Zinc in PDB 4njr: Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa

The structure of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa, PDB code: 4njr was solved by D.D.Nguyen, R.Pandian, D.Y.Kim, S.C.Ha, K.H.Yun, K.S.Kim, J.H.Kim, K.K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.40 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	134.187, 134.187, 328.756, 90.00, 90.00, 120.00
R / Rfree (%)	14.6 / 19.6

The binding sites of Zinc atom in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa (pdb code 4njr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa, PDB code: 4njr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.1 occ:1.00 OE1 A:GLU266 2.0 19.2 1.0 O3 A:CO3503 2.0 51.4 1.0 OD2 A:ASP236 2.0 18.8 1.0 NE2 A:HIS401 2.2 24.4 1.0 C A:CO3503 2.3 52.6 1.0 O2 A:CO3503 2.3 35.2 1.0 OE2 A:GLU266 2.5 18.9 1.0 CD A:GLU266 2.5 18.5 1.0 CG A:ASP236 3.0 20.7 1.0 CD2 A:HIS401 3.1 24.9 1.0 CE1 A:HIS401 3.2 25.4 1.0 O1 A:CO3503 3.3 54.8 1.0 OD1 A:ASP236 3.3 21.3 1.0 ZN A:ZN502 3.4 29.9 1.0 O A:HOH823 3.5 46.1 1.0 CG A:GLU266 4.0 18.7 1.0 OE1 A:GLU265 4.1 51.4 1.0 ND1 A:HIS401 4.3 24.6 1.0 CG A:HIS401 4.3 24.3 1.0 CB A:ASP236 4.3 21.2 1.0 NE2 D:HIS156 4.4 32.6 1.0 CE1 A:HIS82 4.4 16.5 1.0 NE2 A:HIS82 4.5 18.3 1.0 CE1 D:HIS156 4.6 33.2 1.0 CG A:PRO86 4.6 21.7 1.0 CD A:PRO86 4.6 21.0 1.0 O A:HOH601 4.7 24.5 1.0 SD A:MET400 4.7 32.3 1.0 CG A:MET400 4.9 26.3 1.0 CB A:GLU266 5.0 19.7 1.0 CD A:GLU265 5.0 42.7 1.0

Zinc binding site 2 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:29.9 occ:1.00 OD1 A:ASP236 2.1 21.3 1.0 O2 A:CO3503 2.1 35.2 1.0 OD1 A:ASP307 2.2 24.4 1.0 NE2 A:HIS82 2.2 18.3 1.0 OD2 A:ASP307 2.4 20.4 1.0 O A:HOH823 2.4 46.1 1.0 CG A:ASP307 2.6 20.0 1.0 CG A:ASP236 3.0 20.7 1.0 CE1 A:HIS82 3.0 16.5 1.0 C A:CO3503 3.1 52.6 1.0 CD2 A:HIS82 3.3 16.5 1.0 OD2 A:ASP236 3.4 18.8 1.0 ZN A:ZN501 3.4 25.1 1.0 O3 A:CO3503 3.4 51.4 1.0 CB A:ASN237 3.9 23.0 1.0 OE1 A:GLU265 3.9 51.4 1.0 OE1 A:GLU266 4.0 19.2 1.0 CB A:ASP307 4.0 18.6 1.0 O1 A:CO3503 4.1 54.8 1.0 CG A:ASN237 4.2 22.6 1.0 ND1 A:HIS82 4.2 17.6 1.0 CD A:GLU265 4.2 42.7 1.0 OE2 A:GLU265 4.3 52.2 1.0 CB A:ASP236 4.3 21.2 1.0 CG A:HIS82 4.4 18.5 1.0 ND2 A:ASN237 4.6 21.7 1.0 CD A:GLU266 4.6 18.5 1.0 OD1 A:ASN237 4.7 21.3 1.0 N A:ASN308 4.7 20.8 1.0 CA A:ASP236 4.7 20.6 1.0 CA A:ASP307 4.8 18.7 1.0 CA A:ASN237 4.8 21.9 1.0 C A:ASP236 4.8 21.4 1.0 N A:ASN237 4.9 23.4 1.0 OE2 A:GLU266 4.9 18.9 1.0

