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Zinc in PDB 6j6h: Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom:
2.3.2.27;

Other elements in 6j6h:

The structure of Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 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 the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom (pdb code 6j6h). 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 Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom, PDB code: 6j6h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6j6h

Go back to Zinc Binding Sites List in 6j6h
Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 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 the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn400

b:66.9
occ:1.00
 SG Q:CYS74 2.1 38.9 1.0
SG Q:CYS71 2.2 39.5 1.0
SG Q:CYS16 2.6 53.8 1.0
SG Q:CYS13 2.6 54.5 1.0
CB Q:CYS13 3.0 54.5 1.0
CB Q:CYS74 3.2 38.9 1.0
N Q:CYS74 3.4 38.9 1.0
CB Q:CYS71 3.4 39.5 1.0
CA Q:CYS74 3.7 38.9 1.0
N Q:CYS13 3.8 54.5 1.0
CB Q:CYS16 4.0 53.8 1.0
CA Q:CYS13 4.0 54.5 1.0
C Q:CYS74 4.3 38.9 1.0
N Q:MET75 4.3 40.1 1.0
C Q:CYS73 4.5 37.6 1.0
CB Q:CYS73 4.6 37.6 1.0
N Q:LEU76 4.7 42.5 1.0
CA Q:CYS71 4.7 39.5 1.0
N Q:CYS16 4.8 53.8 1.0
N Q:CYS73 4.8 37.6 1.0
CA Q:CYS73 4.9 37.6 1.0
CA Q:CYS16 5.0 53.8 1.0

Zinc binding site 2 out of 6 in 6j6h

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 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 the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn401

b:63.3
occ:1.00
 SG Q:CYS64 2.2 34.6 1.0
SG Q:CYS37 2.3 31.7 1.0
SG Q:CYS34 2.3 31.2 1.0
SG Q:CYS61 2.3 33.1 1.0
CB Q:CYS34 3.0 31.2 1.0
CB Q:CYS64 3.2 34.6 1.0
CB Q:CYS37 3.2 31.7 1.0
N Q:CYS37 3.6 31.7 1.0
CB Q:CYS61 3.6 33.1 1.0
N Q:CYS61 3.9 33.1 1.0
CA Q:CYS37 4.0 31.7 1.0
N Q:CYS64 4.2 34.6 1.0
CA Q:CYS61 4.3 33.1 1.0
CA Q:CYS64 4.3 34.6 1.0
CB Q:ILE36 4.5 30.9 1.0
CA Q:CYS34 4.5 31.2 1.0
C Q:ILE36 4.7 30.9 1.0
C Q:CYS37 4.8 31.7 1.0
O Q:CYS61 4.8 33.1 1.0
N Q:ILE36 4.8 30.9 1.0
C Q:CYS61 4.9 33.1 1.0
CB Q:SER114 4.9 36.8 1.0
CA Q:ILE36 4.9 30.9 1.0
N Q:THR38 5.0 31.1 1.0
C Q:ILE60 5.0 30.4 1.0

Zinc binding site 3 out of 6 in 6j6h

Go back to Zinc Binding Sites List in 6j6h
Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 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 the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:55.4
occ:1.00
 SG R:CYS81 2.3 45.7 1.0
NE2 R:HIS91 2.3 51.3 1.0
SG R:CYS73 2.3 48.6 1.0
SG R:CYS87 2.3 46.6 1.0
CE1 R:HIS91 2.8 51.3 1.0
CB R:CYS73 3.2 48.6 1.0
CB R:CYS87 3.2 46.6 1.0
CB R:CYS81 3.3 45.7 1.0
CD2 R:HIS91 3.5 51.3 1.0
ND1 R:HIS91 4.0 51.3 1.0
CG R:HIS91 4.4 51.3 1.0
N6 E:A35 4.5 69.6 1.0
CA R:CYS73 4.6 48.6 1.0
CA R:CYS81 4.6 45.7 1.0
CA R:CYS87 4.7 46.6 1.0
O R:TYR89 4.8 70.3 1.0
CB R:PHE76 4.8 50.6 1.0
N R:PHE76 4.8 50.6 1.0
O R:GLY84 4.9 51.8 1.0

