Zinc in PDB 3umi: X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc, PDB code: 3umi was solved by S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.44 / 2.40
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	39.757, 39.757, 126.425, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.5

The structure of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc also contains other interesting chemical elements:

Cadmium

(Cd)

9 atoms

The binding sites of Zinc atom in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc (pdb code 3umi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc, PDB code: 3umi:

Zinc binding site 1 out of 1 in the X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the E2 Domain of the Human Amyloid Precursor Protein (App) in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:38.1 occ:0.70 NE2 A:HIS432 2.0 27.6 1.0 O A:HOH79 2.0 35.4 1.0 NE2 A:HIS382 2.0 28.3 1.0 NE2 A:HIS436 2.1 30.6 1.0 CE1 A:HIS432 2.9 23.8 1.0 CD2 A:HIS432 3.0 31.2 1.0 CE1 A:HIS382 3.0 26.1 1.0 CE1 A:HIS436 3.0 31.2 1.0 CD2 A:HIS382 3.0 26.4 1.0 CD2 A:HIS436 3.1 29.4 1.0 ND1 A:HIS432 4.1 24.6 1.0 CG A:HIS432 4.1 28.5 1.0 ND1 A:HIS382 4.1 27.0 1.0 ND1 A:HIS436 4.1 32.3 1.0 CG A:HIS382 4.2 29.4 1.0 CG A:HIS436 4.2 29.2 1.0 ND1 A:HIS313 4.2 54.0 0.0 CD2 A:PHE316 4.4 37.0 1.0 CE2 A:PHE316 4.5 40.2 1.0 CE1 A:HIS313 4.5 54.2 0.0 SD A:MET383 4.7 37.7 1.0

S.O.Dahms, I.Konnig, D.Roeser, K.H.Guhrs, M.C.Mayer, D.Kaden, G.Multhaup, M.E.Than. Metal Binding Dictates Conformation and Function of the Amyloid Precursor Protein (App) E2 Domain. J.Mol.Biol. V. 416 438 2012.
ISSN: ISSN 0022-2836
PubMed: 22245578
DOI: 10.1016/J.JMB.2011.12.057