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Zinc in PDB 3jb9: Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution:
5.2.1.8;

Other elements in 3jb9:

The structure of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution (pdb code 3jb9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution, PDB code: 3jb9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3jb9

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


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 the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn501

b:11.0
occ:1.00
 SG Y:CYS125 1.6 0.7 1.0
SG Y:CYS117 2.4 0.7 1.0
SG Y:CYS131 2.5 0.2 1.0
CB Y:CYS117 2.6 0.9 1.0
NE2 Y:HIS135 3.0 0.3 1.0
CB Y:CYS125 3.0 0.8 1.0
CE1 Y:HIS135 3.2 0.6 1.0
CB Y:CYS131 3.6 0.5 1.0
CD2 Y:HIS135 4.0 0.2 1.0
CA Y:CYS117 4.2 0.2 1.0
ND1 Y:HIS135 4.3 0.2 1.0
N6 N:A23 4.3 0.2 1.0
CA Y:CYS125 4.3 0.7 1.0
N Y:PHE120 4.4 0.7 1.0
CB Y:PHE120 4.5 0.2 1.0
CG Y:HIS135 4.7 0.8 1.0
O Y:TYR133 4.7 0.0 1.0
CA Y:PHE120 4.8 0.5 1.0
C Y:CYS117 4.9 0.7 1.0
CB Y:TYR119 4.9 0.3 1.0
O Y:CYS125 4.9 1.0 1.0
N Y:CYS117 4.9 0.6 1.0
C Y:CYS125 4.9 0.3 1.0
CA Y:CYS131 5.0 0.8 1.0

Zinc binding site 2 out of 7 in 3jb9

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


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 the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn401

b:30.0
occ:1.00
 SG a:CYS70 1.7 85.0 1.0
CB a:CYS70 2.2 93.0 1.0
SG a:CYS44 2.5 89.0 1.0
CB a:CYS47 2.6 92.1 1.0
CB a:CYS44 2.7 98.1 1.0
SG a:CYS47 3.0 90.0 1.0
N a:CYS70 3.1 98.3 1.0
CA a:CYS70 3.1 95.6 1.0
SG a:CYS73 3.2 93.1 1.0
CB a:CYS73 3.7 96.6 1.0
C a:CYS70 3.8 96.4 1.0
O a:CYS70 3.8 0.0 1.0
CA a:CYS47 3.9 91.7 1.0
N a:CYS47 4.0 92.2 1.0
CD a:LYS49 4.1 0.0 1.0
CA a:CYS44 4.2 0.3 1.0
N a:CYS73 4.2 91.5 1.0
C a:ILE69 4.4 0.1 1.0
CG2 a:ILE69 4.4 0.0 1.0
NZ a:LYS49 4.4 0.6 1.0
CA a:CYS73 4.6 93.9 1.0
CE a:LYS49 4.7 0.1 1.0
N a:VAL71 4.8 97.1 1.0
N a:CYS44 4.9 0.9 1.0
C a:CYS47 4.9 91.7 1.0
CA a:ILE69 4.9 0.6 1.0
C a:CYS44 4.9 0.3 1.0
CG a:LYS49 4.9 0.9 1.0

Zinc binding site 3 out of 7 in 3jb9

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


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 the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn402

b:30.0
occ:1.00
 SG a:CYS83 1.6 95.9 1.0
SG a:CYS80 1.8 82.7 1.0
SG a:CYS23 1.8 87.0 1.0
CB a:CYS83 2.7 97.2 1.0
CB a:CYS80 2.8 84.7 1.0
SG a:CYS26 2.9 0.8 1.0
CB a:CYS23 3.3 90.7 1.0
N a:CYS83 3.6 0.9 1.0
OG a:SER82 3.6 88.6 1.0
CA a:CYS83 3.7 99.7 1.0
CB a:CYS26 3.7 0.8 1.0
N a:CYS23 3.9 85.4 1.0
N a:CYS26 4.1 0.7 1.0
CA a:CYS23 4.2 92.0 1.0
CA a:CYS80 4.2 84.9 1.0
CA a:CYS26 4.5 0.7 1.0
CB a:ARG25 4.6 0.6 1.0
C a:CYS23 4.7 0.9 1.0
C a:CYS80 4.7 81.2 1.0
C a:CYS83 4.8 0.3 1.0
C a:SER82 4.8 96.6 1.0
O a:CYS80 4.8 81.5 1.0
O a:CYS23 4.9 0.3 1.0
CB a:SER82 4.9 89.5 1.0
C a:ARG25 4.9 0.9 1.0
N a:ARG25 5.0 0.1 1.0
N a:MET84 5.0 0.8 1.0

Zinc binding site 4 out of 7 in 3jb9

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


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 the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn701

b:30.0
occ:1.00
 NE2 c:HIS502 1.8 0.1 1.0
CD2 c:HIS502 1.9 0.2 1.0
SG c:CYS412 2.1 0.8 1.0
SG c:CYS415 2.2 0.7 1.0
CE1 c:HIS502 2.6 0.8 1.0
CG c:HIS502 2.8 0.9 1.0
ND1 c:HIS502 3.1 0.5 1.0
CD1 c:LEU414 3.2 0.9 1.0
ND1 c:HIS455 3.4 0.6 1.0
CB c:CYS415 3.5 0.5 1.0
CE1 c:HIS455 3.5 1.0 1.0
N c:CYS415 3.5 0.1 1.0
CB c:CYS412 3.7 0.7 1.0
CA c:CYS415 3.8 0.1 1.0
CB c:HIS502 4.0 0.4 1.0
CG c:HIS455 4.3 0.8 1.0
NE2 c:HIS455 4.3 0.2 1.0
CG c:LEU414 4.4 0.8 1.0
C c:LEU414 4.6 0.8 1.0
CD2 c:HIS455 4.8 0.1 1.0
N c:LEU414 4.8 0.5 1.0
CB c:LEU414 4.8 0.0 1.0
CA c:CYS412 4.9 0.9 1.0
CA c:LEU414 4.9 0.4 1.0

