Zinc in PDB 1jk9: Heterodimer Between H48F-YSOD1 and Yccs

All present enzymatic activity of Heterodimer Between H48F-YSOD1 and Yccs:
1.15.1.1;

The structure of Heterodimer Between H48F-YSOD1 and Yccs, PDB code: 1jk9 was solved by A.L.Lamb, A.S.Torres, T.V.O'halloran, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.090, 104.090, 233.710, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26

The binding sites of Zinc atom in the Heterodimer Between H48F-YSOD1 and Yccs (pdb code 1jk9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Heterodimer Between H48F-YSOD1 and Yccs, PDB code: 1jk9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Heterodimer Between H48F-YSOD1 and Yccs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Heterodimer Between H48F-YSOD1 and Yccs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.6 occ:1.00 OD1 A:ASP83 2.0 22.9 1.0 ND1 A:HIS71 2.2 24.4 1.0 ND1 A:HIS80 2.2 21.5 1.0 ND1 A:HIS63 2.3 16.5 1.0 CG A:ASP83 2.7 22.4 1.0 OD2 A:ASP83 2.7 21.4 1.0 CE1 A:HIS71 3.0 23.2 1.0 CE1 A:HIS80 3.1 19.8 1.0 CG A:HIS80 3.1 22.5 1.0 CG A:HIS71 3.2 24.6 1.0 CE1 A:HIS63 3.2 18.1 1.0 CG A:HIS63 3.2 16.5 1.0 CB A:HIS80 3.5 24.1 1.0 CB A:HIS63 3.5 15.2 1.0 CB A:HIS71 3.7 24.2 1.0 CA A:HIS71 3.8 24.1 1.0 O A:LYS136 3.8 28.6 1.0 CB A:ASP83 4.1 22.5 1.0 NE2 A:HIS71 4.1 23.8 1.0 NE2 A:HIS80 4.1 20.2 1.0 CD2 A:HIS80 4.2 22.4 1.0 CD2 A:HIS71 4.3 24.5 1.0 NE2 A:HIS63 4.4 20.3 1.0 CD2 A:HIS63 4.4 17.9 1.0 N A:GLY72 4.6 23.9 1.0 N A:HIS80 4.7 29.1 1.0 CA A:HIS80 4.7 25.9 1.0 CA A:ASP83 4.8 23.9 1.0 N A:HIS71 4.8 23.7 1.0 C A:HIS71 4.8 24.1 1.0 C A:LYS136 5.0 27.4 1.0

Zinc binding site 2 out of 4 in the Heterodimer Between H48F-YSOD1 and Yccs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Heterodimer Between H48F-YSOD1 and Yccs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:22.4 occ:1.00 ND1 B:HIS16 2.2 32.5 1.0 OE2 C:GLU42 2.2 32.4 1.0 OE1 C:GLU42 2.5 33.5 1.0 CD C:GLU42 2.7 31.4 1.0 CE1 B:HIS16 3.1 33.5 1.0 CG B:HIS16 3.1 32.2 1.0 CB B:HIS16 3.5 34.2 1.0 NE2 C:GLN123 4.1 30.8 1.0 NE2 B:HIS16 4.2 34.0 1.0 CG C:GLU42 4.2 28.4 1.0 CD2 B:HIS16 4.2 32.7 1.0 OE1 C:GLN123 4.7 33.7 1.0 CD C:GLN123 4.7 31.1 1.0 OE1 B:GLN44 4.9 23.4 1.0 CA B:HIS16 5.0 36.7 1.0

Zinc binding site 3 out of 4 in the Heterodimer Between H48F-YSOD1 and Yccs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Heterodimer Between H48F-YSOD1 and Yccs within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:19.2 occ:1.00 ND1 C:HIS80 2.1 24.1 1.0 OD1 C:ASP83 2.1 18.1 1.0 ND1 C:HIS71 2.2 20.2 1.0 ND1 C:HIS63 2.2 19.9 1.0 OD2 C:ASP83 2.7 20.0 1.0 CG C:ASP83 2.7 19.7 1.0 CE1 C:HIS80 3.0 22.8 1.0 CG C:HIS80 3.0 23.7 1.0 CE1 C:HIS71 3.0 19.6 1.0 CE1 C:HIS63 3.1 20.9 1.0 CG C:HIS63 3.2 18.7 1.0 CG C:HIS71 3.2 19.9 1.0 CB C:HIS80 3.4 24.9 1.0 CB C:HIS63 3.5 16.6 1.0 CB C:HIS71 3.6 21.7 1.0 O C:LYS136 3.8 31.1 1.0 CA C:HIS71 3.9 23.2 1.0 NE2 C:HIS80 4.0 22.7 1.0 CD2 C:HIS80 4.1 24.3 1.0 NE2 C:HIS71 4.1 19.2 1.0 CB C:ASP83 4.2 20.9 1.0 NE2 C:HIS63 4.2 20.5 1.0 CD2 C:HIS71 4.2 19.1 1.0 CD2 C:HIS63 4.3 20.5 1.0 CA C:HIS80 4.7 26.7 1.0 N C:HIS80 4.7 30.4 1.0 N C:GLY72 4.8 23.4 1.0 CA C:ASP83 4.9 22.0 1.0 N C:HIS71 4.9 23.8 1.0 C C:HIS71 4.9 23.4 1.0 C C:LYS136 5.0 29.7 1.0 N C:ASP83 5.0 22.1 1.0

Zinc binding site 4 out of 4 in the Heterodimer Between H48F-YSOD1 and Yccs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Heterodimer Between H48F-YSOD1 and Yccs within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:25.6 occ:1.00 ND1 D:HIS16 2.1 32.6 1.0 OE2 A:GLU42 2.2 25.1 1.0 OE1 A:GLU42 2.8 25.7 1.0 CD A:GLU42 2.8 23.9 1.0 CG D:HIS16 2.9 32.2 1.0 CE1 D:HIS16 3.1 32.5 1.0 CB D:HIS16 3.2 35.7 1.0 CD2 D:HIS16 4.0 31.7 1.0 NE2 D:HIS16 4.0 32.4 1.0 CG A:GLU42 4.3 22.2 1.0 OE1 A:GLN123 4.3 37.3 1.0 CA D:HIS16 4.7 41.0 1.0 CD A:GLN123 4.9 37.1 1.0 O D:HIS16 5.0 47.0 1.0

A.L.Lamb, A.S.Torres, T.V.O'halloran, A.C.Rosenzweig. Heterodimeric Structure of Superoxide Dismutase in Complex with Its Metallochaperone. Nat.Struct.Biol. V. 8 751 2001.
ISSN: ISSN 1072-8368
PubMed: 11524675
DOI: 10.1038/NSB0901-751