Zinc in PDB 7qcd: Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure)

All present enzymatic activity of Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure):
2.3.2.27;

The binding sites of Zinc atom in the Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure) (pdb code 7qcd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure), PDB code: 7qcd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:50.0 occ:1.00 OG C:SER197 2.1 50.0 1.0 N C:CYS200 2.2 50.0 1.0 SG C:CYS200 2.3 50.0 1.0 CB C:SER197 2.7 50.0 1.0 CB C:CYS200 2.9 50.0 1.0 CA C:CYS200 3.0 50.0 1.0 C C:LYS199 3.0 50.0 1.0 CB C:LYS199 3.1 50.0 1.0 N C:LYS199 3.2 50.0 1.0 CA C:LYS199 3.2 50.0 1.0 C C:CYS200 3.8 50.0 1.0 N C:ASN201 3.8 50.0 1.0 C C:SER197 3.8 50.0 1.0 CA C:SER197 3.9 50.0 1.0 O C:SER197 3.9 50.0 1.0 CG C:LYS199 4.0 50.0 1.0 CG1 C:VAL230 4.1 50.0 1.0 O C:LYS199 4.1 50.0 1.0 CB C:GLN228 4.2 50.0 1.0 CG C:GLN228 4.2 50.0 1.0 C C:ARG198 4.4 50.0 1.0 N C:ARG198 4.4 50.0 1.0 CD C:LYS199 4.5 50.0 1.0 N C:HIS202 4.8 50.0 1.0 O C:CYS200 4.8 50.0 1.0 CD C:GLN228 4.9 50.0 1.0 N C:SER197 4.9 50.0 1.0

Zinc binding site 2 out of 3 in the Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1000 b:50.0 occ:1.00 CB D:CYS271 1.0 50.0 1.0 SG D:CYS271 2.3 50.0 1.0 SG D:CYS274 2.3 50.0 1.0 ND1 D:HIS306 2.3 50.0 1.0 CA D:CYS271 2.4 50.0 1.0 CE1 D:HIS306 2.6 50.0 1.0 N D:LYS276 2.7 50.0 1.0 O D:LYS276 2.8 50.0 1.0 N D:CYS271 2.9 50.0 1.0 N D:HIS275 3.0 50.0 1.0 C D:CYS271 3.3 50.0 1.0 C D:CYS274 3.4 50.0 1.0 CA D:LYS276 3.5 50.0 1.0 C D:LYS276 3.5 50.0 1.0 C D:HIS275 3.6 50.0 1.0 CA D:HIS275 3.6 50.0 1.0 CG D:HIS306 3.7 50.0 1.0 CB D:CYS274 3.7 50.0 1.0 N D:CYS274 3.8 50.0 1.0 CA D:CYS274 3.8 50.0 1.0 CB D:LYS276 3.9 50.0 1.0 NE2 D:HIS306 3.9 50.0 1.0 N D:GLN272 3.9 50.0 1.0 O D:CYS271 4.0 50.0 1.0 O D:CYS274 4.1 50.0 1.0 C D:THR270 4.2 50.0 1.0 N D:HIS306 4.2 50.0 1.0 CD2 D:HIS306 4.4 50.0 1.0 CG D:LYS276 4.5 50.0 1.0 CB D:HIS306 4.5 50.0 1.0 SG D:CYS309 4.6 50.0 1.0 O D:HIS275 4.7 50.0 1.0 N D:ASN273 4.8 50.0 1.0 N D:LEU277 4.8 50.0 1.0 CA D:HIS306 4.9 50.0 1.0 O D:THR270 4.9 50.0 1.0 C D:ASN273 4.9 50.0 1.0

Zinc binding site 3 out of 3 in the Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryoem Structure of the SMC5/6-Holocomplex (Composite Structure) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:50.0 occ:1.00 CB D:CYS289 2.0 50.0 1.0 CB D:CYS324 2.3 50.0 1.0 SG D:CYS321 2.3 50.0 1.0 SG D:CYS324 2.3 50.0 1.0 SG D:CYS289 2.3 50.0 1.0 N D:CYS324 2.5 50.0 1.0 CA D:CYS289 2.8 50.0 1.0 CA D:CYS324 2.9 50.0 1.0 C D:ARG323 3.3 50.0 1.0 CB D:ARG323 3.4 50.0 1.0 CG D:ARG323 3.4 50.0 1.0 N D:CYS289 3.5 50.0 1.0 CB D:CYS321 3.5 50.0 1.0 CA D:ARG323 3.8 50.0 1.0 C D:CYS324 3.9 50.0 1.0 C D:CYS289 4.0 50.0 1.0 N D:GLY325 4.1 50.0 1.0 SG D:CYS284 4.1 50.0 1.0 N D:ARG323 4.1 50.0 1.0 O D:ARG323 4.2 50.0 1.0 CB D:CYS284 4.4 50.0 1.0 C D:SER288 4.4 50.0 1.0 O D:CYS289 4.5 50.0 1.0 OD1 D:ASN286 4.6 50.0 1.0 O D:SER288 4.7 50.0 1.0 OG D:SER288 4.8 50.0 1.0 CA D:CYS321 4.9 50.0 1.0 O D:CYS324 4.9 50.0 1.0 CD D:ARG323 4.9 50.0 1.0 N D:ASP322 5.0 50.0 1.0

S.T.Hallett, I.Campbell Harry, P.Schellenberger, L.Zhou, N.B.Cronin, J.Baxter, T.J.Etheridge, J.M.Murray, A.W.Oliver. Cryo-Em Structure of the SMC5/6 Holo-Complex. Nucleic Acids Res. V. 50 9505 2022.
ISSN: ESSN 1362-4962
PubMed: 35993814
DOI: 10.1093/NAR/GKAC692