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Zinc in PDB 6j6q: Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom

Enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom:
2.3.2.27;

Other elements in 6j6q:

The structure of Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom (pdb code 6j6q). 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 B*-B2 Complex at An Average Resolution of 3.7 Angstrom, PDB code: 6j6q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6j6q

Go back to Zinc Binding Sites List in 6j6q
Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn400

b:74.8
occ:1.00
 SG Q:CYS74 2.3 40.9 1.0
SG Q:CYS71 2.3 38.0 1.0
SG Q:CYS13 2.3 46.9 1.0
SG Q:CYS16 2.3 43.4 1.0
CB Q:CYS13 2.9 46.9 1.0
CB Q:CYS71 3.2 38.0 1.0
CB Q:CYS74 3.3 40.9 1.0
N Q:CYS74 3.4 40.9 1.0
CA Q:CYS74 3.8 40.9 1.0
N Q:CYS13 3.8 46.9 1.0
CA Q:CYS13 3.9 46.9 1.0
CB Q:CYS16 4.0 43.4 1.0
C Q:CYS74 4.3 40.9 1.0
N Q:MET75 4.3 39.5 1.0
C Q:CYS73 4.6 37.8 1.0
CA Q:CYS71 4.6 38.0 1.0
N Q:LEU76 4.7 39.4 1.0
CB Q:CYS73 4.7 37.8 1.0
N Q:CYS16 4.8 43.4 1.0
N Q:CYS73 4.8 37.8 1.0
CA Q:CYS16 4.9 43.4 1.0
CA Q:CYS73 4.9 37.8 1.0
C Q:ILE12 5.0 40.0 1.0

Zinc binding site 2 out of 7 in 6j6q

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn401

b:62.7
occ:1.00
 SG Q:CYS37 2.3 28.1 1.0
SG Q:CYS61 2.3 33.7 1.0
SG Q:CYS64 2.3 34.1 1.0
SG Q:CYS34 2.3 29.3 1.0
CB Q:CYS34 3.0 29.3 1.0
CB Q:CYS64 3.1 34.1 1.0
CB Q:CYS37 3.1 28.1 1.0
N Q:CYS37 3.6 28.1 1.0
CB Q:CYS61 3.6 33.7 1.0
N Q:CYS61 3.9 33.7 1.0
CA Q:CYS37 3.9 28.1 1.0
N Q:CYS64 4.2 34.1 1.0
CA Q:CYS64 4.2 34.1 1.0
CA Q:CYS61 4.3 33.7 1.0
CB Q:ILE36 4.5 29.0 1.0
CA Q:CYS34 4.5 29.3 1.0
C Q:ILE36 4.7 29.0 1.0
C Q:CYS37 4.8 28.1 1.0
N Q:ILE36 4.9 29.0 1.0
C Q:CYS61 4.9 33.7 1.0
O Q:CYS61 4.9 33.7 1.0
CB Q:SER114 4.9 30.1 1.0
CA Q:ILE36 4.9 29.0 1.0
O Q:LEU39 5.0 28.3 1.0

Zinc binding site 3 out of 7 in 6j6q

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn400

b:31.7
occ:1.00
 SG R:CYS81 2.3 31.1 1.0
NE2 R:HIS91 2.3 32.1 1.0
SG R:CYS73 2.3 29.8 1.0
SG R:CYS87 2.3 37.0 1.0
CE1 R:HIS91 2.7 32.1 1.0
CB R:CYS73 3.2 29.8 1.0
CB R:CYS87 3.2 37.0 1.0
CB R:CYS81 3.3 31.1 1.0
CD2 R:HIS91 3.5 32.1 1.0
ND1 R:HIS91 3.9 32.1 1.0
CG R:HIS91 4.3 32.1 1.0
N6 E:A35 4.5 20.4 1.0
CA R:CYS73 4.6 29.8 1.0
CA R:CYS81 4.6 31.1 1.0
CA R:CYS87 4.7 37.0 1.0
N R:PHE76 4.7 30.3 1.0
O R:TYR89 4.7 34.3 1.0
CB R:PHE76 4.9 30.3 1.0
O R:GLY84 4.9 37.4 1.0

Zinc binding site 4 out of 7 in 6j6q

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:42.6
occ:1.00
 SG T:CYS148 2.3 26.3 1.0
SG T:CYS104 2.3 35.5 1.0
SG T:CYS108 2.3 35.3 1.0
SG T:CYS105 2.3 35.9 1.0
CB T:CYS104 3.1 35.5 1.0
CB T:CYS108 3.2 35.3 1.0
N T:CYS105 3.7 35.9 1.0
ZN T:ZN1002 3.8 45.6 1.0
CB T:CYS148 3.8 26.3 1.0
CB T:CYS105 3.8 35.9 1.0
ZN T:ZN1001 3.9 44.3 1.0
C T:CYS104 4.2 35.5 1.0
CA T:CYS104 4.2 35.5 1.0
N T:CYS108 4.3 35.3 1.0
SG T:CYS145 4.3 31.2 1.0
CA T:CYS108 4.3 35.3 1.0
CA T:CYS105 4.4 35.9 1.0
SG T:CYS122 4.5 30.1 1.0
CB T:HIS147 4.5 29.9 1.0
CB T:CYS150 4.7 30.1 1.0
N T:CYS148 4.8 26.3 1.0
CA T:CYS148 4.9 26.3 1.0

