 283.0 1.0
C B:CYS164 4.7 313.3 1.0
N B:PHE163 4.7 289.9 1.0
N B:CYS174 4.7 298.2 1.0
C B:CYS174 4.8 298.2 1.0
CA B:PHE163 4.8 289.9 1.0
CA B:VAL171 4.9 270.6 1.0
N B:GLN165 4.9 308.1 1.0
C B:CYS161 4.9 289.8 1.0
N B:PRO175 5.0 316.4 1.0

Reference:

X.Han, S.Yamashita, K.Tomita. Structural Basis of LIN28-Dependent Pre-Let-7 Oligo-Uridylylation By TUT4 To Be Published.
Page generated: Sun Dec 14 19:35:21 2025

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