Atomistry » Zinc » PDB 6j4f-6jes » 6j6q
Atomistry »
  Zinc »
    PDB 6j4f-6jes »
      6j6q »

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

Go back to Zinc Binding Sites List in 6j6q
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

Go back to Zinc Binding Sites List in 6j6q
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

Go back to Zinc Binding Sites List in 6j6q
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

Go back to Zinc Binding Sites List in 6j6q
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

Go back to Zinc Binding Sites List in 6j6q
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

Go back to Zinc Binding Sites List in 6j6q
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

Last articles

Mg in 2VSC
Mg in 2VPN
Mg in 2VRN
Mg in 2VPQ
Mg in 2VQD
Mg in 2VQ2
Mg in 2VPR
Mg in 2VPO
Mg in 2VP0
Mg in 2VOS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy