Zinc in PDB 4nge: Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40)

The structure of Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40), PDB code: 4nge was solved by J.V.King, W.G.Liang, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.62 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.275, 86.183, 158.611, 90.00, 127.56, 90.00
R / Rfree (%)	19.1 / 23.2

The structure of Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40) also contains other interesting chemical elements:

Arsenic

(As)

5 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40) (pdb code 4nge). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40), PDB code: 4nge:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:44.4 occ:1.00 OE1 A:GLU205 2.0 57.5 1.0 O B:PHE20 2.0 56.2 1.0 NE2 A:HIS108 2.0 55.8 1.0 NE2 A:HIS104 2.1 37.9 1.0 OE2 A:GLU205 2.1 59.8 1.0 CD A:GLU205 2.4 52.2 1.0 CE1 A:HIS108 2.4 39.9 1.0 CE1 A:HIS104 2.9 36.3 1.0 C B:PHE20 3.2 68.5 1.0 CD2 A:HIS104 3.3 38.8 1.0 CD2 A:HIS108 3.4 44.4 1.0 ND1 A:HIS108 3.7 28.3 1.0 CG A:GLU205 3.9 41.0 1.0 CA B:ALA21 3.9 88.5 1.0 O B:ALA21 3.9 76.5 1.0 N B:ALA21 3.9 70.9 1.0 C B:ALA21 3.9 75.2 1.0 ND1 A:HIS104 4.1 34.0 1.0 CE1 A:TYR906 4.1 59.5 1.0 OH A:TYR906 4.2 57.0 1.0 CG A:HIS108 4.2 43.4 1.0 CG A:HIS104 4.3 34.2 1.0 CD1 B:PHE20 4.4 77.5 1.0 CA B:PHE20 4.4 79.2 1.0 CZ A:TYR906 4.5 56.1 1.0 CG2 A:VAL202 4.5 31.4 1.0 NE2 A:GLN107 4.6 40.2 1.0 CB A:GLU205 4.6 38.9 1.0 N B:GLU22 4.6 63.0 1.0 CB B:PHE20 4.8 71.1 1.0 N B:PHE20 4.9 81.1 1.0 CD1 A:TYR906 5.0 54.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Presequence Protease in Complex with Amyloid-Beta (1-40) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:45.5 occ:1.00 O E:PHE20 1.7 56.4 1.0 NE2 D:HIS104 2.0 39.0 1.0 OE1 D:GLU205 2.0 54.7 1.0 OE2 D:GLU205 2.0 46.2 1.0 NE2 D:HIS108 2.1 50.0 1.0 CD D:GLU205 2.3 46.8 1.0 CE1 D:HIS104 2.6 35.1 1.0 CE1 D:HIS108 2.6 49.1 1.0 C E:PHE20 2.8 60.1 1.0 CA E:ALA21 3.1 77.5 1.0 CD2 D:HIS104 3.2 39.4 1.0 CD2 D:HIS108 3.3 44.5 1.0 N E:ALA21 3.3 58.6 1.0 CG D:GLU205 3.8 34.1 1.0 ND1 D:HIS104 3.8 25.1 1.0 ND1 D:HIS108 3.9 39.5 1.0 C E:ALA21 3.9 75.6 1.0 CB E:ALA21 4.1 87.3 1.0 CE1 D:TYR906 4.1 49.5 1.0 CA E:PHE20 4.1 89.2 1.0 CG D:HIS104 4.2 35.8 1.0 CG D:HIS108 4.2 44.3 1.0 OH D:TYR906 4.3 54.7 1.0 N E:GLU22 4.3 78.8 1.0 CG2 D:VAL202 4.4 29.2 1.0 OE1 E:GLU22 4.4 79.6 1.0 NE2 D:GLN107 4.5 41.7 1.0 CZ D:TYR906 4.6 47.8 1.0 CB D:GLU205 4.6 33.8 1.0 O E:ALA21 4.7 68.0 1.0 CB E:PHE20 4.7 76.4 1.0 N E:PHE20 4.7 100.0 1.0 CD1 D:TYR906 5.0 35.3 1.0

J.V.King, W.G.Liang, K.P.Scherpelz, A.B.Schilling, S.C.Meredith, W.J.Tang. Molecular Basis of Substrate Recognition and Degradation By Human Presequence Protease. Structure V. 22 996 2014.
ISSN: ISSN 0969-2126
PubMed: 24931469
DOI: 10.1016/J.STR.2014.05.003