Zinc in PDB 7vpx: The Cryo-Em Structure of the Human Pre-A Complex

All present enzymatic activity of The Cryo-Em Structure of the Human Pre-A Complex:
3.6.4.13;

The binding sites of Zinc atom in the The Cryo-Em Structure of the Human Pre-A Complex (pdb code 7vpx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Cryo-Em Structure of the Human Pre-A Complex, PDB code: 7vpx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:197.7 occ:1.00 NE2 B:HIS72 1.9 201.5 1.0 SG B:CYS56 2.2 166.3 1.0 CD2 B:HIS72 2.3 201.5 1.0 SG B:CYS59 2.5 166.7 1.0 ND1 B:HIS78 2.5 179.7 1.0 CB B:CYS56 2.7 166.3 1.0 CE1 B:HIS78 2.8 179.7 1.0 CB B:CYS59 3.0 166.7 1.0 CE1 B:HIS72 3.2 201.5 1.0 OG1 B:THR61 3.4 173.4 1.0 CG B:HIS72 3.7 201.5 1.0 CG B:HIS78 3.8 179.7 1.0 N B:CYS59 3.9 166.7 1.0 ND1 B:HIS72 4.0 201.5 1.0 CA B:CYS59 4.1 166.7 1.0 NE2 B:HIS78 4.1 179.7 1.0 CE1 B:TYR69 4.1 185.6 1.0 CA B:CYS56 4.2 166.3 1.0 NE2 B:HIS63 4.3 184.6 1.0 CB B:HIS78 4.5 179.7 1.0 CD2 B:HIS78 4.6 179.7 1.0 CD1 B:TYR69 4.7 185.6 1.0 O B:CYS56 4.7 166.3 1.0 C B:CYS56 4.7 166.3 1.0 CB B:THR61 4.7 173.4 1.0 CE1 B:HIS63 4.9 184.6 1.0 CB B:HIS72 4.9 201.5 1.0 C B:CYS59 5.0 166.7 1.0 C B:LEU58 5.0 162.5 1.0

Zinc binding site 2 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:104.8 occ:1.00 NE2 C:HIS425 1.9 91.5 1.0 ND1 C:HIS431 2.3 99.3 1.0 SG C:CYS408 2.5 93.5 1.0 CE1 C:HIS431 2.6 99.3 1.0 CE1 C:HIS425 2.9 91.5 1.0 CB C:CYS408 2.9 93.5 1.0 CD2 C:HIS425 2.9 91.5 1.0 CB C:CYS411 3.3 98.8 1.0 SG C:CYS411 3.4 98.8 1.0 CG C:HIS431 3.6 99.3 1.0 NE2 C:HIS431 3.9 99.3 1.0 ND1 C:HIS425 4.0 91.5 1.0 CG C:HIS425 4.0 91.5 1.0 N C:CYS411 4.0 98.8 1.0 CE2 C:TYR416 4.2 93.9 1.0 CB C:HIS431 4.3 99.3 1.0 CA C:CYS411 4.3 98.8 1.0 CD2 C:HIS431 4.3 99.3 1.0 OH C:TYR416 4.4 93.9 1.0 CA C:CYS408 4.4 93.5 1.0 CE1 C:PHE426 4.5 88.5 1.0 CZ C:TYR416 4.7 93.9 1.0 CD1 C:PHE426 4.7 88.5 1.0 CB C:ILE410 4.7 94.2 1.0 C C:ILE410 4.7 94.2 1.0 C C:CYS408 4.9 93.5 1.0 O C:CYS408 4.9 93.5 1.0 CA C:HIS431 4.9 99.3 1.0

Zinc binding site 3 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn201 b:136.1 occ:1.00 NE2 N:HIS24 1.8 128.6 1.0 ND1 N:HIS30 2.0 152.4 1.0 SG N:CYS9 2.3 127.4 1.0 SG N:CYS6 2.5 175.8 1.0 CE1 N:HIS30 2.6 144.9 1.0 CD2 N:HIS24 2.8 127.0 1.0 CE1 N:HIS24 2.8 128.0 1.0 CG N:HIS30 3.0 154.0 1.0 CB N:CYS6 3.5 158.4 1.0 CB N:HIS30 3.6 165.5 1.0 CB N:CYS9 3.6 128.5 1.0 NE2 N:HIS30 3.6 140.0 1.0 CD2 N:HIS30 3.8 140.1 1.0 ND1 N:HIS24 3.9 130.0 1.0 CG N:HIS24 3.9 131.1 1.0 CA N:HIS30 4.2 175.2 1.0 N N:CYS9 4.2 132.7 1.0 CA N:CYS9 4.5 131.3 1.0 CB N:TYR8 4.7 136.4 1.0 CA N:CYS6 4.8 149.5 1.0 O N:HIS24 4.9 129.0 1.0

