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Zinc in PDB 6exn: Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked

Enzymatic activity of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked

All present enzymatic activity of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked:
2.3.2.27; 3.6.4.13;

Other elements in 6exn:

The structure of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 6exn

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Zinc binding site 1 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:75.7
occ:1.00
SG L:CYS104 2.3 59.6 1.0
SG L:CYS148 2.3 58.3 1.0
SG L:CYS108 2.3 59.7 1.0
SG L:CYS105 2.3 60.6 1.0
CB L:CYS108 2.9 59.7 1.0
CB L:CYS104 3.2 59.6 1.0
N L:CYS105 3.5 60.6 1.0
CB L:CYS105 3.5 60.6 1.0
CB L:CYS148 3.7 58.3 1.0
ZN L:ZN1001 3.7 71.2 1.0
ZN L:ZN1002 3.9 68.6 1.0
N L:CYS108 3.9 59.7 1.0
CA L:CYS105 4.0 60.6 1.0
CA L:CYS108 4.0 59.7 1.0
C L:CYS104 4.0 59.6 1.0
O L:CYS105 4.2 60.6 1.0
CA L:CYS104 4.2 59.6 1.0
SG L:CYS122 4.3 64.2 1.0
C L:CYS105 4.4 60.6 1.0
N L:CYS148 4.4 58.3 1.0
SG L:CYS150 4.4 60.7 1.0
CB L:HIS147 4.5 55.4 1.0
CA L:CYS148 4.6 58.3 1.0
SG L:CYS145 4.7 60.0 1.0
C L:ARG107 4.9 54.3 1.0
O L:CYS104 4.9 59.6 1.0

Zinc binding site 2 out of 7 in 6exn

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Zinc binding site 2 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:71.2
occ:1.00
SG L:CYS153 2.3 60.6 1.0
SG L:CYS122 2.3 64.2 1.0
SG L:CYS150 2.3 60.7 1.0
SG L:CYS104 2.3 59.6 1.0
CB L:CYS104 2.4 59.6 1.0
CB L:CYS122 3.0 64.2 1.0
CB L:CYS153 3.4 60.6 1.0
ZN L:ZN1000 3.7 75.7 1.0
CA L:CYS104 3.8 59.6 1.0
N L:CYS104 3.9 59.6 1.0
ZN L:ZN1002 4.0 68.6 1.0
CB L:CYS150 4.0 60.7 1.0
CB L:CYS108 4.0 59.7 1.0
SG L:CYS148 4.2 58.3 1.0
CA L:CYS122 4.2 64.2 1.0
C L:CYS122 4.3 64.2 1.0
SG L:CYS108 4.4 59.7 1.0
O L:CYS122 4.4 64.2 1.0
CA L:CYS153 4.6 60.6 1.0
N L:CYS153 4.7 60.6 1.0
C L:CYS104 4.8 59.6 1.0
N L:ARG123 4.9 63.1 1.0
N L:CYS105 4.9 60.6 1.0
SG L:CYS145 4.9 60.0 1.0
O L:CYS150 5.0 60.7 1.0
CD L:ARG123 5.0 63.1 1.0

Zinc binding site 3 out of 7 in 6exn

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Zinc binding site 3 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:68.6
occ:1.00
SG L:CYS145 2.3 60.0 1.0
SG L:CYS120 2.3 63.1 1.0
SG L:CYS108 2.3 59.7 1.0
SG L:CYS122 2.3 64.2 1.0
CB L:CYS108 3.0 59.7 1.0
CB L:CYS120 3.2 63.1 1.0
CB L:CYS122 3.6 64.2 1.0
CB L:CYS145 3.7 60.0 1.0
ZN L:ZN1000 3.9 75.7 1.0
ZN L:ZN1001 4.0 71.2 1.0
ND1 L:HIS147 4.0 55.4 1.0
CA L:CYS108 4.1 59.7 1.0
N L:CYS122 4.2 64.2 1.0
CA L:CYS122 4.5 64.2 1.0
SG L:CYS148 4.5 58.3 1.0
SG L:CYS104 4.5 59.6 1.0
CA L:CYS120 4.6 63.1 1.0
N L:ILE121 4.7 62.0 1.0
CE1 L:HIS147 4.8 55.4 1.0
SG L:CYS150 4.8 60.7 1.0
C L:CYS120 4.9 63.1 1.0
O L:CYS108 4.9 59.7 1.0
CA L:CYS145 4.9 60.0 1.0
CG L:HIS147 4.9 55.4 1.0
CB L:HIS147 4.9 55.4 1.0
N L:VAL146 5.0 57.5 1.0

Zinc binding site 4 out of 7 in 6exn

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Zinc binding site 4 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1000

b:72.1
occ:1.00
SG M:CYS73 2.0 62.3 1.0
NE2 M:HIS91 2.0 65.6 1.0
SG M:CYS81 2.3 68.1 1.0
SG M:CYS87 2.3 66.3 1.0
CE1 M:HIS91 2.3 65.6 1.0
CB M:CYS87 2.9 66.3 1.0
CD2 M:HIS91 3.2 65.6 1.0
CB M:CYS73 3.4 62.3 1.0
ND1 M:HIS91 3.5 65.6 1.0
CB M:CYS81 3.7 68.1 1.0
CG M:HIS91 4.0 65.6 1.0
O M:LEU83 4.4 68.8 1.0
N6 6:A35 4.4 67.0 1.0
CA M:CYS87 4.4 66.3 1.0
N M:PHE76 4.6 65.8 1.0
CA M:CYS73 4.6 62.3 1.0
CB M:PHE76 4.9 65.8 1.0
CA M:CYS81 5.0 68.1 1.0

