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Zinc in PDB 5lj5: Overall Structure of the Yeast Spliceosome Immediately After Branching.

Enzymatic activity of Overall Structure of the Yeast Spliceosome Immediately After Branching.

All present enzymatic activity of Overall Structure of the Yeast Spliceosome Immediately After Branching.:
3.6.4.13;

Other elements in 5lj5:

The structure of Overall Structure of the Yeast Spliceosome Immediately After Branching. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Overall Structure of the Yeast Spliceosome Immediately After Branching. (pdb code 5lj5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Overall Structure of the Yeast Spliceosome Immediately After Branching., PDB code: 5lj5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5lj5

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Zinc binding site 1 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:0.4
occ:1.00
 SG D:CYS88 1.6 0.6 1.0
SG D:CYS91 1.7 0.6 1.0
SG D:CYS54 2.2 0.2 1.0
CB D:CYS88 2.6 0.3 1.0
SG D:CYS51 2.6 0.5 1.0
O D:CYS91 2.8 0.3 1.0
CB D:CYS91 3.1 0.4 1.0
N D:CYS91 3.3 0.5 1.0
C D:CYS91 3.4 0.8 1.0
CA D:CYS91 3.4 0.8 1.0
CB D:CYS51 3.7 0.5 1.0
CB D:CYS54 3.9 0.3 1.0
CA D:CYS88 4.0 0.0 1.0
N D:CYS54 4.3 0.8 1.0
C D:CYS88 4.4 0.9 1.0
N D:ASN93 4.5 0.7 1.0
CB D:ASN93 4.5 0.9 1.0
C D:ARG90 4.5 0.8 1.0
N D:ALA92 4.6 0.6 1.0
CA D:CYS54 4.6 0.8 1.0
O D:CYS88 4.6 0.0 1.0
N D:CYS88 4.7 0.5 1.0
CB D:GLU56 4.7 0.4 1.0
N D:ARG90 4.8 0.1 1.0
CB D:GLU53 4.9 0.2 1.0

Zinc binding site 2 out of 7 in 5lj5

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Zinc binding site 2 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:31.1
occ:1.00
 SG L:CYS148 2.0 79.5 1.0
SG L:CYS104 2.1 60.2 1.0
SG L:CYS108 2.5 56.5 1.0
SG L:CYS105 2.6 78.7 1.0
CB L:CYS108 3.0 60.8 1.0
N L:CYS105 3.0 66.7 1.0
CB L:CYS104 3.0 60.6 1.0
CB L:CYS105 3.4 74.5 1.0
ZN L:ZN1001 3.5 38.3 1.0
CB L:CYS148 3.6 84.8 1.0
C L:CYS104 3.7 63.2 1.0
CA L:CYS105 3.7 71.2 1.0
O L:CYS105 3.8 71.1 1.0
CA L:CYS104 3.9 60.9 1.0
ZN L:ZN1002 4.0 15.2 1.0
SG L:CYS150 4.0 94.1 1.0
C L:CYS105 4.1 71.9 1.0
CA L:CYS108 4.2 64.8 1.0
N L:CYS108 4.2 68.9 1.0
O L:CYS104 4.5 65.2 1.0
N L:CYS104 4.6 58.4 1.0
SG L:CYS145 4.7 97.1 1.0
CB L:CYS150 4.7 97.0 1.0
SG L:CYS122 4.7 73.0 1.0
CA L:CYS148 4.7 88.3 1.0
N L:CYS148 4.7 90.6 1.0
CB L:HIS147 4.9 0.1 1.0
O L:CYS148 5.0 95.9 1.0

Zinc binding site 3 out of 7 in 5lj5

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Zinc binding site 3 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:38.3
occ:1.00
 SG L:CYS104 1.9 60.2 1.0
SG L:CYS122 2.2 73.0 1.0
SG L:CYS150 2.6 94.1 1.0
CB L:CYS153 2.8 86.8 1.0
CB L:CYS104 2.8 60.6 1.0
SG L:CYS153 2.9 81.3 1.0
CB L:CYS150 2.9 97.0 1.0
CB L:CYS122 3.0 71.0 1.0
ZN L:ZN1002 3.3 15.2 1.0
ZN L:ZN1000 3.5 31.1 1.0
SG L:CYS108 3.9 56.5 1.0
CA L:CYS104 4.0 60.9 1.0
N L:CYS104 4.1 58.4 1.0
CB L:CYS108 4.2 60.8 1.0
CA L:CYS153 4.2 88.2 1.0
SG L:CYS148 4.2 79.5 1.0
O L:CYS150 4.3 93.0 1.0
CA L:CYS150 4.4 99.8 1.0
CA L:CYS122 4.4 68.7 1.0
C L:CYS122 4.7 69.6 1.0
N L:CYS153 4.7 95.6 1.0
C L:CYS150 4.8 98.8 1.0
N L:CYS105 4.8 66.7 1.0
N L:ARG123 4.9 71.2 1.0
C L:CYS104 5.0 63.2 1.0
SG L:CYS120 5.0 53.5 1.0

