Zinc in PDB 4myp: Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme

The structure of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme, PDB code: 4myp was solved by G.R.Malmirchegini, M.R.Sawaya, R.T.Clubb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.05 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.730, 67.690, 58.480, 90.00, 91.62, 90.00
R / Rfree (%)	19.5 / 22.5

The structure of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme (pdb code 4myp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme, PDB code: 4myp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.0 occ:0.75 OD1 A:ASP294 1.9 34.2 1.0 ND1 A:HIS277 1.9 35.1 1.0 O A:HOH501 2.1 33.3 1.0 CG A:ASP294 2.8 31.1 1.0 CE1 A:HIS277 2.8 34.2 1.0 OD2 A:ASP294 3.0 32.5 1.0 CG A:HIS277 3.1 32.7 1.0 CB A:HIS277 3.6 28.6 1.0 NE2 A:HIS277 4.0 34.3 1.0 CD2 A:HIS277 4.1 34.9 1.0 CB A:ASP294 4.2 27.1 1.0 O A:ALA293 4.2 29.9 1.0 C A:ALA293 4.3 31.0 1.0 CA A:HIS277 4.3 26.9 1.0 N A:ASP294 4.4 27.7 1.0 CA A:ASP294 4.5 26.2 1.0 OE1 A:GLN292 4.6 70.1 1.0 CD1 A:LEU246 4.8 39.4 1.0 O A:HOH519 4.9 41.3 1.0

Zinc binding site 2 out of 4 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.4 occ:1.00 OD1 A:ASP255 2.4 45.7 1.0 O A:HOH502 3.1 47.6 0.5 CB A:ASP257 3.1 42.8 1.0 O A:HOH502 3.1 47.7 0.5 CG A:ASP255 3.2 46.1 1.0 OD2 A:ASP257 3.3 58.3 1.0 OD2 A:ASP255 3.4 49.1 1.0 CG A:ASP257 3.5 56.1 1.0 CA A:ASP257 4.2 40.5 1.0 N A:ASP257 4.2 39.8 1.0 CB A:ASP255 4.5 38.1 1.0 OD1 A:ASP257 4.5 57.5 1.0 N A:ALA258 4.6 35.6 1.0 CA A:ASP255 4.8 37.3 1.0 C A:ASP257 4.8 42.2 1.0 C A:ASP255 5.0 40.7 1.0

Zinc binding site 3 out of 4 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:61.7 occ:1.00 O A:HOH526 2.4 42.9 1.0 OD2 A:ASP257 2.5 58.3 1.0 CG A:ASP257 3.2 56.1 1.0 OD1 A:ASP257 3.3 57.5 1.0 CB A:ASP257 4.6 42.8 1.0

Zinc binding site 4 out of 4 in the Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Central Neat Domain, N2, of the Listerial HBP2 Protein Complexed with Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:27.6 occ:0.70 ND1 B:HIS277 1.9 38.1 1.0 OD1 B:ASP294 1.9 36.1 1.0 O B:HOH501 2.3 33.2 1.0 CG B:ASP294 2.8 39.4 1.0 CE1 B:HIS277 2.8 39.0 1.0 OD2 B:ASP294 2.9 41.7 1.0 CG B:HIS277 3.1 35.7 1.0 CB B:HIS277 3.6 31.3 1.0 NE2 B:HIS277 4.0 39.7 1.0 CD2 B:HIS277 4.1 39.4 1.0 CB B:ASP294 4.1 32.7 1.0 O B:ALA293 4.4 30.9 1.0 C B:ALA293 4.4 33.8 1.0 CA B:HIS277 4.4 29.1 1.0 N B:ASP294 4.4 30.9 1.0 CA B:ASP294 4.5 30.0 1.0 OE1 B:GLN292 4.7 57.4 1.0 CD1 B:LEU246 4.7 38.5 1.0

G.R.Malmirchegini, S.Shnitkind, M.R.Sawaya, J.S.Rosinski, J.S.Olson, P.E.Klebba, R.T.Clubb. Novel Mechanism of Hemin Capture By HBP2, the Hemoglobin-Binding Hemophore From Listeria Monocytogenes J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X