Zinc binding site 4 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn201 b:109.8 occ:1.00 SG 6:CYS46 2.0 86.3 1.0 SG 6:CYS49 2.2 99.0 1.0 SG 6:CYS11 2.4 81.4 1.0 SG 6:CYS85 2.8 77.0 1.0 CB 6:CYS49 3.1 99.0 1.0 CB 6:CYS46 3.2 86.3 1.0 CB 6:CYS11 3.3 81.4 1.0 CB 6:CYS85 3.6 77.0 1.0 N 6:CYS49 4.0 99.0 1.0 CA 6:CYS49 4.1 99.0 1.0 N 6:CYS46 4.2 86.3 1.0 CA 6:CYS46 4.2 86.3 1.0 CB 6:LYS87 4.5 82.0 1.0 C 6:CYS46 4.7 86.3 1.0 CA 6:CYS11 4.8 81.4 1.0 O 6:CYS46 4.8 86.3 1.0

Zinc binding site 5 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn202 b:134.7 occ:1.00 SG 6:CYS75 2.3 80.8 1.0 SG 6:CYS30 2.3 93.8 1.0 SG 6:CYS33 2.6 90.5 1.0 SG 6:CYS72 2.7 84.6 1.0 CB 6:CYS30 2.9 93.8 1.0 CB 6:CYS75 3.3 80.8 1.0 CB 6:CYS72 3.4 84.6 1.0 CB 6:CYS33 3.5 90.5 1.0 N 6:CYS33 3.5 90.5 1.0 N 6:CYS72 3.6 84.6 1.0 CA 6:CYS72 4.1 84.6 1.0 CA 6:CYS33 4.1 90.5 1.0 CB 6:ILE32 4.1 81.7 1.0 N 6:CYS75 4.3 80.8 1.0 CA 6:CYS75 4.3 80.8 1.0 CA 6:CYS30 4.4 93.8 1.0 N 6:ILE32 4.5 81.7 1.0 C 6:ILE32 4.5 81.7 1.0 CA 6:ILE32 4.6 81.7 1.0 C 6:TYR71 4.7 78.8 1.0 C 6:CYS72 4.7 84.6 1.0 O 6:CYS72 4.8 84.6 1.0 CG2 6:ILE32 4.8 81.7 1.0 C 6:CYS33 4.8 90.5 1.0 C 6:CYS30 4.9 93.8 1.0 CA 6:TYR71 5.0 78.8 1.0

Zinc binding site 6 out of 6 in the The Cryo-Em Structure of the Human Pre-A Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Cryo-Em Structure of the Human Pre-A Complex within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn203 b:129.3 occ:1.00 SG 6:CYS58 2.2 109.3 1.0 SG 6:CYS61 2.4 114.8 1.0 SG 6:CYS23 2.6 106.1 1.0 CB 6:CYS58 3.0 109.3 1.0 CB 6:CYS23 3.2 106.1 1.0 CB 6:CYS61 3.2 114.8 1.0 N 6:CYS61 3.3 114.8 1.0 CA 6:CYS61 3.5 114.8 1.0 C 6:CYS61 3.9 114.8 1.0 O 6:CYS61 4.1 114.8 1.0 N 6:CYS23 4.1 106.1 1.0 CA 6:CYS23 4.3 106.1 1.0 C 6:ILE60 4.4 100.3 1.0 CA 6:CYS58 4.4 109.3 1.0 CB 6:ILE60 4.5 100.3 1.0 N 6:GLY62 4.5 114.9 1.0 N 6:GLY63 4.6 112.9 1.0 N 6:ILE60 4.7 100.3 1.0 CD 6:LYS25 4.8 112.6 1.0 CA 6:ILE60 4.8 100.3 1.0 C 6:CYS58 4.9 109.3 1.0

X.Zhang, X.Zhan, Y.Shi. Mechanism For Branch Site Recognition and Proofreading During Prespliceosome Assembly To Be Published.