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Zinc in PDB 6bk8: S. Cerevisiae Spliceosomal Post-Catalytic P Complex

Enzymatic activity of S. Cerevisiae Spliceosomal Post-Catalytic P Complex

All present enzymatic activity of S. Cerevisiae Spliceosomal Post-Catalytic P Complex:
2.3.2.27; 3.6.4.13;

Other elements in 6bk8:

The structure of S. Cerevisiae Spliceosomal Post-Catalytic P Complex also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex (pdb code 6bk8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex, PDB code: 6bk8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6bk8

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Zinc binding site 1 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn501

b:86.5
occ:1.00
 CB F:CYS13 1.5 34.1 1.0
SG F:CYS74 2.2 26.3 1.0
SG F:CYS16 2.4 30.7 1.0
SG F:CYS71 2.5 21.8 1.0
SG F:CYS13 2.6 34.1 1.0
CA F:CYS13 2.8 34.1 1.0
CB F:CYS74 2.9 26.3 1.0
CB F:CYS71 3.1 21.8 1.0
N F:CYS13 3.1 34.1 1.0
CB F:CYS16 3.6 30.7 1.0
C F:CYS13 3.8 34.1 1.0
O F:CYS13 4.2 34.1 1.0
CA F:CYS74 4.2 26.3 1.0
N F:CYS16 4.2 30.7 1.0
N F:CYS74 4.3 26.3 1.0
C F:ILE12 4.5 24.5 1.0
CA F:CYS16 4.5 30.7 1.0
CA F:CYS71 4.6 21.8 1.0
N F:GLU14 4.7 35.1 1.0

Zinc binding site 2 out of 7 in 6bk8

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Zinc binding site 2 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:59.4
occ:1.00
 CB F:CYS61 1.8 18.5 1.0
CB F:CYS37 2.3 17.4 1.0
SG F:CYS64 2.4 17.1 1.0
SG F:CYS37 2.5 17.4 1.0
SG F:CYS34 2.6 17.2 1.0
SG F:CYS61 2.7 18.5 1.0
CB F:CYS34 3.2 17.2 1.0
CA F:CYS61 3.2 18.5 1.0
N F:CYS61 3.4 18.5 1.0
CB F:CYS64 3.5 17.1 1.0
CA F:CYS37 3.8 17.4 1.0
N F:CYS37 4.2 17.4 1.0
C F:CYS61 4.2 18.5 1.0
N F:CYS64 4.3 17.1 1.0
CA F:CYS64 4.5 17.1 1.0
C F:CYS37 4.6 17.4 1.0
CA F:CYS34 4.7 17.2 1.0
C F:ILE60 4.7 14.8 1.0
N F:VAL62 4.8 16.6 1.0
O F:CYS61 4.8 18.5 1.0
O F:LEU39 4.9 16.8 1.0

Zinc binding site 3 out of 7 in 6bk8

Go back to Zinc Binding Sites List in 6bk8
Zinc binding site 3 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:50.8
occ:1.00
 NE2 G:HIS91 2.1 24.2 1.0
SG G:CYS81 2.1 25.0 1.0
SG G:CYS87 2.3 28.1 1.0
SG G:CYS73 2.3 19.8 1.0
CE1 G:HIS91 2.4 24.2 1.0
CB G:CYS73 3.1 19.8 1.0
CB G:CYS87 3.2 28.1 1.0
CD2 G:HIS91 3.2 24.2 1.0
ND1 G:HIS91 3.5 24.2 1.0
CB G:CYS81 3.6 25.0 1.0
CG G:HIS91 4.0 24.2 1.0
CB G:PHE76 4.5 22.4 1.0
N G:PHE76 4.5 22.4 1.0
CA G:CYS73 4.6 19.8 1.0
CA G:CYS87 4.6 28.1 1.0
N6 6:A35 4.7 21.1 1.0
CA G:CYS81 4.8 25.0 1.0
CA G:PHE76 4.9 22.4 1.0
O G:TYR89 5.0 24.3 1.0

Zinc binding site 4 out of 7 in 6bk8

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Zinc binding site 4 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn501

b:62.7
occ:1.00
 SG I:CYS108 2.0 22.5 1.0
SG I:CYS148 2.0 23.0 1.0
SG I:CYS105 2.2 20.2 1.0
SG I:CYS104 2.2 21.4 1.0
CB I:CYS108 3.0 22.5 1.0
CB I:CYS148 3.1 23.0 1.0
ZN I:ZN503 3.4 36.0 1.0
ZN I:ZN502 3.8 40.9 1.0
CB I:CYS104 3.8 21.4 1.0
CB I:CYS105 3.9 20.2 1.0
N I:CYS105 4.0 20.2 1.0
N I:CYS108 4.1 22.5 1.0
CA I:CYS108 4.1 22.5 1.0
N I:CYS148 4.1 23.0 1.0
CA I:CYS148 4.2 23.0 1.0
SG I:CYS122 4.3 18.8 1.0
CB I:HIS147 4.3 19.5 1.0
CA I:CYS105 4.4 20.2 1.0
O I:CYS105 4.5 20.2 1.0
SG I:CYS145 4.5 19.9 1.0
CB I:CYS150 4.5 22.9 1.0
C I:CYS105 4.6 20.2 1.0
C I:CYS104 4.7 21.4 1.0
C I:HIS147 4.8 19.5 1.0
C I:ARG107 4.8 20.9 1.0
CA I:CYS104 4.9 21.4 1.0

