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Zinc in PDB 6j6g: Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 Angstrom:
2.3.2.27;

Other elements in 6j6g:

The structure of Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom (pdb code 6j6g). 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*-A2 Complex at An Average Resolution of 3.2 Angstrom, PDB code: 6j6g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6j6g

Go back to Zinc Binding Sites List in 6j6g
Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 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 6j6g

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 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 6j6g

Go back to Zinc Binding Sites List in 6j6g
Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:42.0
occ:1.00
 SG R:CYS81 2.3 29.8 1.0
NE2 R:HIS91 2.3 33.7 1.0
SG R:CYS73 2.3 28.9 1.0
SG R:CYS87 2.3 33.8 1.0
CE1 R:HIS91 2.4 33.7 1.0
CB R:CYS73 3.3 28.9 1.0
CB R:CYS87 3.3 33.8 1.0
CB R:CYS81 3.3 29.8 1.0
CD2 R:HIS91 3.6 33.7 1.0
ND1 R:HIS91 3.7 33.7 1.0
CG R:HIS91 4.2 33.7 1.0
N6 E:A35 4.6 31.7 1.0
CA R:CYS73 4.7 28.9 1.0
CA R:CYS81 4.7 29.8 1.0
O R:TYR89 4.7 31.2 1.0
N R:PHE76 4.7 27.6 1.0
CA R:CYS87 4.8 33.8 1.0
CB R:PHE76 4.8 27.6 1.0
O R:GLY84 4.9 32.6 1.0
N R:GLY84 5.0 32.6 1.0
CB R:LEU83 5.0 31.5 1.0

Zinc binding site 4 out of 6 in 6j6g

Go back to Zinc Binding Sites List in 6j6g
Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:43.4
occ:1.00
 SG T:CYS148 2.3 26.8 1.0
SG T:CYS104 2.3 31.2 1.0
SG T:CYS108 2.3 29.0 1.0
SG T:CYS105 2.3 27.4 1.0
CB T:CYS108 3.2 29.0 1.0
CB T:CYS104 3.5 31.2 1.0
CB T:CYS105 3.6 27.4 1.0
ZN T:ZN1002 3.8 43.9 1.0
N T:CYS105 3.8 27.4 1.0
CB T:CYS148 3.9 26.8 1.0
C T:CYS104 3.9 31.2 1.0
ZN T:ZN1001 4.0 49.1 1.0
N T:CYS108 4.2 29.0 1.0
CA T:CYS105 4.3 27.4 1.0
CA T:CYS108 4.3 29.0 1.0
SG T:CYS145 4.3 28.5 1.0
CA T:CYS104 4.3 31.2 1.0
O T:CYS104 4.3 31.2 1.0
N T:CYS148 4.5 26.8 1.0
SG T:CYS122 4.5 32.4 1.0
CB T:HIS147 4.6 26.7 1.0
CB T:CYS150 4.6 31.6 1.0
O T:CYS105 4.7 27.4 1.0
C T:CYS105 4.8 27.4 1.0
CA T:CYS148 4.8 26.8 1.0

Zinc binding site 5 out of 6 in 6j6g

Go back to Zinc Binding Sites List in 6j6g
Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:49.1
occ:1.00
 CB T:CYS104 2.2 31.2 1.0
SG T:CYS153 2.3 32.2 1.0
SG T:CYS150 2.3 31.6 1.0
SG T:CYS122 2.3 32.4 1.0
SG T:CYS104 2.3 31.2 1.0
CB T:CYS150 2.4 31.6 1.0
CB T:CYS122 3.2 32.4 1.0
CA T:CYS104 3.7 31.2 1.0
ZN T:ZN1002 3.8 43.9 1.0
CB T:CYS153 3.9 32.2 1.0
CA T:CYS150 3.9 31.6 1.0
ZN T:ZN1000 4.0 43.4 1.0
N T:CYS153 4.1 32.2 1.0
O T:CYS122 4.4 32.4 1.0
SG T:CYS108 4.4 29.0 1.0
N T:CYS104 4.4 31.2 1.0
CA T:CYS122 4.4 32.4 1.0
C T:CYS122 4.4 32.4 1.0
C T:CYS150 4.5 31.6 1.0
CA T:CYS153 4.5 32.2 1.0
SG T:CYS145 4.6 28.5 1.0
N T:GLY152 4.6 34.2 1.0
C T:GLY152 4.6 34.2 1.0
N T:CYS150 4.7 31.6 1.0
C T:CYS104 4.7 31.2 1.0
N T:ARG151 4.7 34.8 1.0
CB T:CYS108 4.7 29.0 1.0
SG T:CYS148 4.8 26.8 1.0

Zinc binding site 6 out of 6 in 6j6g

Go back to Zinc Binding Sites List in 6j6g
Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-A2 Complex at An Average Resolution of 3.2 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*-A2 Complex at An Average Resolution of 3.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:43.9
occ:1.00
 SG T:CYS122 2.3 32.4 1.0
SG T:CYS108 2.3 29.0 1.0
SG T:CYS120 2.3 29.2 1.0
SG T:CYS145 2.3 28.5 1.0
CB T:CYS145 2.9 28.5 1.0
CB T:CYS120 3.1 29.2 1.0
CB T:CYS108 3.5 29.0 1.0
CB T:CYS122 3.6 32.4 1.0
ZN T:ZN1000 3.8 43.4 1.0
ZN T:ZN1001 3.8 49.1 1.0
SG T:CYS104 4.3 31.2 1.0
CA T:CYS145 4.4 28.5 1.0
N T:CYS122 4.4 32.4 1.0
CB T:CYS150 4.4 31.6 1.0
CD2 T:HIS147 4.4 26.7 1.0
SG T:CYS148 4.5 26.8 1.0
CA T:CYS120 4.6 29.2 1.0
CA T:CYS122 4.6 32.4 1.0
CA T:CYS108 4.6 29.0 1.0
CB T:HIS147 4.7 26.7 1.0
CG T:HIS147 4.9 26.7 1.0
C T:CYS120 5.0 29.2 1.0
C T:CYS145 5.0 28.5 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 00:48:00 2024

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