Zinc in PDB 6gym: Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)

All present enzymatic activity of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist):
2.7.7.6; 3.6.4.12;

The structure of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Iron	(Fe)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) (pdb code 6gym). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist), PDB code: 6gym:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 3:Zn401 b:0.0 occ:1.00 N 3:CYS16 2.3 0.0 1.0 SG 3:CYS16 2.5 0.0 1.0 CB 3:ILE15 2.6 0.0 1.0 SG 3:CYS13 2.6 0.0 1.0 C 3:ILE15 2.7 0.0 1.0 SG 3:CYS42 2.8 0.0 1.0 CB 3:CYS16 2.9 0.0 1.0 CA 3:ILE15 3.1 0.0 1.0 CA 3:CYS16 3.1 0.0 1.0 CG2 3:ILE15 3.2 0.0 1.0 NZ W:LYS110 3.4 0.0 1.0 N 3:ILE15 3.5 0.0 1.0 O 3:ILE15 3.6 0.0 1.0 CG1 3:ILE15 3.8 0.0 1.0 CB 3:CYS13 4.1 0.0 1.0 SG 3:CYS39 4.2 0.0 1.0 C 3:CYS16 4.2 0.0 1.0 CB 3:CYS42 4.4 0.0 1.0 CD1 3:ILE15 4.4 0.0 1.0 O 3:CYS16 4.6 0.0 1.0 CE W:LYS110 4.6 0.0 1.0 C 3:PRO14 4.9 0.0 1.0

Zinc binding site 2 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 3:Zn402 b:0.0 occ:1.00 ND1 3:HIS36 2.4 0.0 1.0 CE1 3:HIS36 2.4 0.0 1.0 SG 3:CYS54 2.5 0.0 1.0 SG 3:CYS59 2.6 0.0 1.0 CB 3:CYS34 2.9 0.0 1.0 SG 3:CYS34 3.0 0.0 1.0 CE 3:LYS61 3.4 0.0 1.0 CA 3:CYS34 3.5 0.0 1.0 NE2 3:HIS36 3.7 0.0 1.0 CB 3:CYS59 3.7 0.0 1.0 CG 3:HIS36 3.7 0.0 1.0 CB 3:LYS61 3.8 0.0 1.0 O 3:LYS61 3.8 0.0 1.0 NZ 3:LYS61 3.9 0.0 1.0 O 3:CYS34 4.0 0.0 1.0 C 3:CYS34 4.1 0.0 1.0 CB 3:CYS54 4.2 0.0 1.0 CD2 3:HIS36 4.3 0.0 1.0 CD 3:LYS61 4.4 0.0 1.0 N 3:LYS61 4.5 0.0 1.0 CA 3:LYS61 4.5 0.0 1.0 CG 3:LYS61 4.6 0.0 1.0 C 3:LYS61 4.6 0.0 1.0 N 3:CYS54 4.6 0.0 1.0 CB 3:HIS36 4.6 0.0 1.0 O 3:CYS54 4.7 0.0 1.0 O 3:GLU33 4.7 0.0 1.0 N 3:CYS34 4.7 0.0 1.0 CA 3:CYS54 4.9 0.0 1.0 CB 3:TYR56 5.0 0.0 1.0

Zinc binding site 3 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn401 b:0.0 occ:1.00 SG 4:CYS289 2.5 0.0 1.0 CB 4:SER290 2.6 0.0 1.0 SG 4:CYS308 2.6 0.0 1.0 SG 4:CYS305 2.7 0.0 1.0 N 4:SER290 2.9 0.0 1.0 CA 4:SER290 3.1 0.0 1.0 CB 4:SER310 3.4 0.0 1.0 O 4:SER290 3.5 0.0 1.0 C 4:SER290 3.7 0.0 1.0 CB 4:CYS305 3.7 0.0 1.0 SG 4:CYS292 3.7 0.0 1.0 CB 4:CYS289 3.9 0.0 1.0 C 4:CYS289 4.0 0.0 1.0 CB 4:CYS308 4.4 0.0 1.0 CB 4:CYS292 4.4 0.0 1.0 CA 4:CYS289 4.5 0.0 1.0 CA 4:SER310 4.6 0.0 1.0 N 4:SER310 4.8 0.0 1.0 N 4:CYS308 4.9 0.0 1.0 N 4:VAL291 4.9 0.0 1.0 CA 4:CYS308 5.0 0.0 1.0

