Atomistry » Zinc » PDB 3iqs-3jck » 3jb9
Atomistry »
  Zinc »
    PDB 3iqs-3jck »
      3jb9 »

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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Go back to Zinc Binding Sites List in 3jb9
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy