Zinc in PDB 4l3t: Crystal Structure of Substrate-Free Human Presequence Protease

The structure of Crystal Structure of Substrate-Free Human Presequence Protease, PDB code: 4l3t 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)	42.55 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	245.782, 85.093, 158.459, 90.00, 127.54, 90.00
R / Rfree (%)	17.1 / 21

The structure of Crystal Structure of Substrate-Free Human Presequence Protease also contains other interesting chemical elements:

Arsenic

(As)

12 atoms

The binding sites of Zinc atom in the Crystal Structure of Substrate-Free Human Presequence Protease (pdb code 4l3t). 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 Substrate-Free Human Presequence Protease, PDB code: 4l3t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Substrate-Free Human Presequence Protease


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 Substrate-Free Human Presequence Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:28.2 occ:1.00 O A:ACT1108 1.9 35.2 1.0 NE2 A:HIS104 1.9 23.8 1.0 OE1 A:GLU205 2.1 19.6 1.0 NE2 A:HIS108 2.1 25.1 1.0 OE2 A:GLU205 2.1 25.9 1.0 CD A:GLU205 2.4 21.4 1.0 OXT A:ACT1108 2.5 35.4 1.0 C A:ACT1108 2.5 36.5 1.0 CE1 A:HIS104 2.8 21.3 1.0 CE1 A:HIS108 3.0 25.9 1.0 CD2 A:HIS104 3.0 20.9 1.0 CD2 A:HIS108 3.2 19.6 1.0 CG A:GLU205 3.9 22.8 1.0 ND1 A:HIS104 4.0 23.5 1.0 CH3 A:ACT1108 4.0 34.4 1.0 CG A:HIS104 4.1 25.3 1.0 ND1 A:HIS108 4.1 26.5 1.0 CG A:HIS108 4.3 20.2 1.0 CE1 A:TYR906 4.3 23.5 1.0 CG2 A:VAL202 4.5 25.5 1.0 O A:HOH1544 4.6 34.3 1.0 OH A:TYR906 4.6 33.8 1.0 CB A:GLU205 4.7 22.1 1.0 NE2 A:GLN107 4.8 31.6 1.0 CZ A:TYR906 4.9 34.0 1.0 O A:HOH1566 4.9 31.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Substrate-Free Human Presequence Protease


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 Substrate-Free Human Presequence Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:25.3 occ:1.00 OE1 B:GLU205 2.0 24.9 1.0 NE2 B:HIS104 2.0 22.8 1.0 NE2 B:HIS108 2.1 21.4 1.0 OE2 B:GLU205 2.1 28.1 1.0 O B:ACT1108 2.2 40.6 1.0 CD B:GLU205 2.4 25.6 1.0 OXT B:ACT1108 2.4 38.4 1.0 C B:ACT1108 2.7 43.5 1.0 CE1 B:HIS108 2.9 27.0 1.0 CE1 B:HIS104 3.0 19.0 1.0 CD2 B:HIS104 3.1 19.9 1.0 CD2 B:HIS108 3.2 17.3 1.0 CG B:GLU205 3.9 27.4 1.0 ND1 B:HIS108 4.1 26.3 1.0 ND1 B:HIS104 4.1 21.0 1.0 CE1 B:TYR906 4.2 31.2 1.0 CG B:HIS104 4.2 21.3 1.0 CH3 B:ACT1108 4.2 47.5 1.0 CG B:HIS108 4.2 23.8 1.0 OH B:TYR906 4.4 27.9 1.0 CG2 B:VAL202 4.4 21.6 1.0 O B:HOH1528 4.5 37.0 1.0 CZ B:TYR906 4.7 30.2 1.0 CB B:GLU205 4.7 18.7 1.0 NE2 B:GLN107 4.7 31.6 1.0 O B:HOH1525 4.8 37.8 1.0 OE1 B:GLN107 4.9 33.7 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