Zinc in PDB 6n13: UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin

All present enzymatic activity of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin:
2.3.2.23; 2.3.2.31;

The binding sites of Zinc atom in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin (pdb code 6n13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin, PDB code: 6n13:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:10.0 occ:1.00 ND1 B:HIS257 1.8 10.0 1.0 SG B:CYS293 1.9 10.0 1.0 SG B:CYS253 2.0 10.0 1.0 SG B:CYS289 2.0 10.0 1.0 CE1 B:HIS257 2.7 10.0 1.0 CG B:HIS257 2.9 10.0 1.0 CB B:CYS253 3.1 10.0 1.0 CB B:CYS289 3.2 10.0 1.0 CB B:CYS293 3.3 10.0 1.0 CB B:HIS257 3.4 10.0 1.0 HG B:SER255 3.8 10.0 1.0 NE2 B:HIS257 3.9 10.0 1.0 CD2 B:HIS257 4.0 10.0 1.0 H B:HIS257 4.0 10.0 1.0 H B:ARG256 4.1 10.0 1.0 H B:GLY292 4.2 10.0 1.0 N B:HIS257 4.2 10.0 1.0 H B:ALA291 4.3 10.0 1.0 OG B:SER255 4.4 10.0 1.0 CA B:HIS257 4.4 10.0 1.0 CB B:ALA291 4.4 10.0 1.0 CA B:CYS253 4.5 10.0 1.0 CA B:CYS289 4.6 10.0 1.0 CA B:CYS293 4.6 10.0 1.0 H B:ASN254 4.6 10.0 1.0 N B:ARG256 4.7 10.0 1.0 HE2 B:HIS257 4.8 10.0 1.0 N B:CYS293 4.8 10.0 1.0 C B:ARG256 4.8 10.0 1.0 H B:CYS293 4.9 10.0 1.0 H B:VAL290 4.9 10.0 1.0 C B:CYS253 5.0 10.0 1.0 N B:ALA291 5.0 10.0 1.0

Zinc binding site 2 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:10.0 occ:1.00 SG B:CYS377 1.9 10.0 1.0 NE2 B:HIS373 2.9 10.0 1.0 OE1 B:GLU370 2.9 10.0 1.0 CD B:GLU370 3.0 10.0 1.0 OE2 B:GLU370 3.2 10.0 1.0 CD2 B:HIS373 3.3 10.0 1.0 CE1 B:HIS373 3.5 10.0 1.0 CB B:CYS377 3.6 10.0 1.0 SG B:CYS368 3.8 10.0 1.0 CG B:GLU370 3.8 10.0 1.0 CG B:HIS373 4.2 10.0 1.0 ND1 B:HIS373 4.2 10.0 1.0 CA B:CYS377 4.2 10.0 1.0 CB B:GLU370 4.2 10.0 1.0 O B:GLU376 4.3 10.0 1.0 N B:CYS377 4.5 10.0 1.0 CB B:CYS368 4.6 10.0 1.0 C B:GLU376 4.6 10.0 1.0 HD1 B:HIS373 5.0 10.0 1.0

Zinc binding site 3 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:10.0 occ:1.00 SG B:CYS449 1.9 10.0 1.0 SG B:CYS457 2.0 10.0 1.0 CB B:CYS449 3.2 10.0 1.0 CB B:CYS457 3.6 10.0 1.0 HD22 B:ASN454 4.0 10.0 1.0 NE2 B:HIS461 4.0 10.0 1.0 SG B:CYS451 4.1 10.0 1.0 CA B:CYS457 4.2 10.0 1.0 H B:CYS457 4.4 10.0 1.0 N B:CYS457 4.5 10.0 1.0 CA B:CYS449 4.5 10.0 1.0 ND2 B:ASN454 4.8 10.0 1.0 H B:CYS449 4.9 10.0 1.0 CD2 B:HIS461 4.9 10.0 1.0

Zinc binding site 4 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:10.0 occ:1.00 SG B:CYS196 1.9 10.0 1.0 SG B:CYS201 1.9 10.0 1.0 SG B:CYS166 2.0 10.0 1.0 SG B:CYS169 2.0 10.0 1.0 CB B:CYS166 3.0 10.0 1.0 CB B:CYS201 3.1 10.0 1.0 CB B:CYS196 3.3 10.0 1.0 H B:CYS169 3.3 10.0 1.0 CB B:CYS169 3.6 10.0 1.0 N B:CYS169 4.1 10.0 1.0 H B:ARG170 4.2 10.0 1.0 H B:GLY203 4.3 10.0 1.0 H B:THR168 4.4 10.0 1.0 CA B:CYS169 4.4 10.0 1.0 CA B:CYS201 4.4 10.0 1.0 CA B:CYS166 4.4 10.0 1.0 O B:CYS201 4.5 10.0 1.0 O B:GLY203 4.7 10.0 1.0 CA B:CYS196 4.7 10.0 1.0 C B:CYS201 4.7 10.0 1.0 N B:ARG170 4.9 10.0 1.0 H B:SER167 4.9 10.0 1.0 H B:GLN171 4.9 10.0 1.0

