Zinc in PDB 8hk1: The Cryo-Em Structure of Human Pre-17S U2 Snrnp

Enzymatic activity of The Cryo-Em Structure of Human Pre-17S U2 Snrnp

All present enzymatic activity of The Cryo-Em Structure of Human Pre-17S U2 Snrnp:
3.6.4.13;

Zinc Binding Sites:

The binding sites of Zinc atom in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp (pdb code 8hk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp, PDB code: 8hk1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8hk1

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Zinc binding site 1 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn201

b:55.0
occ:1.00
 SG 6:CYS61 2.4 32.3 1.0
SG 6:CYS23 2.4 30.0 1.0
SG 6:CYS26 2.5 30.5 1.0
SG 6:CYS58 2.6 30.1 1.0
CB 6:CYS61 3.2 32.3 1.0
CB 6:CYS58 3.4 30.1 1.0
CB 6:CYS26 3.5 30.5 1.0
CB 6:CYS23 3.6 30.0 1.0
CE 6:LYS25 3.9 33.6 1.0
N 6:CYS61 3.9 32.3 1.0
CA 6:CYS61 4.2 32.3 1.0
NZ 6:LYS25 4.3 33.6 1.0
N 6:CYS26 4.3 30.5 1.0
N 6:CYS23 4.4 30.0 1.0
CA 6:CYS26 4.5 30.5 1.0
CA 6:CYS23 4.5 30.0 1.0
N 6:GLY62 4.7 32.2 1.0
CB 6:ILE60 4.7 27.4 1.0
C 6:CYS61 4.9 32.3 1.0
CG2 6:ILE60 4.9 27.4 1.0
CA 6:CYS58 4.9 30.1 1.0
CB 6:LYS25 4.9 33.6 1.0
N 6:GLY63 4.9 31.2 1.0
C 6:ILE60 4.9 27.4 1.0

Zinc binding site 2 out of 4 in 8hk1

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Zinc binding site 2 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn202

b:44.0
occ:1.00
 SG 6:CYS11 2.4 25.7 1.0
SG 6:CYS46 2.4 22.6 1.0
SG 6:CYS85 2.4 22.1 1.0
SG 6:CYS49 2.6 35.4 1.0
CB 6:CYS85 2.7 22.1 1.0
CB 6:CYS11 3.0 25.7 1.0
CB 6:CYS46 3.6 22.6 1.0
CB 6:CYS49 3.8 35.4 1.0
OE1 6:GLU48 3.9 34.7 1.0
N 6:CYS46 4.1 22.6 1.0
CA 6:CYS85 4.2 22.1 1.0
CB 6:LYS13 4.4 22.7 1.0
CA 6:CYS46 4.5 22.6 1.0
CA 6:CYS11 4.5 25.7 1.0
CB 6:LYS87 4.5 28.4 1.0
C 6:CYS85 4.6 22.1 1.0
O 6:CYS85 4.7 22.1 1.0
N 6:CYS49 4.7 35.4 1.0
CG 6:GLU48 4.8 34.7 1.0
CD 6:GLU48 4.8 34.7 1.0
N 6:LYS13 4.8 22.7 1.0
CD 6:LYS13 4.8 22.7 1.0
CA 6:CYS49 4.9 35.4 1.0
C 6:CYS11 4.9 25.7 1.0
CG 6:LYS13 4.9 22.7 1.0
N 6:CYS85 4.9 22.1 1.0
N 6:ARG12 5.0 22.3 1.0

Zinc binding site 3 out of 4 in 8hk1

Go back to Zinc Binding Sites List in 8hk1
Zinc binding site 3 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn203

b:40.8
occ:1.00
 SG 6:CYS33 2.4 21.2 1.0
SG 6:CYS30 2.4 19.7 1.0
SG 6:CYS72 2.4 15.2 1.0
SG 6:CYS75 2.5 15.2 1.0
CB 6:CYS75 3.2 15.2 1.0
CB 6:CYS33 3.4 21.2 1.0
CB 6:CYS72 3.6 15.2 1.0
CB 6:CYS30 3.6 19.7 1.0
N 6:CYS33 3.8 21.2 1.0
N 6:CYS72 3.9 15.2 1.0
N 6:CYS75 4.2 15.2 1.0
CA 6:CYS33 4.2 21.2 1.0
CA 6:CYS75 4.3 15.2 1.0
CA 6:CYS72 4.3 15.2 1.0
CB 6:ILE32 4.6 19.9 1.0
C 6:ILE32 4.8 19.9 1.0
O 6:CYS72 4.9 15.2 1.0
N 6:ILE32 4.9 19.9 1.0
C 6:CYS72 4.9 15.2 1.0
C 6:CYS33 5.0 21.2 1.0

Zinc binding site 4 out of 4 in 8hk1

Go back to Zinc Binding Sites List in 8hk1
Zinc binding site 4 out of 4 in the The Cryo-Em Structure of Human Pre-17S U2 Snrnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Cryo-Em Structure of Human Pre-17S U2 Snrnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1000

b:104.8
occ:1.00
 NE2 C:HIS425 2.3 91.5 1.0
ND1 C:HIS431 2.3 99.3 1.0
SG C:CYS408 2.5 93.5 1.0
CE1 C:HIS431 2.6 99.3 1.0
CB C:CYS408 2.9 93.5 1.0
CD2 C:HIS425 2.9 91.5 1.0
CE1 C:HIS425 3.3 91.5 1.0
CB C:CYS411 3.3 98.8 1.0
SG C:CYS411 3.4 98.8 1.0
CG C:HIS431 3.6 99.3 1.0
NE2 C:HIS431 3.9 99.3 1.0
N C:CYS411 4.0 98.8 1.0
CG C:HIS425 4.1 91.5 1.0
CE2 C:TYR416 4.2 93.9 1.0
ND1 C:HIS425 4.3 91.5 1.0
CB C:HIS431 4.3 99.3 1.0
CA C:CYS411 4.3 98.8 1.0
CD2 C:HIS431 4.3 99.3 1.0
OH C:TYR416 4.4 93.9 1.0
CA C:CYS408 4.4 93.5 1.0
CE1 C:PHE426 4.5 88.5 1.0
CZ C:TYR416 4.7 93.9 1.0
CD1 C:PHE426 4.7 88.5 1.0
CB C:ILE410 4.7 94.2 1.0
C C:ILE410 4.7 94.2 1.0
C C:CYS408 4.9 93.5 1.0
O C:CYS408 4.9 93.5 1.0
CA C:HIS431 4.9 99.3 1.0

Reference:

F.Yang, T.Bian, X.Zhan, Z.Chen, Z.Xing, N.A.Larsen, X.Zhang, Y.Shi. Mechanisms of the Rna Helicases DDX42 and DDX46 in Human U2 Snrnp Assembly. Nat Commun V. 14 897 2023.
ISSN: ESSN 2041-1723
PubMed: 36797247
DOI: 10.1038/S41467-023-36489-X
Page generated: Sat Apr 8 09:19:54 2023

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