Zinc in PDB 5lj3: Structure of the Core of the Yeast Spliceosome Immediately After Branching

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of the Core of the Yeast Spliceosome Immediately After Branching (pdb code 5lj3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of the Core of the Yeast Spliceosome Immediately After Branching, PDB code: 5lj3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of the Core 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 Structure of the Core 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 SG D:CYS51 2.5 0.5 1.0 CB D:CYS88 2.6 0.3 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 the Structure of the Core 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 Structure of the Core 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 the Structure of the Core 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 Structure of the Core 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 the Structure of the Core 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 Structure of the Core 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 the Structure of the Core 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 Structure of the Core 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 the Structure of the Core 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 Structure of the Core 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: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 SG N:CYS64 3.6 0.7 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 the Structure of the Core 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 Structure of the Core 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

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