Zinc binding site 4 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn501 b:0.0 occ:1.00 SG 6:CYS366 2.6 0.0 1.0 SG 6:CYS352 2.6 0.0 1.0 SG 6:CYS363 2.6 0.0 1.0 SG 6:CYS349 2.6 0.0 1.0 CB 6:CYS363 2.9 0.0 1.0 CB 6:CYS349 3.4 0.0 1.0 N 6:CYS366 3.6 0.0 1.0 CB 6:CYS366 3.7 0.0 1.0 CB 6:CYS352 4.0 0.0 1.0 CA 6:CYS363 4.1 0.0 1.0 CA 6:CYS366 4.2 0.0 1.0 CB 6:CYS365 4.3 0.0 1.0 C 6:CYS365 4.3 0.0 1.0 C 6:CYS363 4.3 0.0 1.0 N 6:CYS365 4.3 0.0 1.0 O 6:CYS363 4.3 0.0 1.0 N 6:CYS352 4.4 0.0 1.0 CA 6:CYS365 4.5 0.0 1.0 C 6:CYS366 4.7 0.0 1.0 N 6:ASP367 4.7 0.0 1.0 N 6:LEU368 4.7 0.0 1.0 CB 6:LEU368 4.7 0.0 1.0 O 6:LEU368 4.7 0.0 1.0 CA 6:CYS352 4.8 0.0 1.0 CA 6:CYS349 4.8 0.0 1.0 N 6:CYS363 4.9 0.0 1.0 N 6:PRO364 4.9 0.0 1.0

Zinc binding site 5 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn502 b:0.0 occ:1.00 SG 6:CYS406 2.6 0.0 1.0 SG 6:CYS403 2.6 0.0 1.0 SG 6:CYS437 2.6 0.0 1.0 CB 6:CYS403 3.0 0.0 1.0 SG 6:CYS440 3.0 0.0 1.0 CB 6:SER408 3.5 0.0 1.0 CB 6:CYS440 4.0 0.0 1.0 CB 6:CYS437 4.0 0.0 1.0 N 6:SER408 4.2 0.0 1.0 CB 6:CYS406 4.2 0.0 1.0 CA 6:SER408 4.4 0.0 1.0 N 6:CYS406 4.4 0.0 1.0 CA 6:CYS403 4.5 0.0 1.0 N 6:GLN407 4.5 0.0 1.0 N 6:CYS437 4.6 0.0 1.0 N 6:CYS440 4.6 0.0 1.0 CA 6:CYS406 4.7 0.0 1.0 C 6:GLN407 4.8 0.0 1.0 C 6:CYS406 4.8 0.0 1.0 CA 6:CYS437 4.9 0.0 1.0 CA 6:CYS440 5.0 0.0 1.0

Zinc binding site 6 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


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 Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn503 b:0.0 occ:1.00 SG 6:CYS451 2.6 0.0 1.0 SG 6:CYS454 2.6 0.0 1.0 SG 6:CYS432 2.6 0.0 1.0 SG 6:CYS429 2.8 0.0 1.0 CB 6:CYS451 2.9 0.0 1.0 CB 6:ASP431 3.6 0.0 1.0 CB 6:CYS429 3.8 0.0 1.0 N 6:CYS454 3.8 0.0 1.0 CB 6:CYS432 3.8 0.0 1.0 N 6:CYS432 4.0 0.0 1.0 CB 6:CYS454 4.1 0.0 1.0 C 6:ASP431 4.2 0.0 1.0 C 6:GLY453 4.2 0.0 1.0 CA 6:CYS451 4.2 0.0 1.0 CA 6:CYS454 4.2 0.0 1.0 O 6:CYS451 4.2 0.0 1.0 CA 6:ASP431 4.3 0.0 1.0 C 6:CYS451 4.4 0.0 1.0 N 6:ASP431 4.5 0.0 1.0 N 6:GLY453 4.5 0.0 1.0 CA 6:GLY453 4.5 0.0 1.0 CA 6:CYS432 4.5 0.0 1.0 O 6:ASN450 4.6 0.0 1.0 O 6:ASP431 4.8 0.0 1.0 O 6:GLY453 4.9 0.0 1.0 O 6:CYS429 5.0 0.0 1.0

Zinc binding site 7 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:0.0 occ:1.00 SG A:CYS167 2.5 0.0 1.0 SG A:CYS110 2.5 0.0 1.0 SG A:CYS107 2.5 0.0 1.0 SG A:CYS148 2.6 0.0 1.0 CB A:CYS107 3.0 0.0 1.0 CB A:CYS167 3.0 0.0 1.0 CB A:CYS148 3.2 0.0 1.0 CB A:CYS110 3.8 0.0 1.0 N A:CYS110 4.2 0.0 1.0 NE2 A:GLN171 4.2 0.0 1.0 N A:GLY168 4.4 0.0 1.0 CA A:CYS167 4.4 0.0 1.0 CA A:CYS107 4.4 0.0 1.0 O A:GLY166 4.5 0.0 1.0 CA A:CYS110 4.5 0.0 1.0 CA A:CYS148 4.7 0.0 1.0 NH2 A:ARG164 4.7 0.0 1.0 N A:GLY111 4.7 0.0 1.0 C A:CYS167 4.8 0.0 1.0 N A:LYS112 4.9 0.0 1.0 C A:CYS110 5.0 0.0 1.0 N A:ASN169 5.0 0.0 1.0

