Zinc in PDB 2m48: Solution Structure of Ibr-RING2 Tandem Domain From Parkin

The binding sites of Zinc atom in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin (pdb code 2m48). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin, PDB code: 2m48:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of Ibr-RING2 Tandem Domain From Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.0 occ:1.00 SG A:CYS353 2.2 0.0 1.0 SG A:CYS377 2.2 0.0 1.0 SG A:CYS373 2.2 0.0 1.0 SG A:CYS358 2.5 0.0 1.0 H A:CYS377 2.9 0.0 1.0 HB2 A:CYS353 3.0 0.0 1.0 HB2 A:CYS358 3.0 0.0 1.0 CB A:CYS353 3.0 0.0 1.0 HB2 A:CYS373 3.1 0.0 1.0 HB3 A:CYS353 3.1 0.0 1.0 CB A:CYS373 3.2 0.0 1.0 CB A:CYS358 3.2 0.0 1.0 HB3 A:CYS358 3.5 0.0 1.0 HB3 A:CYS373 3.5 0.0 1.0 HE3 A:MET360 3.5 0.0 1.0 N A:CYS377 3.6 0.0 1.0 O A:CYS377 3.6 0.0 1.0 CB A:CYS377 3.6 0.0 1.0 HB2 A:CYS377 4.0 0.0 1.0 HB3 A:GLN355 4.0 0.0 1.0 CA A:CYS377 4.0 0.0 1.0 HA3 A:GLY376 4.1 0.0 1.0 C A:CYS377 4.1 0.0 1.0 HE2 A:TYR379 4.2 0.0 1.0 H A:GLY359 4.2 0.0 1.0 HB2 A:GLN355 4.3 0.0 1.0 HD21 A:LEU362 4.4 0.0 1.0 HB3 A:CYS377 4.5 0.0 1.0 CA A:CYS353 4.5 0.0 1.0 CE A:MET360 4.6 0.0 1.0 C A:GLY376 4.6 0.0 1.0 CB A:GLN355 4.7 0.0 1.0 CA A:CYS373 4.7 0.0 1.0 CA A:CYS358 4.7 0.0 1.0 H A:GLN355 4.7 0.0 1.0 HE1 A:MET360 4.8 0.0 1.0 HA A:CYS353 4.8 0.0 1.0 CE2 A:TYR379 4.8 0.0 1.0 CA A:GLY376 4.8 0.0 1.0 HA A:CYS373 4.8 0.0 1.0 HA A:CYS358 4.9 0.0 1.0 H A:MET360 5.0 0.0 1.0 HG3 A:MET360 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of Ibr-RING2 Tandem Domain From Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.0 occ:1.00 SG A:CYS385 2.1 0.0 1.0 NE2 A:HIS390 2.2 0.0 1.0 SG A:CYS382 2.2 0.0 1.0 SG A:CYS394 2.2 0.0 1.0 CD2 A:HIS390 2.9 0.0 1.0 HB2 A:ASN384 2.9 0.0 1.0 HD2 A:HIS390 3.0 0.0 1.0 CB A:CYS394 3.0 0.0 1.0 HB3 A:CYS394 3.0 0.0 1.0 HB2 A:CYS394 3.0 0.0 1.0 HB3 A:CYS382 3.2 0.0 1.0 CB A:CYS382 3.2 0.0 1.0 H A:CYS385 3.3 0.0 1.0 CE1 A:HIS390 3.3 0.0 1.0 HB2 A:CYS382 3.4 0.0 1.0 H A:ASN384 3.6 0.0 1.0 HE1 A:HIS390 3.7 0.0 1.0 CB A:CYS385 3.7 0.0 1.0 N A:CYS385 3.7 0.0 1.0 CB A:ASN384 4.0 0.0 1.0 HD21 A:ASN384 4.0 0.0 1.0 HB3 A:CYS385 4.0 0.0 1.0 CG A:HIS390 4.1 0.0 1.0 CA A:CYS385 4.3 0.0 1.0 ND1 A:HIS390 4.3 0.0 1.0 HB2 A:GLN387 4.3 0.0 1.0 N A:ASN384 4.3 0.0 1.0 C A:ASN384 4.4 0.0 1.0 CA A:ASN384 4.5 0.0 1.0 HB2 A:CYS385 4.5 0.0 1.0 CA A:CYS394 4.5 0.0 1.0 HB3 A:ASN384 4.5 0.0 1.0 H A:ARG383 4.5 0.0 1.0 HG2 A:GLN387 4.6 0.0 1.0 CA A:CYS382 4.6 0.0 1.0 HG3 A:GLN387 4.7 0.0 1.0 ND2 A:ASN384 4.7 0.0 1.0 H A:GLN387 4.8 0.0 1.0 CG A:ASN384 4.8 0.0 1.0 C A:CYS385 4.9 0.0 1.0 O A:CYS385 4.9 0.0 1.0 H A:HIS390 4.9 0.0 1.0 N A:ARG383 5.0 0.0 1.0 HA A:CYS382 5.0 0.0 1.0 O A:GLU393 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structure of Ibr-RING2 Tandem Domain From Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.0 occ:1.00 SG A:CYS454 2.2 0.0 1.0 SG A:CYS439 2.3 0.0 1.0 SG A:CYS436 2.3 0.0 1.0 SG A:CYS459 2.3 0.0 1.0 H A:CYS439 2.8 0.0 1.0 HB3 A:CYS454 3.1 0.0 1.0 HB2 A:CYS436 3.1 0.0 1.0 HG1 A:THR441 3.1 0.0 1.0 CB A:CYS454 3.2 0.0 1.0 CB A:CYS436 3.2 0.0 1.0 CB A:CYS459 3.2 0.0 1.0 HB2 A:CYS459 3.2 0.0 1.0 HB3 A:LYS438 3.2 0.0 1.0 HB3 A:CYS459 3.3 0.0 1.0 HB3 A:CYS436 3.3 0.0 1.0 HB2 A:CYS454 3.4 0.0 1.0 HB2 A:ARG456 3.5 0.0 1.0 CB A:CYS439 3.7 0.0 1.0 N A:CYS439 3.7 0.0 1.0 OG1 A:THR441 3.8 0.0 1.0 HB3 A:CYS439 3.8 0.0 1.0 HB3 A:PHE461 3.8 0.0 1.0 HG3 A:ARG456 3.9 0.0 1.0 HB3 A:ARG456 4.0 0.0 1.0 H A:PHE461 4.1 0.0 1.0 H A:LYS438 4.1 0.0 1.0 HD2 A:LYS438 4.1 0.0 1.0 H A:THR441 4.1 0.0 1.0 CB A:ARG456 4.2 0.0 1.0 CA A:CYS439 4.2 0.0 1.0 H A:ARG440 4.3 0.0 1.0 CB A:LYS438 4.3 0.0 1.0 H A:GLY460 4.4 0.0 1.0 HB2 A:CYS439 4.5 0.0 1.0 CA A:CYS454 4.6 0.0 1.0 CG A:ARG456 4.6 0.0 1.0 HB2 A:PHE461 4.6 0.0 1.0 CA A:CYS436 4.6 0.0 1.0 CA A:CYS459 4.7 0.0 1.0 HD2 A:PRO437 4.7 0.0 1.0 CB A:PHE461 4.7 0.0 1.0 HB2 A:LYS438 4.8 0.0 1.0 C A:LYS438 4.8 0.0 1.0 O A:CYS454 4.8 0.0 1.0 N A:ARG440 4.9 0.0 1.0 N A:LYS438 4.9 0.0 1.0 HD3 A:LYS438 4.9 0.0 1.0 CA A:LYS438 4.9 0.0 1.0 CD A:LYS438 4.9 0.0 1.0 C A:CYS454 4.9 0.0 1.0 C A:CYS439 4.9 0.0 1.0 HG23 A:THR441 4.9 0.0 1.0 HA A:CYS436 4.9 0.0 1.0 HA A:CYS454 5.0 0.0 1.0 N A:PHE461 5.0 0.0 1.0 HA A:CYS459 5.0 0.0 1.0 N A:GLY460 5.0 0.0 1.0

