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Zinc in PDB 5mq0: Structure of A Spliceosome Remodeled For Exon Ligation

Enzymatic activity of Structure of A Spliceosome Remodeled For Exon Ligation

All present enzymatic activity of Structure of A Spliceosome Remodeled For Exon Ligation:
3.6.4.13;

Other elements in 5mq0:

The structure of Structure of A Spliceosome Remodeled For Exon Ligation also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Spliceosome Remodeled For Exon Ligation (pdb code 5mq0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Spliceosome Remodeled For Exon Ligation, PDB code: 5mq0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 1 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1000

b:80.7
occ:1.00
 SG L:CYS104 2.3 75.4 1.0
SG L:CYS148 2.3 84.4 1.0
SG L:CYS108 2.3 75.0 1.0
SG L:CYS105 2.3 94.6 1.0
CB L:CYS148 3.3 86.2 1.0
CB L:CYS108 3.3 78.8 1.0
N L:CYS105 3.4 89.2 1.0
CB L:CYS105 3.4 91.2 1.0
CB L:CYS104 3.4 80.6 1.0
CA L:CYS105 3.7 90.2 1.0
O L:CYS105 3.8 90.0 1.0
ZN L:ZN1001 4.0 83.7 1.0
ZN L:ZN1002 4.0 80.2 1.0
C L:CYS105 4.0 89.7 1.0
N L:CYS108 4.0 87.6 1.0
C L:CYS104 4.0 90.0 1.0
CA L:CYS108 4.3 82.2 1.0
CA L:CYS104 4.3 84.8 1.0
N L:CYS148 4.3 91.8 1.0
CA L:CYS148 4.4 91.3 1.0
CB L:HIS147 4.8 0.9 1.0
C L:HIS147 4.8 90.9 1.0
O L:CYS104 4.9 96.5 1.0
C L:ARG107 4.9 91.2 1.0
SG L:CYS145 4.9 99.5 1.0
N L:LEU106 5.0 87.1 1.0

Zinc binding site 2 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 2 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1001

b:83.7
occ:1.00
 SG L:CYS104 2.3 75.4 1.0
SG L:CYS150 2.3 83.9 1.0
SG L:CYS122 2.3 79.1 1.0
SG L:CYS153 2.3 0.4 1.0
ZN L:ZN1002 2.9 80.2 1.0
CB L:CYS153 3.2 0.9 1.0
CB L:CYS122 3.2 80.6 1.0
CB L:CYS150 3.3 89.3 1.0
CB L:CYS104 3.3 80.6 1.0
SG L:CYS108 3.6 75.0 1.0
CB L:CYS108 3.8 78.8 1.0
ZN L:ZN1000 4.0 80.7 1.0
CA L:CYS153 4.0 0.5 1.0
SG L:CYS148 4.2 84.4 1.0
N L:CYS104 4.3 82.9 1.0
CA L:CYS104 4.4 84.8 1.0
CA L:CYS122 4.5 82.1 1.0
N L:CYS153 4.6 0.2 1.0
CD L:ARG123 4.6 83.5 1.0
SG L:CYS120 4.7 81.6 1.0
C L:CYS122 4.7 85.2 1.0
CA L:CYS150 4.7 92.4 1.0
N L:ARG123 4.9 85.9 1.0
SG L:CYS145 4.9 99.5 1.0

Zinc binding site 3 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 3 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1002

b:80.2
occ:1.00
 SG L:CYS108 2.3 75.0 1.0
SG L:CYS122 2.3 79.1 1.0
SG L:CYS120 2.3 81.6 1.0
SG L:CYS145 2.3 99.5 1.0
ZN L:ZN1001 2.9 83.7 1.0
CB L:CYS108 3.4 78.8 1.0
CB L:CYS122 3.4 80.6 1.0
CB L:CYS145 3.4 0.5 1.0
CB L:CYS120 3.4 84.7 1.0
CB L:CYS150 3.7 89.3 1.0
SG L:CYS148 4.0 84.4 1.0
ZN L:ZN1000 4.0 80.7 1.0
SG L:CYS104 4.0 75.4 1.0
SG L:CYS150 4.1 83.9 1.0
CA L:CYS108 4.5 82.2 1.0
CA L:CYS122 4.6 82.1 1.0
N L:CYS122 4.6 80.6 1.0
O L:CYS148 4.8 99.5 1.0
CA L:CYS145 4.8 0.0 1.0
CA L:CYS120 4.8 87.0 1.0
N L:CYS148 4.9 91.8 1.0

