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Zinc in PDB 5z58: Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.

Enzymatic activity of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.

All present enzymatic activity of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.:
3.6.4.13; 5.2.1.8;

Other elements in 5z58:

The structure of Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. (pdb code 5z58). 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 A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom., PDB code: 5z58:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5z58

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


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 A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn201

b:0.0
occ:1.00
 SG 6:CYS23 2.4 0.1 1.0
SG 6:CYS26 2.5 0.4 1.0
SG 6:CYS58 2.5 0.7 1.0
SG 6:CYS61 2.7 0.5 1.0
NZ 6:LYS25 2.7 0.9 1.0
CE 6:LYS25 3.2 0.5 1.0
CB 6:CYS26 3.4 0.7 1.0
CB 6:CYS61 3.4 0.5 1.0
N 6:CYS61 3.6 0.5 1.0
N 6:CYS26 3.6 0.1 1.0
CB 6:CYS58 3.8 0.2 1.0
CB 6:CYS23 3.9 0.9 1.0
CB 6:LYS25 4.0 0.4 1.0
CA 6:CYS26 4.1 0.4 1.0
CB 6:ILE60 4.1 0.3 1.0
CA 6:CYS61 4.1 0.4 1.0
CD 6:LYS25 4.4 0.7 1.0
CG 6:LYS25 4.4 0.9 1.0
N 6:CYS23 4.6 0.3 1.0
C 6:LYS25 4.6 1.0 1.0
C 6:ILE60 4.7 0.4 1.0
CA 6:LYS25 4.7 1.0 1.0
CG2 6:ILE60 4.8 0.2 1.0
CA 6:ILE60 4.8 0.1 1.0
CA 6:CYS23 4.8 0.2 1.0
N 6:ILE60 4.9 0.4 1.0
N 6:LYS25 4.9 0.2 1.0
CG1 6:ILE60 4.9 0.4 1.0

Zinc binding site 2 out of 4 in 5z58

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


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 A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn202

b:0.3
occ:1.00
 SG 6:CYS49 2.3 0.3 1.0
SG 6:CYS46 2.5 0.1 1.0
CD 6:LYS13 2.5 0.5 1.0
CB 6:LYS13 2.5 0.8 1.0
CG 6:LYS13 2.8 0.9 1.0
SG 6:CYS85 3.1 0.7 1.0
SG 6:CYS11 3.4 0.9 1.0
CB 6:CYS49 3.6 0.8 1.0
N 6:CYS49 3.7 0.4 1.0
CA 6:LYS13 3.7 0.9 1.0
CE 6:LYS13 3.8 0.9 1.0
N 6:LYS13 3.9 0.3 1.0
CB 6:GLU48 4.1 0.8 1.0
CA 6:CYS49 4.1 0.7 1.0
CB 6:CYS11 4.2 0.1 1.0
CB 6:CYS46 4.2 0.8 1.0
C 6:GLU48 4.3 0.4 1.0
NZ 6:LYS13 4.4 0.0 1.0
C 6:LYS13 4.5 0.3 1.0
CA 6:GLU48 4.7 0.5 1.0
CB 6:CYS85 4.8 0.6 1.0
O 6:LYS13 4.8 0.3 1.0
O 6:GLU48 4.9 96.0 1.0

Zinc binding site 3 out of 4 in 5z58

Go back to Zinc Binding Sites List in 5z58
Zinc binding site 3 out of 4 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


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 A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn203

b:0.7
occ:1.00
 SG 6:CYS33 2.3 0.3 1.0
SG 6:CYS75 2.4 0.6 1.0
SG 6:CYS30 2.5 0.9 1.0
SG 6:CYS72 2.5 0.4 1.0
CB 6:CYS33 2.7 0.5 1.0
N 6:CYS33 3.0 0.4 1.0
CA 6:CYS33 3.4 0.2 1.0
CB 6:CYS75 3.4 1.0 1.0
CB 6:CYS30 3.7 0.1 1.0
CB 6:CYS72 3.7 0.8 1.0
N 6:CYS72 4.1 0.3 1.0
C 6:ILE32 4.1 0.3 1.0
N 6:CYS75 4.3 0.7 1.0
N 6:ILE32 4.3 0.1 1.0
C 6:CYS33 4.5 0.4 1.0
CA 6:CYS75 4.5 0.2 1.0
CA 6:CYS72 4.5 0.1 1.0
CA 6:ILE32 4.5 0.3 1.0
CB 6:ILE32 4.5 0.8 1.0
C 6:CYS30 4.6 0.2 1.0
CA 6:CYS30 4.8 0.2 1.0
O 6:CYS30 4.8 0.8 1.0
N 6:ASP34 4.8 0.7 1.0
N 6:VAL31 4.9 0.2 1.0

Zinc binding site 4 out of 4 in 5z58

Go back to Zinc Binding Sites List in 5z58
Zinc binding site 4 out of 4 in the Cryo-Em Structure of A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom.


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 A Human Activated Spliceosome (Early Bact) at 4.9 Angstrom. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn500

b:60.1
occ:1.00
 SG M:CYS217 2.2 0.9 1.0
SG M:CYS202 2.2 31.2 1.0
SG M:CYS211 2.5 94.9 1.0
CB M:CYS202 3.0 61.4 1.0
NE2 M:HIS221 3.0 0.5 1.0
CD2 M:HIS221 3.2 1.0 1.0
CB M:CYS217 3.3 0.6 1.0
CB M:CYS211 3.4 0.6 1.0
N2 G:G1 3.4 99.5 1.0
N1 G:G1 3.8 0.2 1.0
C2 G:G1 4.1 0.1 1.0
CE1 M:HIS221 4.2 86.1 1.0
CB M:TYR205 4.4 0.5 1.0
CA M:CYS202 4.4 86.2 1.0
CG M:HIS221 4.4 0.0 1.0
CA M:CYS211 4.5 0.3 1.0
CA M:CYS217 4.7 0.3 1.0
CB M:PHE219 4.7 0.0 1.0
ND1 M:HIS221 4.9 86.4 1.0
N M:TYR205 4.9 0.8 1.0
C6 G:G1 5.0 0.3 1.0

Reference:

X.Zhang, C.Yan, X.Zhan, L.Li, J.Lei, Y.Shi. Structure of the Human Activated Spliceosome in Three Conformational States. Cell Res. V. 28 307 2018.
ISSN: ISSN 1748-7838
PubMed: 29360106
DOI: 10.1038/CR.2018.14
Page generated: Mon Oct 28 16:33:26 2024

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