Zinc in PDB 6nw5: Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors

The structure of Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors, PDB code: 6nw5 was solved by R.Dutoit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.60 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	131.152, 131.152, 285.610, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 16.4

The structure of Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors also contains other interesting chemical elements:

Cobalt

(Co)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors (pdb code 6nw5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors, PDB code: 6nw5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors


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 TMPEP1050 Aminopeptidase with Its Metal Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.4 occ:0.87 OD1 A:ASP168 2.0 15.9 1.0 NE2 A:HIS60 2.0 14.7 1.0 OD1 A:ASP220 2.1 17.5 1.0 O A:HOH771 2.3 26.2 1.0 OD2 A:ASP220 2.5 18.8 1.0 CG A:ASP220 2.6 17.6 1.0 CE1 A:HIS60 3.0 14.2 1.0 CG A:ASP168 3.0 22.9 1.0 CD2 A:HIS60 3.1 15.7 1.0 OD2 A:ASP168 3.3 23.1 1.0 OE1 A:GLU197 3.8 18.5 1.0 CO A:CO402 3.8 59.9 0.3 CB A:ASP169 3.9 13.8 1.0 OE2 A:GLU198 4.0 21.1 1.0 ND1 A:HIS60 4.1 15.0 1.0 CD A:GLU197 4.1 21.6 1.0 CG A:HIS60 4.2 13.3 1.0 CB A:ASP220 4.2 16.0 1.0 O A:HOH655 4.3 34.5 1.0 OE2 A:GLU197 4.3 21.1 1.0 CB A:ASP168 4.3 14.3 1.0 CG A:ASP169 4.4 14.8 1.0 CG2 A:VAL221 4.5 15.9 1.0 O A:HOH766 4.5 50.3 1.0 OD2 A:ASP169 4.6 14.5 1.0 CA A:ASP168 4.6 13.9 1.0 N A:VAL221 4.6 14.7 1.0 O A:HOH578 4.7 16.8 1.0 CD A:GLU198 4.7 19.1 1.0 C A:ASP168 4.7 16.0 1.0 CA A:ASP169 4.7 12.7 1.0 N A:ASP169 4.8 15.3 1.0 O A:HOH533 4.8 37.6 1.0 CA A:ASP220 4.9 13.1 1.0 OD1 A:ASP169 5.0 14.1 1.0 CG A:GLU197 5.0 18.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors


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 TMPEP1050 Aminopeptidase with Its Metal Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:18.6 occ:0.87 OD1 B:ASP168 2.0 18.5 1.0 NE2 B:HIS60 2.0 16.2 1.0 OD1 B:ASP220 2.1 20.1 1.0 O B:HOH789 2.2 26.8 1.0 OD2 B:ASP220 2.5 19.4 1.0 CG B:ASP220 2.6 18.7 1.0 CG B:ASP168 3.0 21.9 1.0 CE1 B:HIS60 3.0 15.3 1.0 CD2 B:HIS60 3.1 17.9 1.0 OD2 B:ASP168 3.3 24.2 1.0 OE1 B:GLU197 3.8 19.2 1.0 CO B:CO402 3.9 44.8 0.3 CB B:ASP169 3.9 13.9 1.0 OE2 B:GLU198 4.0 21.0 1.0 ND1 B:HIS60 4.1 16.8 1.0 CD B:GLU197 4.2 23.1 1.0 CB B:ASP220 4.2 16.1 1.0 CG B:HIS60 4.2 16.2 1.0 CB B:ASP168 4.3 14.3 1.0 OE2 B:GLU197 4.3 22.4 1.0 CG B:ASP169 4.3 18.1 1.0 O B:HOH691 4.4 37.0 1.0 CG2 B:VAL221 4.5 17.6 1.0 OD2 B:ASP169 4.6 17.2 1.0 CA B:ASP168 4.6 16.7 1.0 N B:VAL221 4.6 17.2 1.0 O B:HOH590 4.7 19.6 1.0 CA B:ASP169 4.7 14.7 1.0 C B:ASP168 4.7 18.8 1.0 CD B:GLU198 4.7 18.1 1.0 N B:ASP169 4.8 15.5 1.0 CA B:ASP220 4.9 14.4 1.0 O B:HOH545 4.9 37.9 1.0 OD1 B:ASP169 5.0 15.7 1.0 CG B:GLU197 5.0 18.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:20.6 occ:0.91 OD1 C:ASP168 2.0 19.9 1.0 NE2 C:HIS60 2.0 17.0 1.0 OD1 C:ASP220 2.1 19.6 1.0 O C:HOH751 2.4 28.7 1.0 OD2 C:ASP220 2.5 21.2 1.0 CG C:ASP220 2.6 20.2 1.0 CG C:ASP168 3.0 26.2 1.0 CE1 C:HIS60 3.0 16.4 1.0 CD2 C:HIS60 3.1 15.4 1.0 OD2 C:ASP168 3.4 24.2 1.0 OE1 C:GLU197 3.8 21.4 1.0 CO C:CO402 3.9 49.5 0.3 CB C:ASP169 3.9 15.4 1.0 OE2 C:GLU198 4.1 22.8 1.0 ND1 C:HIS60 4.1 16.3 1.0 CD C:GLU197 4.2 23.7 1.0 CB C:ASP220 4.2 16.8 1.0 CG C:HIS60 4.2 17.7 1.0 CB C:ASP168 4.3 15.9 1.0 CG C:ASP169 4.4 19.9 1.0 OE2 C:GLU197 4.4 22.9 1.0 O C:HOH727 4.5 42.3 1.0 CG2 C:VAL221 4.5 19.8 1.0 OD2 C:ASP169 4.5 19.3 1.0 N C:VAL221 4.6 16.7 1.0 CA C:ASP168 4.6 16.4 1.0 O C:HOH571 4.7 19.1 1.0 CA C:ASP169 4.7 17.1 1.0 C C:ASP168 4.7 17.4 1.0 CD C:GLU198 4.8 22.1 1.0 N C:ASP169 4.8 17.9 1.0 O C:HOH774 4.8 53.3 1.0 CA C:ASP220 4.9 18.1 1.0 CG C:GLU197 4.9 19.2 1.0 OD1 C:ASP169 4.9 17.5 1.0 O C:HOH528 5.0 37.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TMPEP1050 Aminopeptidase with Its Metal Cofactors within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:18.2 occ:0.88 OD1 D:ASP168 1.9 17.5 1.0 NE2 D:HIS60 2.0 14.8 1.0 O D:OH409 2.1 29.2 1.0 OD1 D:ASP220 2.1 18.2 1.0 OD2 D:ASP220 2.5 18.6 1.0 CG D:ASP220 2.6 17.8 1.0 CG D:ASP168 3.0 21.8 1.0 CE1 D:HIS60 3.0 17.2 1.0 CD2 D:HIS60 3.1 16.5 1.0 OD2 D:ASP168 3.3 23.5 1.0 OE1 D:GLU197 3.8 18.8 1.0 CB D:ASP169 3.9 13.5 1.0 CO D:CO402 3.9 42.8 0.3 OE2 D:GLU198 4.0 23.5 1.0 ND1 D:HIS60 4.1 17.7 1.0 CD D:GLU197 4.2 21.8 1.0 CG D:HIS60 4.2 16.4 1.0 CB D:ASP220 4.2 15.2 1.0 CB D:ASP168 4.3 16.0 1.0 O D:HOH650 4.3 39.7 1.0 CG D:ASP169 4.3 15.5 1.0 OE2 D:GLU197 4.4 24.0 1.0 CG2 D:VAL221 4.4 16.0 1.0 O D:HOH781 4.5 47.4 1.0 OD2 D:ASP169 4.5 15.8 1.0 CA D:ASP168 4.6 16.4 1.0 N D:VAL221 4.6 15.1 1.0 O D:HOH568 4.7 49.2 1.0 CD D:GLU198 4.7 21.5 1.0 CA D:ASP169 4.7 13.6 1.0 O D:HOH615 4.7 17.6 1.0 C D:ASP168 4.7 16.8 1.0 N D:ASP169 4.8 15.3 1.0 CA D:ASP220 4.9 14.3 1.0 O D:HOH576 4.9 36.1 1.0 OD1 D:ASP169 4.9 16.5 1.0 CG D:GLU197 5.0 17.7 1.0

R.Dutoit, T.Van Gompel, N.Brandt, D.Van Elder, J.Van Dyck, F.Sobott, L.Droogmans. How Metal Cofactors Drive Dimer-Dodecamer Transition of the M42 Aminopeptidase TMPEP1050 Ofthermotoga Maritima. J.Biol.Chem. V. 294 17777 2019.
ISSN: ESSN 1083-351X
PubMed: 31611236
DOI: 10.1074/JBC.RA119.009281