Atomistry » Zinc » PDB 5wqa-5x6h » 5wsg
Atomistry »
  Zinc »
    PDB 5wqa-5x6h »
      5wsg »

Zinc in PDB 5wsg: Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution

Enzymatic activity of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution:
3.6.4.13;

Other elements in 5wsg:

The structure of Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution 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 the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution (pdb code 5wsg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution, PDB code: 5wsg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn400

b:30.0
occ:1.00
 SG Q:CYS73 2.3 0.0 1.0
SG Q:CYS13 2.3 0.0 1.0
SG Q:CYS71 2.3 0.0 1.0
SG Q:CYS74 2.3 0.0 1.0
CB Q:CYS13 2.3 0.0 1.0
N Q:CYS74 3.0 0.0 1.0
CB Q:CYS74 3.1 0.0 1.0
N Q:CYS13 3.3 0.0 1.0
CA Q:CYS13 3.4 0.0 1.0
CB Q:CYS71 3.5 0.0 1.0
CA Q:CYS74 3.5 0.0 1.0
CB Q:CYS16 3.6 0.0 1.0
CB Q:CYS73 3.9 0.0 1.0
C Q:CYS73 4.1 0.0 1.0
SG Q:CYS16 4.3 0.0 1.0
CA Q:CYS73 4.3 0.0 1.0
N Q:CYS73 4.3 0.0 1.0
C Q:CYS13 4.5 0.0 1.0
C Q:ILE12 4.5 0.0 1.0
CG2 Q:ILE12 4.6 0.0 1.0
CA Q:CYS16 4.7 0.0 1.0
N Q:LEU17 4.7 0.0 1.0
CA Q:CYS71 4.7 0.0 1.0
C Q:CYS71 4.8 0.0 1.0
N Q:CYS16 4.8 0.0 1.0
O Q:CYS13 4.8 0.0 1.0
O Q:CYS71 4.9 0.0 1.0
CA Q:ILE12 4.9 0.0 1.0
C Q:CYS74 4.9 0.0 1.0
C Q:CYS16 4.9 0.0 1.0

Zinc binding site 2 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn401

b:30.0
occ:1.00
 SG Q:CYS37 2.2 0.0 1.0
SG Q:CYS34 2.3 0.0 1.0
SG Q:CYS64 2.3 0.0 1.0
SG Q:CYS61 2.3 0.0 1.0
CB Q:CYS61 3.0 0.0 1.0
CB Q:CYS37 3.1 0.0 1.0
CB Q:CYS34 3.2 0.0 1.0
CB Q:CYS64 3.4 0.0 1.0
N Q:CYS61 3.7 0.0 1.0
CA Q:CYS61 3.9 0.0 1.0
N Q:CYS37 4.2 0.0 1.0
CA Q:CYS37 4.2 0.0 1.0
NH1 Q:ARG63 4.2 0.0 1.0
N Q:CYS64 4.4 0.0 1.0
CA Q:CYS64 4.5 0.0 1.0
CA Q:CYS34 4.5 0.0 1.0
C Q:ILE60 4.8 0.0 1.0
C Q:CYS37 4.8 0.0 1.0
N Q:CYS34 4.8 0.0 1.0
O Q:LEU39 4.9 0.0 1.0
N Q:THR38 4.9 0.0 1.0
CZ Q:ARG63 4.9 0.0 1.0
N Q:LEU39 5.0 0.0 1.0

Zinc binding site 3 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:30.0
occ:1.00
 SG R:CYS87 2.3 0.0 1.0
SG R:CYS81 2.3 0.0 1.0
SG R:CYS73 2.3 0.0 1.0
NE2 R:HIS91 2.3 0.0 1.0
CB R:CYS87 2.9 0.0 1.0
CB R:CYS81 3.0 0.0 1.0
CE1 R:HIS91 3.1 0.0 1.0
CD2 R:HIS91 3.1 0.0 1.0
CB R:CYS73 3.2 0.0 1.0
N6 E:A35 4.0 0.4 1.0
ND1 R:HIS91 4.0 0.0 1.0
O R:TYR89 4.1 0.0 1.0
CG R:HIS91 4.1 0.0 1.0
CB R:PHE76 4.3 0.0 1.0
CA R:CYS87 4.4 0.0 1.0
N R:PHE76 4.4 0.0 1.0
CA R:CYS81 4.5 0.0 1.0
CA R:CYS73 4.7 0.0 1.0
CA R:PHE76 4.8 0.0 1.0
C R:PHE75 4.9 0.0 1.0