Zinc binding site 4 out of 4 in the Solution Structure of Ibr-RING2 Tandem Domain From Parkin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Solution Structure of Ibr-RING2 Tandem Domain From Parkin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:0.0 occ:1.00 SG A:CYS467 2.2 0.0 1.0 NE2 A:HIS479 2.2 0.0 1.0 SG A:CYS464 2.2 0.0 1.0 SG A:CYS475 2.2 0.0 1.0 CE1 A:HIS479 3.0 0.0 1.0 CB A:CYS464 3.1 0.0 1.0 HB3 A:CYS464 3.1 0.0 1.0 H A:CYS467 3.1 0.0 1.0 HB2 A:CYS464 3.1 0.0 1.0 HE1 A:HIS479 3.1 0.0 1.0 CD2 A:HIS479 3.2 0.0 1.0 HD2 A:HIS479 3.6 0.0 1.0 CB A:CYS475 3.7 0.0 1.0 O A:CYS467 3.7 0.0 1.0 CB A:CYS467 3.8 0.0 1.0 HB3 A:CYS475 3.8 0.0 1.0 HB2 A:CYS475 3.9 0.0 1.0 N A:CYS467 3.9 0.0 1.0 HB A:VAL466 3.9 0.0 1.0 ND1 A:HIS479 4.1 0.0 1.0 CA A:CYS467 4.2 0.0 1.0 HB2 A:CYS467 4.3 0.0 1.0 CG A:HIS479 4.3 0.0 1.0 C A:CYS467 4.4 0.0 1.0 HB3 A:CYS467 4.5 0.0 1.0 CA A:CYS464 4.5 0.0 1.0 HG1 A:THR469 4.5 0.0 1.0 H A:HIS479 4.8 0.0 1.0 H A:VAL466 4.8 0.0 1.0 HA A:CYS464 4.9 0.0 1.0 HE3 A:TRP480 4.9 0.0 1.0 OG1 A:THR469 4.9 0.0 1.0 CB A:VAL466 4.9 0.0 1.0 CA A:CYS475 5.0 0.0 1.0 HD1 A:HIS479 5.0 0.0 1.0 C A:VAL466 5.0 0.0 1.0

D.E.Spratt, R.Julio Martinez-Torres, Y.J.Noh, P.Mercier, N.Manczyk, K.R.Barber, J.D.Aguirre, L.Burchell, A.Purkiss, H.Walden, G.S.Shaw. A Molecular Explanation For the Recessive Nature of Parkin-Linked Parkinson'S Disease. Nat Commun V. 4 1983 2013.
ISSN: ESSN 2041-1723
PubMed: 23770917
DOI: 10.1038/NCOMMS2983