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Zinc in PDB 6j6n: Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 Angstrom:
2.3.2.27;

Other elements in 6j6n:

The structure of Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom (pdb code 6j6n). 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*-B1 Complex at An Average Resolution of 3.86 Angstrom, PDB code: 6j6n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6j6n

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn400

b:87.2
occ:1.00
 SG Q:CYS74 2.3 31.7 1.0
SG Q:CYS71 2.3 28.9 1.0
SG Q:CYS13 2.3 38.6 1.0
SG Q:CYS16 2.3 34.8 1.0
CB Q:CYS13 2.9 38.6 1.0
CB Q:CYS71 3.2 28.9 1.0
CB Q:CYS74 3.3 31.7 1.0
N Q:CYS74 3.4 31.7 1.0
CA Q:CYS74 3.8 31.7 1.0
N Q:CYS13 3.9 38.6 1.0
CB Q:CYS16 4.0 34.8 1.0
CA Q:CYS13 4.0 38.6 1.0
C Q:CYS74 4.2 31.7 1.0
N Q:MET75 4.2 29.0 1.0
C Q:CYS73 4.6 27.5 1.0
N Q:LEU76 4.6 31.1 1.0
CA Q:CYS71 4.6 28.9 1.0
CB Q:CYS73 4.6 27.5 1.0
N Q:CYS73 4.8 27.5 1.0
N Q:CYS16 4.9 34.8 1.0
CA Q:CYS73 4.9 27.5 1.0
CA Q:CYS16 4.9 34.8 1.0
CB Q:LEU76 5.0 31.1 1.0
N Q:CYS71 5.0 28.9 1.0
O Q:LEU76 5.0 31.1 1.0

Zinc binding site 2 out of 6 in 6j6n

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn401

b:0.1
occ:1.00
 SG Q:CYS37 2.3 25.1 1.0
SG Q:CYS61 2.3 30.9 1.0
SG Q:CYS64 2.3 32.3 1.0
SG Q:CYS34 2.3 27.7 1.0
CB Q:CYS34 3.0 27.7 1.0
CB Q:CYS37 3.1 25.1 1.0
CB Q:CYS64 3.1 32.3 1.0
N Q:CYS37 3.5 25.1 1.0
CB Q:CYS61 3.6 30.9 1.0
CA Q:CYS37 3.9 25.1 1.0
N Q:CYS61 4.0 30.9 1.0
N Q:CYS64 4.2 32.3 1.0
CA Q:CYS64 4.3 32.3 1.0
CA Q:CYS61 4.3 30.9 1.0
CA Q:CYS34 4.5 27.7 1.0
CB Q:ILE36 4.5 23.8 1.0
C Q:ILE36 4.6 23.8 1.0
C Q:CYS37 4.7 25.1 1.0
N Q:ILE36 4.9 23.8 1.0
CB Q:SER114 4.9 23.0 1.0
CA Q:ILE36 4.9 23.8 1.0
C Q:CYS61 4.9 30.9 1.0
O Q:CYS61 5.0 30.9 1.0

Zinc binding site 3 out of 6 in 6j6n

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:48.7
occ:1.00
 SG R:CYS81 2.3 26.7 1.0
NE2 R:HIS91 2.3 29.8 1.0
SG R:CYS73 2.3 29.8 1.0
SG R:CYS87 2.3 35.3 1.0
CE1 R:HIS91 2.8 29.8 1.0
CB R:CYS87 3.1 35.3 1.0
CB R:CYS73 3.2 29.8 1.0
CB R:CYS81 3.2 26.7 1.0
CD2 R:HIS91 3.5 29.8 1.0
ND1 R:HIS91 4.0 29.8 1.0
CG R:HIS91 4.4 29.8 1.0
N6 E:A35 4.5 24.6 1.0
CA R:CYS73 4.6 29.8 1.0
CA R:CYS87 4.6 35.3 1.0
CA R:CYS81 4.6 26.7 1.0
N R:PHE76 4.7 21.8 1.0
O R:TYR89 4.8 38.1 1.0
O R:GLY84 4.9 29.6 1.0
CB R:PHE76 4.9 21.8 1.0