Zinc binding site 5 out of 7 in 3jb9

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn201

b:30.0
occ:1.00
 SG e:CYS102 1.7 55.4 1.0
SG e:CYS137 1.9 64.5 1.0
SG e:CYS101 2.5 54.5 1.0
SG e:CYS139 2.7 88.4 1.0
SG e:CYS105 2.8 58.8 1.0
CB e:CYS102 2.9 62.4 1.0
CB e:CYS101 2.9 56.3 1.0
N e:CYS102 3.0 60.4 1.0
CB e:CYS137 3.3 69.0 1.0
ZN e:ZN202 3.5 30.0 1.0
CA e:CYS102 3.5 62.6 1.0
C e:CYS101 3.7 56.9 1.0
CB e:CYS105 3.9 64.0 1.0
CA e:CYS101 4.0 56.5 1.0
O e:CYS102 4.2 67.8 1.0
ZN e:ZN203 4.3 30.0 1.0
C e:CYS102 4.3 65.7 1.0
CB e:CYS139 4.3 92.1 1.0
O e:CYS101 4.6 58.2 1.0
CA e:CYS137 4.6 69.2 1.0
N e:CYS137 4.7 70.4 1.0
N e:CYS101 4.8 57.8 1.0
N e:CYS139 4.9 81.5 1.0
SG e:CYS142 4.9 55.5 1.0
CA e:CYS139 4.9 87.0 1.0
N e:CYS105 4.9 64.3 1.0
SG e:CYS119 5.0 53.2 1.0

Zinc binding site 6 out of 7 in 3jb9

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn202

b:30.0
occ:1.00
 SG e:CYS142 1.4 55.5 1.0
SG e:CYS101 1.7 54.5 1.0
SG e:CYS139 2.1 88.4 1.0
CB e:CYS139 2.5 92.1 1.0
CB e:CYS101 2.6 56.3 1.0
SG e:CYS119 2.7 53.2 1.0
CB e:CYS142 3.0 69.9 1.0
ZN e:ZN201 3.5 30.0 1.0
CA e:CYS139 3.5 87.0 1.0
CB e:CYS119 3.6 59.2 1.0
SG e:CYS105 3.9 58.8 1.0
CA e:CYS101 3.9 56.5 1.0
ZN e:ZN203 4.0 30.0 1.0
N e:CYS101 4.1 57.8 1.0
CA e:CYS142 4.2 78.3 1.0
SG e:CYS137 4.3 64.5 1.0
N e:CYS142 4.4 86.4 1.0
N e:CYS139 4.5 81.5 1.0
N e:ASN140 4.5 88.0 1.0
C e:CYS139 4.5 84.8 1.0
CB e:CYS105 4.7 64.0 1.0
N e:CYS102 4.7 60.4 1.0
SG e:CYS117 4.8 42.5 1.0
C e:CYS101 4.9 56.9 1.0

Zinc binding site 7 out of 7 in 3jb9

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the Yeast Spliceosome at 3.6 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Zn203

b:30.0
occ:1.00
 SG e:CYS117 1.3 42.5 1.0
SG e:CYS134 2.1 98.9 1.0
SG e:CYS139 2.4 88.4 1.0
SG e:CYS105 2.4 58.8 1.0
CB e:CYS134 2.5 93.7 1.0
CB e:CYS117 2.8 49.6 1.0
SG e:CYS119 2.8 53.2 1.0
CB e:CYS139 3.3 92.1 1.0
CB e:CYS119 3.4 59.2 1.0
CB e:CYS105 3.8 64.0 1.0
CA e:CYS134 3.9 90.8 1.0
ZN e:ZN202 4.0 30.0 1.0
SG e:CYS137 4.1 64.5 1.0
CA e:CYS117 4.1 50.2 1.0
ZN e:ZN201 4.3 30.0 1.0
N e:CYS119 4.4 56.3 1.0
C e:CYS117 4.5 53.4 1.0
SG e:CYS101 4.5 54.5 1.0
CA e:CYS139 4.5 87.0 1.0
N e:CYS139 4.5 81.5 1.0
CA e:CYS119 4.5 58.3 1.0
CD2 e:HIS136 4.7 97.8 1.0
O e:CYS117 4.7 53.0 1.0
N e:CYS134 4.8 95.8 1.0
CA e:CYS105 4.9 61.4 1.0
C e:CYS134 4.9 82.9 1.0
SG e:CYS142 4.9 55.5 1.0

Reference:

C.Yan, J.Hang, R.Wan, M.Huang, C.Wong, Y.Shi. Structure of A Yeast Spliceosome at 3.6-Angstrom Resolution Science V. 349 1182 2015.
ISSN: ISSN 0036-8075
PubMed: 26292707
DOI: 10.1126/SCIENCE.AAC7629
Page generated: Sat Oct 26 07:26:02 2024

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