Zinc binding site 4 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:0.0
occ:1.00
 CB T:CYS104 2.2 0.0 1.0
SG T:CYS148 2.3 0.0 1.0
SG T:CYS105 2.3 0.0 1.0
SG T:CYS108 2.3 0.0 1.0
SG T:CYS104 2.3 0.0 1.0
CB T:CYS148 3.1 0.0 1.0
CB T:CYS105 3.1 0.0 1.0
CA T:CYS104 3.6 0.0 1.0
CB T:CYS108 3.7 0.0 1.0
ZN T:ZN1002 3.8 0.0 1.0
N T:CYS105 3.8 0.0 1.0
C T:CYS104 3.9 0.0 1.0
ZN T:ZN1001 4.0 0.0 1.0
CA T:CYS105 4.1 0.0 1.0
SG T:CYS122 4.1 0.0 1.0
CA T:CYS148 4.5 0.0 1.0
O T:CYS104 4.6 0.0 1.0
CB T:CYS150 4.6 0.0 1.0
SG T:CYS145 4.7 0.0 1.0
N T:CYS104 4.7 0.0 1.0
N T:CYS108 4.9 0.0 1.0
CA T:CYS108 4.9 0.0 1.0
N T:CYS148 4.9 0.0 1.0

Zinc binding site 5 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:0.0
occ:1.00
 CB T:CYS153 2.3 0.0 1.0
SG T:CYS104 2.3 0.0 1.0
SG T:CYS122 2.3 0.0 1.0
SG T:CYS150 2.3 0.0 1.0
SG T:CYS153 2.3 0.0 1.0
CB T:CYS150 2.5 0.0 1.0
CB T:CYS104 3.2 0.0 1.0
CA T:CYS153 3.6 0.0 1.0
O T:CYS122 3.7 0.0 1.0
CB T:CYS122 3.8 0.0 1.0
CA T:CYS150 3.9 0.0 1.0
N T:CYS104 4.0 0.0 1.0
ZN T:ZN1000 4.0 0.0 1.0
CA T:CYS104 4.1 0.0 1.0
C T:CYS122 4.1 0.0 1.0
N T:CYS153 4.3 0.0 1.0
ZN T:ZN1002 4.3 0.0 1.0
CA T:CYS122 4.3 0.0 1.0
CG n:PRO68 4.6 0.7 1.0
SG T:CYS108 4.6 0.0 1.0
C T:CYS150 4.7 0.0 1.0
CB T:CYS108 4.7 0.0 1.0
C T:CYS153 4.8 0.0 1.0
N T:CYS150 4.8 0.0 1.0
CB n:PRO68 4.9 0.1 1.0
N T:ARG123 5.0 0.0 1.0

Zinc binding site 6 out of 6 in 5wsg

Go back to Zinc Binding Sites List in 5wsg
Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Catalytic Step II Spliceosome (C* Complex) at 4.0 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 Catalytic Step II Spliceosome (C* Complex) at 4.0 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:0.0
occ:1.00
 SG T:CYS108 2.3 0.0 1.0
SG T:CYS145 2.3 0.0 1.0
SG T:CYS120 2.3 0.0 1.0
SG T:CYS122 2.3 0.0 1.0
CB T:CYS122 2.5 0.0 1.0
CB T:CYS108 2.7 0.0 1.0
CB T:CYS120 3.3 0.0 1.0
CB T:CYS145 3.5 0.0 1.0
CA T:CYS108 3.6 0.0 1.0
ZN T:ZN1000 3.8 0.0 1.0
CA T:CYS122 4.0 0.0 1.0
CD2 T:HIS147 4.2 0.0 1.0
ZN T:ZN1001 4.3 0.0 1.0
SG T:CYS148 4.4 0.0 1.0
SG T:CYS104 4.5 0.0 1.0
N T:CYS108 4.5 0.0 1.0
N T:CYS122 4.5 0.0 1.0
CA T:CYS120 4.6 0.0 1.0
O T:CYS108 4.6 0.0 1.0
C T:CYS108 4.6 0.0 1.0
CB T:CYS150 4.7 0.0 1.0
C T:CYS122 4.8 0.0 1.0
N T:CYS120 4.8 0.0 1.0
CA T:CYS145 4.9 0.0 1.0
CB T:HIS147 4.9 0.0 1.0
CG T:HIS147 4.9 0.0 1.0
CB T:CYS104 4.9 0.0 1.0
CB T:CYS148 5.0 0.0 1.0

Reference:

C.Yan, R.Wan, R.Bai, G.Huang, Y.Shi. Structure of A Yeast Step II Catalytically Activated Spliceosome Science V. 355 149 2017.
ISSN: ESSN 1095-9203
PubMed: 27980089
DOI: 10.1126/SCIENCE.AAK9979
Page generated: Mon Oct 28 14:37:52 2024

Last articles

Fe in 6EL4
Fe in 6EL0
Fe in 6EKZ
Fe in 6EKY
Fe in 6EKX
Fe in 6EKW
Fe in 6EHA
Fe in 6EFN
Fe in 6ECJ
Fe in 6EGZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy