Zinc in PDB 5gmk: Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution

The structure of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution (pdb code 5gmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution, PDB code: 5gmk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn400 b:30.0 occ:1.00 SG Q:CYS71 2.3 0.0 1.0 SG Q:CYS74 2.3 0.0 1.0 SG Q:CYS13 2.3 0.0 1.0 SG Q:CYS73 2.3 0.0 1.0 CB Q:CYS13 3.0 0.0 1.0 CB Q:CYS74 3.2 0.0 1.0 N Q:CYS74 3.2 0.0 1.0 CB Q:CYS16 3.5 0.0 1.0 N Q:CYS13 3.5 0.0 1.0 CB Q:CYS71 3.7 0.0 1.0 CA Q:CYS74 3.7 0.0 1.0 CA Q:CYS13 3.8 0.0 1.0 CB Q:CYS73 3.9 0.0 1.0 C Q:CYS73 4.1 0.0 1.0 N Q:CYS16 4.3 0.0 1.0 CA Q:CYS73 4.4 0.0 1.0 CG2 Q:ILE12 4.4 0.0 1.0 N Q:CYS73 4.4 0.0 1.0 CA Q:CYS16 4.4 0.0 1.0 SG Q:CYS16 4.6 0.0 1.0 C Q:CYS13 4.6 0.0 1.0 O Q:CYS13 4.7 0.0 1.0 C Q:ILE12 4.7 0.0 1.0 CA Q:CYS71 4.9 0.0 1.0

Zinc binding site 2 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn401 b:30.0 occ:1.00 SG Q:CYS34 2.3 0.0 1.0 SG Q:CYS37 2.3 0.0 1.0 SG Q:CYS64 2.3 0.0 1.0 SG Q:CYS61 2.3 0.0 1.0 CB Q:CYS61 2.9 0.0 1.0 CB Q:CYS37 2.9 0.0 1.0 CB Q:CYS34 3.2 0.0 1.0 CB Q:CYS64 3.4 0.0 1.0 N Q:CYS61 3.7 0.0 1.0 CA Q:CYS61 3.8 0.0 1.0 N Q:CYS37 4.0 0.0 1.0 CA Q:CYS37 4.0 0.0 1.0 CA Q:CYS34 4.5 0.0 1.0 N Q:CYS64 4.5 0.0 1.0 CA Q:CYS64 4.6 0.0 1.0 N Q:CYS34 4.7 0.0 1.0 O Q:LEU39 4.8 0.0 1.0 C Q:CYS37 4.8 0.0 1.0 C Q:ILE60 4.8 0.0 1.0 N Q:THR38 4.8 0.0 1.0 N Q:LEU39 4.9 0.0 1.0

Zinc binding site 3 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn400 b:30.0 occ:1.00 CE1 R:HIS91 2.2 0.0 1.0 SG R:CYS81 2.3 0.0 1.0 SG R:CYS73 2.3 0.0 1.0 NE2 R:HIS91 2.3 0.0 1.0 SG R:CYS87 2.3 0.0 1.0 CB R:CYS81 3.0 0.0 1.0 CB R:CYS73 3.2 0.0 1.0 CB R:CYS87 3.3 0.0 1.0 ND1 R:HIS91 3.5 0.0 1.0 CD2 R:HIS91 3.6 0.0 1.0 CG R:HIS91 4.2 0.0 1.0 N6 E:A35 4.4 0.4 1.0 N R:PHE76 4.5 0.0 1.0 CB R:PHE76 4.5 0.0 1.0 CA R:CYS81 4.5 0.0 1.0 CA R:CYS73 4.6 0.0 1.0 CA R:CYS87 4.7 0.0 1.0 O R:TYR89 4.9 0.0 1.0 CA R:PHE76 5.0 0.0 1.0

Zinc binding site 4 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn1000 b:0.0 occ:1.00 CB T:CYS104 2.2 0.0 1.0 SG T:CYS148 2.3 0.0 1.0 SG T:CYS105 2.3 0.0 1.0 SG T:CYS108 2.3 0.0 1.0 SG T:CYS104 2.3 0.0 1.0 CB T:CYS148 3.1 0.0 1.0 CB T:CYS105 3.3 0.0 1.0 CA T:CYS104 3.6 0.0 1.0 N T:CYS105 3.7 0.0 1.0 ZN T:ZN1002 3.8 0.0 1.0 C T:CYS104 3.9 0.0 1.0 ZN T:ZN1001 3.9 0.0 1.0 CB T:CYS108 3.9 0.0 1.0 CA T:CYS105 4.2 0.0 1.0 SG T:CYS122 4.3 0.0 1.0 CA T:CYS148 4.4 0.0 1.0 SG T:CYS145 4.6 0.0 1.0 N T:CYS104 4.6 0.0 1.0 O T:CYS104 4.7 0.0 1.0 CB T:CYS150 4.7 0.0 1.0 SG T:CYS153 4.8 0.0 1.0 N T:CYS108 4.9 0.0 1.0 CA T:CYS108 4.9 0.0 1.0

Zinc binding site 5 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn1001 b:0.0 occ:1.00 SG T:CYS153 2.3 0.0 1.0 CB T:CYS150 2.3 0.0 1.0 SG T:CYS150 2.3 0.0 1.0 SG T:CYS122 2.3 0.0 1.0 SG T:CYS104 2.3 0.0 1.0 CB T:CYS104 3.2 0.0 1.0 CB T:CYS153 3.5 0.0 1.0 CA T:CYS150 3.8 0.0 1.0 O T:CYS122 3.8 0.0 1.0 CB T:CYS122 3.8 0.0 1.0 ZN T:ZN1000 3.9 0.0 1.0 N T:CYS153 3.9 0.0 1.0 CA T:CYS153 4.1 0.0 1.0 ZN T:ZN1002 4.1 0.0 1.0 CA T:CYS104 4.2 0.0 1.0 N T:CYS104 4.2 0.0 1.0 SG T:CYS108 4.3 0.0 1.0 C T:CYS122 4.4 0.0 1.0 CA T:CYS122 4.5 0.0 1.0 C T:CYS150 4.5 0.0 1.0 N T:CYS150 4.6 0.0 1.0 CG n:PRO68 4.6 0.7 1.0 N T:ARG151 4.9 0.0 1.0 CB T:CYS108 5.0 0.0 1.0 CB T:CYS145 5.0 0.0 1.0

Zinc binding site 6 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn1002 b:0.0 occ:1.00 SG T:CYS145 2.3 0.0 1.0 SG T:CYS122 2.3 0.0 1.0 SG T:CYS108 2.3 0.0 1.0 SG T:CYS120 2.3 0.0 1.0 CB T:CYS122 2.8 0.0 1.0 CB T:CYS108 3.0 0.0 1.0 CB T:CYS120 3.2 0.0 1.0 CB T:CYS145 3.4 0.0 1.0 ZN T:ZN1000 3.8 0.0 1.0 CA T:CYS108 3.8 0.0 1.0 SG T:CYS148 3.9 0.0 1.0 ZN T:ZN1001 4.1 0.0 1.0 CA T:CYS122 4.3 0.0 1.0 SG T:CYS104 4.6 0.0 1.0 CD2 T:HIS147 4.6 0.0 1.0 CA T:CYS120 4.7 0.0 1.0 N T:CYS108 4.7 0.0 1.0 CA T:CYS145 4.8 0.0 1.0 N T:CYS122 4.8 0.0 1.0 C T:CYS108 4.9 0.0 1.0 CB T:CYS148 4.9 0.0 1.0 C T:CYS122 4.9 0.0 1.0 O T:CYS108 4.9 0.0 1.0 CB T:CYS104 5.0 0.0 1.0 CB T:CYS150 5.0 0.0 1.0

Zinc binding site 7 out of 7 in the Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the Catalytic Step I Spliceosome (C Complex) at 3.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn300 b:30.0 occ:1.00 SG F:CYS91 2.3 20.0 1.0 SG F:CYS54 2.3 20.0 1.0 SG F:CYS88 2.3 20.0 1.0 SG F:CYS51 2.3 20.0 1.0 CB F:CYS88 3.3 20.0 1.0 CB F:CYS51 3.4 20.0 1.0 CB F:CYS91 3.7 20.0 1.0 CB F:CYS54 3.7 20.0 1.0 N F:CYS54 3.8 8.8 1.0 N F:CYS91 4.0 10.3 1.0 CA F:CYS54 4.3 9.4 1.0 CB F:GLU56 4.3 20.0 1.0 CA F:CYS91 4.4 10.8 1.0 CB F:GLU53 4.4 20.0 1.0 CB F:ARG90 4.6 20.0 1.0 O F:CYS91 4.7 9.8 1.0 CA F:CYS88 4.7 9.4 1.0 N F:GLU56 4.8 9.3 1.0 C F:GLU53 4.8 9.1 1.0 C F:CYS54 4.8 8.7 1.0 CA F:CYS51 4.8 6.2 1.0 C F:CYS91 4.8 10.0 1.0 OE1 F:GLU53 4.8 20.0 1.0 CB F:ASN93 4.9 20.0 1.0 N F:GLU53 4.9 7.8 1.0 N F:ARG90 4.9 9.3 1.0 N F:ASN55 5.0 8.2 1.0 CA F:GLU53 5.0 8.1 1.0 C F:ARG90 5.0 11.6 1.0

R.Wan, C.Yan, R.Bai, G.Huang, Y.Shi. Structure of A Yeast Catalytic Step I Spliceosome at 3.4 Angstrom Resolution Science V. 353 895 2016.
ISSN: ESSN 1095-9203
PubMed: 27445308
DOI: 10.1126/SCIENCE.AAG2235