Zinc binding site 4 out of 7 in 5lj5

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Zinc binding site 4 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:15.2
occ:1.00
 SG L:CYS120 2.1 53.5 1.0
SG L:CYS108 2.3 56.5 1.0
SG L:CYS145 2.6 97.1 1.0
SG L:CYS122 2.7 73.0 1.0
SG L:CYS150 2.8 94.1 1.0
CB L:CYS122 3.1 71.0 1.0
CB L:CYS120 3.1 56.8 1.0
CB L:CYS145 3.2 93.4 1.0
ZN L:ZN1001 3.3 38.3 1.0
CB L:CYS108 3.5 60.8 1.0
ZN L:ZN1000 4.0 31.1 1.0
SG L:CYS104 4.1 60.2 1.0
N L:CYS122 4.1 64.2 1.0
CA L:CYS122 4.2 68.7 1.0
SG L:CYS148 4.2 79.5 1.0
CB L:CYS150 4.5 97.0 1.0
CA L:CYS120 4.5 57.9 1.0
CA L:CYS108 4.6 64.8 1.0
CA L:CYS145 4.6 92.5 1.0
O L:CYS148 4.7 95.9 1.0
C L:CYS120 4.8 59.2 1.0
N L:ILE121 4.9 61.5 1.0
N L:CYS145 5.0 95.0 1.0

Zinc binding site 5 out of 7 in 5lj5

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Zinc binding site 5 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1000

b:43.7
occ:1.00
 SG M:CYS81 1.9 73.0 1.0
SG M:CYS73 2.1 66.5 1.0
SG M:CYS87 2.4 90.2 1.0
NE2 M:HIS91 2.8 60.7 1.0
CB M:CYS81 3.0 75.1 1.0
CB M:CYS73 3.3 65.9 1.0
CB M:CYS87 3.4 93.1 1.0
N6 V:A35 3.6 79.0 1.0
CE1 M:HIS91 3.7 60.9 1.0
CD2 M:HIS91 3.8 60.0 1.0
N1 V:A34 4.0 0.3 1.0
CA M:CYS81 4.1 78.4 1.0
CB M:PHE75 4.3 79.8 1.0
N M:PHE76 4.4 82.7 1.0
CA M:CYS73 4.6 66.2 1.0
CB M:PHE76 4.7 79.4 1.0
CA M:CYS87 4.7 94.5 1.0
C2 V:A34 4.8 0.1 1.0
O M:TYR89 4.8 89.8 1.0
N6 V:A34 4.8 0.7 1.0
ND1 M:HIS91 4.8 60.2 1.0
C M:CYS81 4.8 81.2 1.0
CB M:TYR89 4.8 93.4 1.0
C6 V:A35 4.9 77.6 1.0
C6 V:A34 4.9 0.8 1.0
CG M:HIS91 4.9 59.8 1.0
CB M:LEU83 5.0 0.5 1.0

Zinc binding site 6 out of 7 in 5lj5

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Zinc binding site 6 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:74.7
occ:1.00
 SG N:CYS61 1.5 93.2 1.0
SG N:CYS37 1.8 84.2 1.0
SG N:CYS64 2.4 0.7 1.0
SG N:CYS34 2.7 0.9 1.0
CB N:CYS37 2.8 75.0 1.0
CB N:CYS61 3.1 82.9 1.0
CB N:CYS34 3.5 98.2 1.0
CB N:CYS64 3.6 97.3 1.0
NH2 N:ARG63 3.8 0.5 1.0
CB N:SER114 3.8 87.4 1.0
CA N:CYS37 4.1 72.0 1.0
OG N:SER114 4.1 90.5 1.0
CA N:CYS61 4.2 77.8 1.0
N N:CYS61 4.2 72.8 1.0
N N:CYS37 4.2 75.8 1.0
N N:CYS64 4.4 88.7 1.0
CA N:CYS64 4.6 91.8 1.0
CB N:LEU39 4.7 63.7 1.0
C N:CYS61 4.8 79.2 1.0
O N:CYS61 4.8 80.9 1.0
C N:CYS37 4.9 67.0 1.0
O N:LEU39 5.0 57.4 1.0

Zinc binding site 7 out of 7 in 5lj5

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Zinc binding site 7 out of 7 in the Overall Structure of the Yeast Spliceosome Immediately After Branching.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Overall Structure of the Yeast Spliceosome Immediately After Branching. within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:0.5
occ:1.00
 SG N:CYS71 1.8 0.2 1.0
SG N:CYS74 2.0 0.1 1.0
SG N:CYS13 2.2 0.5 1.0
CB N:CYS16 2.2 0.8 1.0
CB N:CYS71 2.7 0.1 1.0
CB N:CYS74 2.8 97.4 1.0
SG N:CYS16 3.0 0.1 1.0
CB N:CYS13 3.2 0.1 1.0
CA N:CYS16 3.4 0.1 1.0
N N:CYS74 3.5 90.6 1.0
N N:CYS13 3.7 0.5 1.0
CA N:CYS74 3.7 92.8 1.0
N N:CYS16 3.7 0.2 1.0
CA N:CYS13 3.9 0.7 1.0
CA N:CYS71 4.2 96.5 1.0
C N:CYS13 4.5 0.3 1.0
CB N:CYS73 4.6 88.6 1.0
C N:CYS73 4.6 88.7 1.0
O N:CYS13 4.6 0.9 1.0
C N:CYS16 4.6 0.4 1.0
C N:CYS71 4.8 89.5 1.0
N N:CYS73 4.8 82.3 1.0
C N:ILE12 4.9 0.8 1.0
C N:CYS74 4.9 92.2 1.0
CG2 N:ILE12 4.9 0.0 1.0
CA N:CYS73 5.0 86.8 1.0
CG N:GLN15 5.0 0.7 1.0

Reference:

W.P.Galej, M.E.Wilkinson, S.M.Fica, C.Oubridge, A.J.Newman, K.Nagai. Cryo-Em Structure of the Spliceosome Immediately After Branching. Nature V. 537 197 2016.
ISSN: ESSN 1476-4687
PubMed: 27459055
DOI: 10.1038/NATURE19316
Page generated: Sun Oct 27 21:02:17 2024

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