Zinc binding site 4 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 4 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1000

b:88.4
occ:1.00
 NE2 M:HIS91 2.1 0.5 1.0
SG M:CYS73 2.3 81.6 1.0
CE1 M:HIS91 2.3 0.5 1.0
SG M:CYS87 2.3 0.8 1.0
SG M:CYS81 2.3 83.6 1.0
CB M:CYS87 3.1 0.1 1.0
CB M:CYS73 3.2 84.9 1.0
CD2 M:HIS91 3.3 0.9 1.0
CB M:CYS81 3.3 83.1 1.0
ND1 M:HIS91 3.5 97.8 1.0
CG M:HIS91 4.0 96.0 1.0
O M:TYR89 4.0 94.4 1.0
N6 6:A35 4.2 0.9 1.0
CA M:CYS87 4.5 0.8 1.0
CA M:CYS73 4.6 87.2 1.0
CA M:CYS81 4.7 84.0 1.0
CB M:TYR89 4.8 0.5 1.0
O M:GLY84 4.8 0.0 1.0
CB M:LEU83 4.9 0.6 1.0
C M:TYR89 4.9 97.0 1.0
O M:LEU90 4.9 96.5 1.0
N M:PHE76 4.9 0.6 1.0

Zinc binding site 5 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 5 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:85.2
occ:1.00
 SG N:CYS34 2.3 79.2 1.0
SG N:CYS64 2.3 0.8 1.0
SG N:CYS37 2.3 94.6 1.0
SG N:CYS61 2.3 90.5 1.0
CB N:CYS34 3.2 86.1 1.0
CB N:CYS64 3.3 98.8 1.0
CB N:CYS61 3.4 86.4 1.0
CB N:CYS37 3.4 94.2 1.0
N N:CYS37 3.5 85.0 1.0
N N:CYS61 3.8 75.3 1.0
CA N:CYS37 4.0 86.5 1.0
OG N:SER114 4.1 93.2 1.0
CB N:ILE36 4.2 78.5 1.0
CA N:CYS61 4.2 81.5 1.0
CA N:CYS64 4.5 97.0 1.0
C N:ILE36 4.5 82.7 1.0
N N:ILE36 4.6 78.9 1.0
CA N:CYS34 4.6 88.3 1.0
CA N:ILE36 4.6 79.5 1.0
C N:CYS37 4.7 80.6 1.0
N N:CYS64 4.7 97.2 1.0
CB N:SER114 4.8 98.5 1.0
CG2 N:ILE36 4.8 79.8 1.0
C N:ILE60 4.9 70.3 1.0
C N:CYS61 4.9 82.5 1.0
CB N:LEU39 4.9 85.8 1.0
O N:CYS61 4.9 82.1 1.0
CB N:ILE60 4.9 71.9 1.0

Zinc binding site 6 out of 6 in 5mq0

Go back to Zinc Binding Sites List in 5mq0
Zinc binding site 6 out of 6 in the Structure of A Spliceosome Remodeled For Exon Ligation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Spliceosome Remodeled For Exon Ligation within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:0.1
occ:1.00
 SG N:CYS71 2.3 0.3 1.0
SG N:CYS16 2.3 0.8 1.0
SG N:CYS74 2.3 0.1 1.0
SG N:CYS13 2.3 0.9 1.0
CB N:CYS16 2.7 0.8 1.0
CB N:CYS71 3.3 0.6 1.0
CB N:CYS74 3.4 0.5 1.0
CB N:CYS13 3.5 0.7 1.0
N N:CYS13 3.5 0.2 1.0
N N:CYS74 3.6 0.2 1.0
CA N:CYS13 3.9 1.0 1.0
CG2 N:ILE12 4.0 0.3 1.0
CB N:CYS73 4.0 0.9 1.0
CA N:CYS74 4.1 0.3 1.0
CA N:CYS16 4.3 0.4 1.0
C N:CYS13 4.4 0.6 1.0
O N:CYS13 4.4 0.9 1.0
C N:CYS73 4.4 0.5 1.0
N N:CYS73 4.5 0.5 1.0
CA N:CYS73 4.6 0.7 1.0
C N:ILE12 4.6 0.0 1.0
CA N:CYS71 4.6 0.8 1.0
CA N:ILE12 4.7 0.0 1.0
N N:CYS16 4.8 0.0 1.0

Reference:

S.M.Fica, C.Oubridge, W.P.Galej, M.E.Wilkinson, X.C.Bai, A.J.Newman, K.Nagai. Structure of A Spliceosome Remodelled For Exon Ligation. Nature V. 542 377 2017.
ISSN: ESSN 1476-4687
PubMed: 28076345
DOI: 10.1038/NATURE21078
Page generated: Sun Oct 27 22:13:23 2024

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