Zinc binding site 5 out of 7 in 6j6q

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:44.3
occ:1.00
 SG T:CYS153 2.3 33.6 1.0
SG T:CYS150 2.3 30.1 1.0
SG T:CYS122 2.3 30.1 1.0
SG T:CYS104 2.3 35.5 1.0
CB T:CYS150 2.3 30.1 1.0
CB T:CYS104 2.7 35.5 1.0
CB T:CYS122 3.2 30.1 1.0
CA T:CYS104 3.8 35.5 1.0
ZN T:ZN1002 3.8 45.6 1.0
CA T:CYS150 3.9 30.1 1.0
ZN T:ZN1000 3.9 42.6 1.0
CB T:CYS153 3.9 33.6 1.0
N T:CYS153 4.2 33.6 1.0
O T:CYS122 4.4 30.1 1.0
SG T:CYS108 4.4 35.3 1.0
CA T:CYS122 4.4 30.1 1.0
N T:CYS104 4.5 35.5 1.0
C T:CYS122 4.5 30.1 1.0
C T:CYS150 4.5 30.1 1.0
SG T:CYS145 4.5 31.2 1.0
N T:GLY152 4.6 32.1 1.0
CA T:CYS153 4.6 33.6 1.0
N T:CYS150 4.6 30.1 1.0
C T:GLY152 4.7 32.1 1.0
N T:ARG151 4.7 32.9 1.0
SG T:CYS148 4.8 26.3 1.0
CB T:CYS108 4.8 35.3 1.0
CB n:PRO68 4.9 33.4 1.0
CA T:GLY152 5.0 32.1 1.0

Zinc binding site 6 out of 7 in 6j6q

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 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*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:45.6
occ:1.00
 SG T:CYS122 2.3 30.1 1.0
SG T:CYS120 2.3 32.1 1.0
SG T:CYS108 2.3 35.3 1.0
SG T:CYS145 2.3 31.2 1.0
CB T:CYS145 3.0 31.2 1.0
CB T:CYS120 3.2 32.1 1.0
CB T:CYS108 3.5 35.3 1.0
CB T:CYS122 3.5 30.1 1.0
ZN T:ZN1000 3.8 42.6 1.0
ZN T:ZN1001 3.8 44.3 1.0
N T:CYS122 4.3 30.1 1.0
SG T:CYS148 4.4 26.3 1.0
CD2 T:HIS147 4.4 29.9 1.0
SG T:CYS104 4.4 35.5 1.0
CB T:CYS150 4.4 30.1 1.0
CA T:CYS122 4.5 30.1 1.0
CA T:CYS145 4.5 31.2 1.0
CA T:CYS108 4.6 35.3 1.0
CA T:CYS120 4.6 32.1 1.0
CB T:HIS147 4.7 29.9 1.0
CG T:HIS147 4.9 29.9 1.0
C T:CYS120 5.0 32.1 1.0

Zinc binding site 7 out of 7 in 6j6q

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of the Yeast B*-B2 Complex at An Average Resolution of 3.7 Angstrom


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 B*-B2 Complex at An Average Resolution of 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:97.6
occ:1.00
 SG F:CYS54 2.3 71.5 1.0
SG F:CYS88 2.3 65.8 1.0
SG F:CYS91 2.3 77.0 1.0
SG F:CYS51 2.3 69.3 1.0
CB F:CYS51 3.3 69.3 1.0
CB F:CYS88 3.4 65.8 1.0
CB F:CYS91 3.6 77.0 1.0
CB F:CYS54 3.7 71.5 1.0
N F:CYS54 3.9 71.5 1.0
N F:CYS91 3.9 77.0 1.0
CA F:CYS91 4.3 77.0 1.0
CA F:CYS54 4.3 71.5 1.0
CB F:GLU56 4.6 66.8 1.0
O F:CYS91 4.6 77.0 1.0
CB F:ARG90 4.7 85.7 1.0
C F:CYS91 4.7 77.0 1.0
C F:CYS54 4.8 71.5 1.0
CA F:CYS51 4.8 69.3 1.0
CA F:CYS88 4.8 65.8 1.0
CB F:GLU53 4.8 72.2 1.0
CB F:ASN93 4.9 59.2 1.0
N F:GLU56 4.9 66.8 1.0
C F:ARG90 5.0 85.7 1.0
N F:ARG90 5.0 85.7 1.0
C F:GLU53 5.0 72.2 1.0
N F:GLU53 5.0 72.2 1.0
N F:ASN55 5.0 65.2 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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