Zinc binding site 4 out of 6 in 6j6h

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 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 the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:46.5
occ:1.00
 SG T:CYS148 2.3 49.6 1.0
SG T:CYS104 2.3 46.0 1.0
SG T:CYS108 2.3 69.6 1.0
SG T:CYS105 2.3 48.4 1.0
CB T:CYS108 3.2 69.6 1.0
CB T:CYS104 3.4 46.0 1.0
CB T:CYS105 3.7 48.4 1.0
N T:CYS105 3.8 48.4 1.0
CB T:CYS148 3.8 49.6 1.0
C T:CYS104 3.8 46.0 1.0
ZN T:ZN1002 3.9 54.5 1.0
ZN T:ZN1001 3.9 51.7 1.0
O T:CYS104 4.1 46.0 1.0
CA T:CYS104 4.2 46.0 1.0
N T:CYS108 4.2 69.6 1.0
CA T:CYS105 4.2 48.4 1.0
CA T:CYS108 4.3 69.6 1.0
SG T:CYS122 4.4 37.9 1.0
SG T:CYS145 4.4 57.0 1.0
CB T:CYS150 4.6 46.2 1.0
N T:CYS148 4.6 49.6 1.0
O T:CYS105 4.6 48.4 1.0
C T:CYS105 4.7 48.4 1.0
CB T:HIS147 4.7 69.6 1.0
CA T:CYS148 4.8 49.6 1.0

Zinc binding site 5 out of 6 in 6j6h

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom


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 B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:51.7
occ:1.00
 SG T:CYS153 2.3 42.3 1.0
SG T:CYS150 2.3 46.2 1.0
SG T:CYS122 2.3 37.9 1.0
SG T:CYS104 2.3 46.0 1.0
CB T:CYS104 2.3 46.0 1.0
CB T:CYS150 2.3 46.2 1.0
CB T:CYS122 3.1 37.9 1.0
CA T:CYS104 3.7 46.0 1.0
CA T:CYS150 3.8 46.2 1.0
ZN T:ZN1000 3.9 46.5 1.0
CB T:CYS153 3.9 42.3 1.0
ZN T:ZN1002 4.1 54.5 1.0
O T:CYS122 4.2 37.9 1.0
N T:CYS153 4.2 42.3 1.0
CA T:CYS122 4.3 37.9 1.0
C T:CYS122 4.3 37.9 1.0
SG T:CYS108 4.3 69.6 1.0
N T:CYS104 4.4 46.0 1.0
C T:CYS150 4.5 46.2 1.0
SG T:CYS145 4.6 57.0 1.0
CA T:CYS153 4.6 42.3 1.0
N T:CYS150 4.6 46.2 1.0
N T:GLY152 4.7 41.7 1.0
C T:GLY152 4.7 41.7 1.0
C T:CYS104 4.7 46.0 1.0
CB T:CYS108 4.7 69.6 1.0
N T:ARG151 4.7 46.2 1.0
SG T:CYS148 4.7 49.6 1.0

Zinc binding site 6 out of 6 in 6j6h

Go back to Zinc Binding Sites List in 6j6h
Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-A1 Complex at An Average Resolution of 3.6 Angstrom


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 B*-A1 Complex at An Average Resolution of 3.6 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:54.5
occ:1.00
 SG T:CYS120 2.4 43.4 1.0
SG T:CYS108 2.4 69.6 1.0
SG T:CYS122 2.4 37.9 1.0
SG T:CYS145 2.5 57.0 1.0
CB T:CYS145 2.7 57.0 1.0
CB T:CYS120 3.3 43.4 1.0
CB T:CYS122 3.7 37.9 1.0
CB T:CYS108 3.7 69.6 1.0
ZN T:ZN1000 3.9 46.5 1.0
ZN T:ZN1001 4.1 51.7 1.0
CA T:CYS145 4.2 57.0 1.0
SG T:CYS148 4.3 49.6 1.0
CD2 T:HIS147 4.3 69.6 1.0
N T:CYS122 4.4 37.9 1.0
CB T:CYS150 4.5 46.2 1.0
CB T:HIS147 4.5 69.6 1.0
SG T:CYS104 4.6 46.0 1.0
CA T:CYS122 4.7 37.9 1.0
C T:CYS145 4.7 57.0 1.0
CA T:CYS120 4.7 43.4 1.0
CA T:CYS108 4.8 69.6 1.0
CG T:HIS147 4.8 69.6 1.0
N T:HIS147 4.9 69.6 1.0

Reference:

R.Wan, R.Bai, C.Yan, J.Lei, Y.Shi. Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell V. 177 339 2019.
ISSN: ISSN 1097-4172
PubMed: 30879786
DOI: 10.1016/J.CELL.2019.02.006
Page generated: Tue Oct 29 00:54:33 2024

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