Zinc binding site 5 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:10.0 occ:1.00 SG B:CYS241 1.9 10.0 1.0 SG B:CYS263 1.9 10.0 1.0 SG B:CYS260 2.0 10.0 1.0 SG B:CYS238 2.0 10.0 1.0 CB B:CYS238 3.0 10.0 1.0 CB B:CYS263 3.3 10.0 1.0 H B:CYS241 3.5 10.0 1.0 CB B:CYS241 3.6 10.0 1.0 CB B:CYS260 3.7 10.0 1.0 H B:CYS260 3.8 10.0 1.0 H B:CYS263 4.0 10.0 1.0 N B:CYS241 4.1 10.0 1.0 CA B:CYS241 4.4 10.0 1.0 N B:CYS260 4.4 10.0 1.0 O B:CYS241 4.4 10.0 1.0 CG1 B:ILE259 4.4 10.0 1.0 CA B:CYS238 4.4 10.0 1.0 CB B:THR240 4.4 10.0 1.0 CA B:CYS260 4.5 10.0 1.0 CA B:CYS263 4.5 10.0 1.0 O B:CYS260 4.6 10.0 1.0 N B:CYS263 4.6 10.0 1.0 H B:THR240 4.7 10.0 1.0 C B:CYS260 4.8 10.0 1.0 C B:CYS241 4.8 10.0 1.0 C B:THR240 4.9 10.0 1.0

Zinc binding site 6 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:10.0 occ:1.00 O B:LEU358 1.7 10.0 1.0 SG B:CYS337 1.9 10.0 1.0 SG B:CYS352 1.9 10.0 1.0 SG B:CYS360 2.0 10.0 1.0 C B:LEU358 2.9 10.0 1.0 CB B:CYS337 3.5 10.0 1.0 CA B:GLY359 3.6 10.0 1.0 CB B:CYS360 3.6 10.0 1.0 H B:CYS360 3.6 10.0 1.0 N B:GLY359 3.7 10.0 1.0 CB B:CYS352 3.7 10.0 1.0 N B:CYS360 3.7 10.0 1.0 C B:GLY359 3.8 10.0 1.0 CA B:LEU358 4.1 10.0 1.0 CA B:CYS360 4.2 10.0 1.0 CG2 A:THR9 4.3 10.0 1.0 CB B:ALA339 4.4 10.0 1.0 OG1 A:THR9 4.5 10.0 1.0 O B:GLY359 4.6 10.0 1.0 H B:GLY359 4.6 10.0 1.0 CA B:CYS337 4.6 10.0 1.0 CA B:CYS352 4.7 10.0 1.0 C B:CYS360 4.8 10.0 1.0 O B:CYS352 4.8 10.0 1.0 O B:CYS360 4.9 10.0 1.0 C B:CYS352 4.9 10.0 1.0 N B:LEU358 4.9 10.0 1.0 HH11 B:ARG334 5.0 10.0 1.0

Zinc binding site 7 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:10.0 occ:1.00 SG B:CYS418 1.9 10.0 1.0 SG B:CYS436 1.9 10.0 1.0 SG B:CYS421 1.9 10.0 1.0 CB B:CYS418 2.6 10.0 1.0 O B:ARG420 3.0 10.0 1.0 CB B:CYS436 3.2 10.0 1.0 CB B:CYS421 3.3 10.0 1.0 C B:ARG420 3.7 10.0 1.0 SG B:CYS441 3.8 10.0 1.0 CA B:CYS418 4.0 10.0 1.0 H B:HIS422 4.1 10.0 1.0 CA B:CYS421 4.2 10.0 1.0 HG B:CYS441 4.3 10.0 1.0 H B:VAL423 4.3 10.0 1.0 H B:ARG420 4.3 10.0 1.0 N B:CYS421 4.3 10.0 1.0 C B:CYS418 4.4 10.0 1.0 CA B:CYS436 4.5 10.0 1.0 N B:ARG420 4.6 10.0 1.0 HE1 B:TRP445 4.6 10.0 1.0 O B:CYS418 4.6 10.0 1.0 CB B:CYS441 4.7 10.0 1.0 H B:CYS418 4.7 10.0 1.0 N B:HIS422 4.7 10.0 1.0 CA B:ARG420 4.7 10.0 1.0 NE1 B:TRP445 4.7 10.0 1.0 N B:CYS418 4.9 10.0 1.0 O B:VAL423 4.9 10.0 1.0 C B:CYS436 5.0 10.0 1.0 C B:CYS421 5.0 10.0 1.0 CD1 B:TRP445 5.0 10.0 1.0 O B:CYS436 5.0 10.0 1.0

Zinc binding site 8 out of 8 in the UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of UBCH7-Ub Complex with R0RBR Parkin and Phosphoubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn508 b:10.0 occ:1.00 SG B:CYS212 1.9 10.0 1.0 SG B:CYS150 1.9 10.0 1.0 SG B:CYS154 2.0 10.0 1.0 CB B:CYS150 2.8 10.0 1.0 CB B:CYS212 2.9 10.0 1.0 NE2 B:HIS215 3.2 10.0 1.0 CB B:CYS154 3.5 10.0 1.0 O B:GLY152 3.8 10.0 1.0 CE1 B:HIS215 3.8 10.0 1.0 CD2 B:HIS215 3.9 10.0 1.0 CA B:CYS150 4.3 10.0 1.0 H B:CYS154 4.3 10.0 1.0 CG B:GLN158 4.3 10.0 1.0 CA B:CYS212 4.4 10.0 1.0 H B:HIS215 4.6 10.0 1.0 CA B:CYS154 4.7 10.0 1.0 N B:CYS154 4.7 10.0 1.0 C B:GLY152 4.7 10.0 1.0 ND1 B:HIS215 4.7 10.0 1.0 CG B:HIS215 4.8 10.0 1.0 C B:CYS150 4.8 10.0 1.0 O B:CYS150 4.8 10.0 1.0 CB B:GLN158 4.9 10.0 1.0 C B:CYS212 4.9 10.0 1.0

T.E.Condos, K.M.Dunkerley, E.A.Freeman, K.R.Barber, J.D.Aguirre, V.K.Chaugule, Y.Xiao, L.Konermann, H.Walden, G.S.Shaw. Synergistic Recruitment of UBCH7~Ub and Phosphorylated Ubl Domain Triggers Parkin Activation. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 30446597
DOI: 10.15252/EMBJ.2018100014