Zinc binding site 5 out of 7 in 6bk8

Go back to Zinc Binding Sites List in 6bk8
Zinc binding site 5 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn502

b:40.9
occ:1.00
 SG I:CYS153 2.1 21.4 1.0
SG I:CYS150 2.2 22.9 1.0
SG I:CYS104 2.3 21.4 1.0
SG I:CYS122 2.5 18.8 1.0
CB I:CYS104 2.6 21.4 1.0
CB I:CYS150 2.7 22.9 1.0
CB I:CYS153 3.0 21.4 1.0
CB I:CYS122 3.5 18.8 1.0
ZN I:ZN501 3.8 62.7 1.0
CA I:CYS104 3.8 21.4 1.0
N I:CYS104 3.8 21.4 1.0
ZN I:ZN503 4.1 36.0 1.0
CA I:CYS150 4.2 22.9 1.0
SG I:CYS108 4.3 22.5 1.0
CA I:CYS153 4.3 21.4 1.0
N I:CYS153 4.4 21.4 1.0
CB I:CYS108 4.5 22.5 1.0
N I:CYS105 4.8 20.2 1.0
C I:CYS104 4.8 21.4 1.0
CA I:CYS122 4.8 18.8 1.0
SG I:CYS148 4.9 23.0 1.0
C I:CYS150 4.9 22.9 1.0
C I:CYS122 4.9 18.8 1.0
CB I:CYS148 5.0 23.0 1.0

Zinc binding site 6 out of 7 in 6bk8

Go back to Zinc Binding Sites List in 6bk8
Zinc binding site 6 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn503

b:36.0
occ:1.00
 SG I:CYS120 2.1 18.6 1.0
SG I:CYS108 2.2 22.5 1.0
SG I:CYS145 2.3 19.9 1.0
SG I:CYS122 2.5 18.8 1.0
CB I:CYS120 3.0 18.6 1.0
CB I:CYS145 3.4 19.9 1.0
ZN I:ZN501 3.4 62.7 1.0
CB I:CYS108 3.5 22.5 1.0
CB I:CYS122 3.5 18.8 1.0
ZN I:ZN502 4.1 40.9 1.0
N I:CYS122 4.1 18.8 1.0
CB I:CYS150 4.3 22.9 1.0
CA I:CYS120 4.4 18.6 1.0
CA I:CYS122 4.5 18.8 1.0
SG I:CYS104 4.5 21.4 1.0
CA I:CYS108 4.6 22.5 1.0
N I:ILE121 4.6 19.3 1.0
C I:CYS120 4.6 18.6 1.0
CA I:CYS145 4.8 19.9 1.0
CD2 I:HIS147 5.0 19.5 1.0

Zinc binding site 7 out of 7 in 6bk8

Go back to Zinc Binding Sites List in 6bk8
Zinc binding site 7 out of 7 in the S. Cerevisiae Spliceosomal Post-Catalytic P Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S. Cerevisiae Spliceosomal Post-Catalytic P Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn501

b:91.5
occ:1.00
 NE2 O:HIS130 2.1 52.3 1.0
SG O:CYS125 2.2 61.1 1.0
SG O:CYS122 2.3 67.7 1.0
SG O:CYS135 2.3 49.3 1.0
CB O:CYS122 2.4 67.7 1.0
CB O:CYS125 2.6 61.1 1.0
CB O:CYS135 2.6 49.3 1.0
CD2 O:HIS130 2.9 52.3 1.0
CE1 O:HIS130 3.1 52.3 1.0
N O:CYS125 3.6 61.1 1.0
CA O:CYS135 3.6 49.3 1.0
OD1 O:ASN124 3.7 56.0 1.0
CA O:CYS125 3.7 61.1 1.0
CA O:CYS122 3.9 67.7 1.0
CG O:HIS130 4.0 52.3 1.0
ND1 O:HIS130 4.1 52.3 1.0
C O:CYS122 4.4 67.7 1.0
N O:CYS135 4.4 49.3 1.0
O O:LYS131 4.6 54.8 1.0
C O:CYS125 4.7 61.1 1.0
N O:GLY126 4.7 60.0 1.0
N O:CYS122 4.8 67.7 1.0
O O:CYS122 4.8 67.7 1.0
C O:CYS135 4.8 49.3 1.0
C O:ASN124 4.8 56.0 1.0
CG O:ASN124 4.9 56.0 1.0
N O:ARG123 4.9 58.7 1.0
N O:ASN124 4.9 56.0 1.0

Reference:

S.Liu, X.Li, L.Zhang, J.Jiang, R.C.Hill, Y.Cui, K.C.Hansen, Z.H.Zhou, R.Zhao. Structure of the Yeast Spliceosomal Postcatalytic P Complex. Science V. 358 1278 2017.
ISSN: ESSN 1095-9203
PubMed: 29146870
DOI: 10.1126/SCIENCE.AAR3462
Page generated: Mon Oct 28 17:59:22 2024

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