Zinc binding site 8 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:0.0 occ:1.00 NE2 A:HIS80 2.3 0.0 1.0 SG A:CYS77 2.5 0.0 1.0 CB A:CYS70 2.5 0.0 1.0 SG A:CYS67 2.8 0.0 1.0 CE1 A:HIS80 3.0 0.0 1.0 CD2 A:HIS80 3.0 0.0 1.0 CA A:GLY59 3.1 0.0 1.0 SG A:CYS70 3.3 0.0 1.0 N A:GLY59 3.7 0.0 1.0 CA A:CYS70 3.8 0.0 1.0 CB A:CYS77 3.8 0.0 1.0 ND1 A:HIS80 3.9 0.0 1.0 N A:CYS70 3.9 0.0 1.0 CG A:HIS80 3.9 0.0 1.0 CA A:GLY79 4.0 0.0 1.0 CB A:CYS67 4.0 0.0 1.0 N A:GLY79 4.1 0.0 1.0 C A:GLY79 4.2 0.0 1.0 C A:LEU58 4.3 0.0 1.0 O A:LEU58 4.3 0.0 1.0 C A:GLY59 4.4 0.0 1.0 O A:GLY79 4.5 0.0 1.0 N A:SER60 4.5 0.0 1.0 N A:HIS80 4.7 0.0 1.0 C A:CYS70 4.8 0.0 1.0 CA A:CYS77 4.9 0.0 1.0

Zinc binding site 9 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:0.0 occ:1.00 SG B:CYS1163 2.5 0.0 1.0 SG B:CYS1182 2.5 0.0 1.0 SG B:CYS1166 2.6 0.0 1.0 CB B:CYS1185 2.6 0.0 1.0 CB B:CYS1163 2.7 0.0 1.0 SG B:CYS1185 2.9 0.0 1.0 CB B:CYS1182 3.6 0.0 1.0 CA B:CYS1185 3.9 0.0 1.0 N B:CYS1185 4.1 0.0 1.0 O B:CYS1166 4.1 0.0 1.0 N B:CYS1166 4.2 0.0 1.0 CB B:CYS1166 4.2 0.0 1.0 CA B:CYS1163 4.3 0.0 1.0 O B:LYS1183 4.5 0.0 1.0 CA B:CYS1166 4.6 0.0 1.0 O B:CYS1182 4.8 0.0 1.0 CB B:ILE1165 4.8 0.0 1.0 C B:CYS1166 4.8 0.0 1.0 CA B:CYS1182 4.9 0.0 1.0 C B:CYS1185 4.9 0.0 1.0 C B:CYS1182 4.9 0.0 1.0 C B:CYS1163 4.9 0.0 1.0 N B:ILE1165 5.0 0.0 1.0

Zinc binding site 10 out of 16 in the Structure of A Yeast Closed Complex with Distorted Dna (Ccdist)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of A Yeast Closed Complex with Distorted Dna (Ccdist) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:0.0 occ:1.00 N C:CYS92 2.2 0.0 1.0 C C:HIS91 2.5 0.0 1.0 SG C:CYS95 2.5 0.0 1.0 SG C:CYS88 2.5 0.0 1.0 CB C:CYS92 2.7 0.0 1.0 SG C:CYS92 2.7 0.0 1.0 SG C:CYS86 2.8 0.0 1.0 CA C:CYS92 2.9 0.0 1.0 CA C:HIS91 3.1 0.0 1.0 O C:HIS91 3.1 0.0 1.0 C C:CYS92 3.8 0.0 1.0 CB C:CYS88 3.9 0.0 1.0 N C:HIS91 3.9 0.0 1.0 CB C:CYS86 4.0 0.0 1.0 O C:CYS92 4.1 0.0 1.0 CB C:CYS95 4.1 0.0 1.0 CB C:HIS91 4.3 0.0 1.0 O C:CYS88 4.5 0.0 1.0 C C:ASP90 4.6 0.0 1.0 O C:ASP90 4.7 0.0 1.0 O C:GLU89 4.7 0.0 1.0 C C:CYS88 4.7 0.0 1.0 N C:ASP93 4.8 0.0 1.0 CA C:CYS88 4.8 0.0 1.0 N C:CYS95 4.9 0.0 1.0

C.Dienemann, B.Schwalb, S.Schilbach, P.Cramer. Promoter Distortion and Opening in the Rna Polymerase II Cleft. Mol. Cell V. 73 97 2019.
ISSN: ISSN 1097-4164
PubMed: 30472190
DOI: 10.1016/J.MOLCEL.2018.10.014