Zinc binding site 4 out of 6 in 6j6n

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:35.5
occ:1.00
 SG T:CYS148 2.3 28.6 1.0
SG T:CYS104 2.3 34.4 1.0
SG T:CYS108 2.3 27.1 1.0
SG T:CYS105 2.3 32.6 1.0
CB T:CYS104 2.8 34.4 1.0
CB T:CYS105 3.1 32.6 1.0
CB T:CYS148 3.1 28.6 1.0
C T:CYS104 3.6 34.4 1.0
N T:CYS105 3.6 32.6 1.0
ZN T:ZN1002 3.6 52.6 1.0
CA T:CYS104 3.8 34.4 1.0
ZN T:ZN1001 3.8 55.0 1.0
O T:HIS147 3.9 26.3 1.0
CB T:CYS108 3.9 27.1 1.0
CA T:CYS105 3.9 32.6 1.0
O T:CYS104 4.1 34.4 1.0
SG T:CYS122 4.4 37.5 1.0
CB T:CYS150 4.5 32.5 1.0
CA T:CYS148 4.5 28.6 1.0
C T:HIS147 4.6 26.3 1.0
SG T:CYS145 4.7 29.9 1.0
N T:CYS148 4.9 28.6 1.0
CA T:CYS108 4.9 27.1 1.0
N T:CYS108 4.9 27.1 1.0
N T:CYS104 5.0 34.4 1.0

Zinc binding site 5 out of 6 in 6j6n

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:55.0
occ:1.00
 CB T:CYS150 2.1 32.5 1.0
SG T:CYS153 2.3 16.1 1.0
SG T:CYS150 2.3 32.5 1.0
SG T:CYS122 2.3 37.5 1.0
SG T:CYS104 2.3 34.4 1.0
CB T:CYS104 2.5 34.4 1.0
CB T:CYS122 3.3 37.5 1.0
O T:CYS122 3.5 37.5 1.0
CA T:CYS150 3.7 32.5 1.0
CA T:CYS104 3.7 34.4 1.0
ZN T:ZN1000 3.8 35.5 1.0
CB T:CYS153 3.9 16.1 1.0
ZN T:ZN1002 3.9 52.6 1.0
N T:CYS153 4.0 16.1 1.0
C T:CYS122 4.3 37.5 1.0
SG T:CYS108 4.3 27.1 1.0
N T:CYS104 4.3 34.4 1.0
SG T:CYS148 4.4 28.6 1.0
C T:CYS150 4.4 32.5 1.0
CA T:CYS122 4.4 37.5 1.0
N T:CYS150 4.4 32.5 1.0
CA T:CYS153 4.4 16.1 1.0
C T:GLY152 4.7 33.8 1.0
N T:ARG151 4.7 55.0 1.0
N T:GLY152 4.8 33.8 1.0
C T:CYS104 4.9 34.4 1.0

Zinc binding site 6 out of 6 in 6j6n

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Yeast B*-B1 Complex at An Average Resolution of 3.86 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*-B1 Complex at An Average Resolution of 3.86 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:52.6
occ:1.00
 SG T:CYS120 2.3 35.6 1.0
SG T:CYS122 2.3 37.5 1.0
SG T:CYS108 2.3 27.1 1.0
SG T:CYS145 2.3 29.9 1.0
CB T:CYS108 3.2 27.1 1.0
CB T:CYS145 3.4 29.9 1.0
CB T:CYS120 3.4 35.6 1.0
ZN T:ZN1000 3.6 35.5 1.0
SG T:CYS148 3.7 28.6 1.0
CB T:CYS122 3.7 37.5 1.0
ZN T:ZN1001 3.9 55.0 1.0
CA T:CYS108 4.1 27.1 1.0
CD2 T:HIS147 4.4 26.3 1.0
N T:CYS122 4.5 37.5 1.0
SG T:CYS104 4.5 34.4 1.0
CA T:CYS122 4.5 37.5 1.0
CB T:CYS104 4.6 34.4 1.0
CA T:CYS120 4.7 35.6 1.0
CB T:CYS150 4.8 32.5 1.0
C T:CYS122 4.8 37.5 1.0
CA T:CYS145 4.8 29.9 1.0
NE2 T:HIS147 4.8 26.3 1.0
C T:CYS120 4.9 35.6 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 00:55:23 2024

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