Zinc binding site 5 out of 7 in 6exn

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Zinc binding site 5 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:77.0
occ:1.00
SG N:CYS64 2.3 65.8 1.0
SG N:CYS34 2.3 55.3 1.0
SG N:CYS37 2.3 57.0 1.0
SG N:CYS61 2.3 64.5 1.0
CB N:CYS37 3.3 57.0 1.0
CB N:CYS64 3.3 65.8 1.0
CB N:CYS34 3.5 55.3 1.0
N N:CYS37 3.6 57.0 1.0
CB N:CYS61 3.9 64.5 1.0
CA N:CYS37 4.0 57.0 1.0
N N:CYS61 4.2 64.5 1.0
CB N:SER114 4.4 60.0 1.0
CB N:ILE36 4.4 58.5 1.0
N N:CYS64 4.5 65.8 1.0
CA N:CYS64 4.5 65.8 1.0
C N:ILE36 4.6 58.5 1.0
CA N:CYS61 4.6 64.5 1.0
C N:CYS37 4.6 57.0 1.0
OG N:SER114 4.7 60.0 1.0
CA N:CYS34 4.8 55.3 1.0
N N:THR38 4.8 53.7 1.0
CG N:ARG63 4.8 66.5 1.0
CA N:ILE36 4.9 58.5 1.0
N N:ILE36 4.9 58.5 1.0
CG2 N:ILE36 4.9 58.5 1.0

Zinc binding site 6 out of 7 in 6exn

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Zinc binding site 6 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:88.5
occ:1.00
SG N:CYS74 2.3 71.7 1.0
SG N:CYS16 2.3 71.5 1.0
SG N:CYS71 2.3 68.1 1.0
SG N:CYS13 2.3 72.8 1.0
CB N:CYS74 2.8 71.7 1.0
N N:CYS74 3.3 71.7 1.0
CA N:CYS74 3.5 71.7 1.0
CB N:CYS71 3.6 68.1 1.0
CB N:CYS13 3.8 72.8 1.0
CB N:CYS16 3.9 71.5 1.0
N N:CYS13 4.1 72.8 1.0
C N:CYS74 4.2 71.7 1.0
CD2 N:HIS81 4.4 77.7 1.0
N N:MET75 4.4 69.3 1.0
N N:CYS16 4.4 71.5 1.0
C N:CYS73 4.5 68.9 1.0
CA N:CYS13 4.5 72.8 1.0
NE2 N:HIS81 4.6 77.7 1.0
CA N:CYS16 4.7 71.5 1.0
N N:CYS73 4.9 68.9 1.0
CB N:CYS73 4.9 68.9 1.0
CA N:CYS71 4.9 68.1 1.0
N N:LEU76 4.9 73.0 1.0
O N:CYS74 4.9 71.7 1.0
CA N:CYS73 5.0 68.9 1.0
C N:CYS13 5.0 72.8 1.0

Zinc binding site 7 out of 7 in 6exn

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Zinc binding site 7 out of 7 in the Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Post-Catalytic P Complex Spliceosome with 3' Splice Site Docked within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Zn400

b:91.3
occ:1.00
NE2 c:HIS130 2.0 74.7 1.0
SG c:CYS122 2.3 84.2 1.0
SG c:CYS125 2.3 79.0 1.0
SG c:CYS135 2.3 64.5 1.0
CD2 c:HIS130 2.8 74.7 1.0
CB c:CYS122 3.0 84.2 1.0
CE1 c:HIS130 3.1 74.7 1.0
CB c:CYS135 3.2 64.5 1.0
CB c:CYS125 3.6 79.0 1.0
N c:CYS125 3.8 79.0 1.0
CA c:CYS135 3.9 64.5 1.0
CG c:HIS130 4.0 74.7 1.0
ND1 c:HIS130 4.1 74.7 1.0
CB c:ASN124 4.2 74.5 1.0
CA c:CYS125 4.3 79.0 1.0
CA c:CYS122 4.5 84.2 1.0
N c:MET136 4.6 59.8 1.0
O c:LYS131 4.7 66.2 1.0
C c:ASN124 4.8 74.5 1.0
C c:CYS135 4.8 64.5 1.0
CA c:ASN124 4.9 74.5 1.0
N c:ASN124 4.9 74.5 1.0
ND2 c:ASN124 4.9 74.5 1.0
N c:GLY126 5.0 84.8 1.0
N c:CYS135 5.0 64.5 1.0
CG c:ASN124 5.0 74.5 1.0

Reference:

M.E.Wilkinson, S.M.Fica, W.P.Galej, C.M.Norman, A.J.Newman, K.Nagai. Postcatalytic Spliceosome Structure Reveals Mechanism of 3'-Splice Site Selection. Science V. 358 1283 2017.
ISSN: ESSN 1095-9203
PubMed: 29146871
DOI: 10.1126/SCIENCE.AAR3729
Page generated: Wed Dec 16 11:45:04 2020

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