Zinc binding site 3 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:29.8 occ:1.00 OD1 B:ASP307 2.0 23.7 1.0 O1 B:CO3503 2.1 38.3 1.0 OD1 B:ASP236 2.1 17.4 1.0 NE2 B:HIS82 2.2 19.8 1.0 O B:HOH818 2.3 43.1 1.0 OD2 B:ASP307 2.4 20.6 1.0 CG B:ASP307 2.6 20.6 1.0 CG B:ASP236 3.0 18.1 1.0 CE1 B:HIS82 3.0 18.1 1.0 C B:CO3503 3.2 51.1 1.0 CD2 B:HIS82 3.3 18.1 1.0 ZN B:ZN502 3.3 27.0 1.0 OD2 B:ASP236 3.3 15.9 1.0 O3 B:CO3503 3.6 48.3 1.0 OE1 B:GLU265 3.7 46.1 1.0 OE1 B:GLU266 3.8 22.3 1.0 CB B:ASN237 3.9 21.4 1.0 CB B:ASP307 4.1 18.2 1.0 O2 B:CO3503 4.1 55.7 1.0 ND1 B:HIS82 4.2 19.1 1.0 CD B:GLU265 4.2 37.1 1.0 CB B:ASP236 4.3 18.1 1.0 CG B:HIS82 4.4 19.6 1.0 CG B:ASN237 4.4 22.4 1.0 OE2 B:GLU265 4.4 42.1 1.0 CD B:GLU266 4.6 22.0 1.0 ND2 B:ASN237 4.7 22.4 1.0 CA B:ASP236 4.7 17.6 1.0 N B:ASN308 4.8 21.8 1.0 CA B:ASP307 4.8 18.3 1.0 C B:ASP236 4.8 19.0 1.0 OD1 B:ASN237 4.9 23.5 1.0 CA B:ASN237 4.9 19.8 1.0 N B:ASN237 5.0 19.6 1.0

Zinc binding site 4 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:27.0 occ:1.00 OE1 B:GLU266 1.8 22.3 1.0 OD2 B:ASP236 2.0 15.9 1.0 O3 B:CO3503 2.1 48.3 1.0 NE2 B:HIS401 2.1 21.0 1.0 O1 B:CO3503 2.2 38.3 1.0 C B:CO3503 2.3 51.1 1.0 CD B:GLU266 2.5 22.0 1.0 OE2 B:GLU266 2.6 23.0 1.0 CG B:ASP236 3.0 18.1 1.0 CE1 B:HIS401 3.1 21.9 1.0 CD2 B:HIS401 3.1 21.1 1.0 O B:HOH818 3.2 43.1 1.0 OD1 B:ASP236 3.3 17.4 1.0 ZN B:ZN501 3.3 29.8 1.0 O2 B:CO3503 3.3 55.7 1.0 CG B:GLU266 4.0 20.1 1.0 OE1 B:GLU265 4.0 46.1 1.0 ND1 B:HIS401 4.2 21.7 1.0 CG B:HIS401 4.3 20.3 1.0 CE1 B:HIS82 4.4 18.1 1.0 CB B:ASP236 4.4 18.1 1.0 NE2 B:HIS82 4.5 19.8 1.0 CD B:PRO86 4.6 18.7 1.0 CG B:PRO86 4.7 19.2 1.0 SD B:MET400 4.8 32.4 1.0 O B:HOH661 4.8 23.6 1.0 CB B:GLU266 4.9 20.3 1.0

Zinc binding site 5 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:26.0 occ:1.00 OE2 C:GLU266 2.0 21.9 1.0 OD2 C:ASP236 2.0 17.0 1.0 O3 C:CO3503 2.2 51.9 1.0 NE2 C:HIS401 2.2 22.5 1.0 O1 C:CO3503 2.3 45.0 1.0 C C:CO3503 2.5 58.0 1.0 OE1 C:GLU266 2.5 22.1 1.0 CD C:GLU266 2.5 20.6 1.0 CG C:ASP236 3.0 17.7 1.0 CD2 C:HIS401 3.1 23.8 1.0 CE1 C:HIS401 3.2 25.2 1.0 OD1 C:ASP236 3.3 17.5 1.0 ZN C:ZN502 3.3 29.0 1.0 O C:HOH819 3.3 46.2 1.0 O2 C:CO3503 3.6 57.5 1.0 CG C:GLU266 4.0 20.7 1.0 OE1 C:GLU265 4.1 44.3 1.0 CG C:HIS401 4.3 22.2 1.0 ND1 C:HIS401 4.3 24.8 1.0 CE1 C:HIS82 4.3 18.6 1.0 CB C:ASP236 4.3 18.8 1.0 NE2 C:HIS82 4.5 19.6 1.0 CD C:PRO86 4.6 21.8 1.0 CG C:PRO86 4.7 21.8 1.0 SD C:MET400 4.8 29.5 1.0 O C:HOH644 4.9 17.7 1.0 CG C:MET400 4.9 24.4 1.0 CB C:GLU266 4.9 21.8 1.0 CD C:GLU265 5.0 39.7 1.0

Zinc binding site 6 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:29.0 occ:1.00 OD1 C:ASP236 2.1 17.5 1.0 OD1 C:ASP307 2.1 22.8 1.0 NE2 C:HIS82 2.2 19.6 1.0 O1 C:CO3503 2.2 45.0 1.0 O C:HOH819 2.3 46.2 1.0 OD2 C:ASP307 2.4 22.9 1.0 CG C:ASP307 2.6 21.3 1.0 CE1 C:HIS82 2.9 18.6 1.0 CG C:ASP236 3.0 17.7 1.0 OD2 C:ASP236 3.3 17.0 1.0 ZN C:ZN501 3.3 26.0 1.0 C C:CO3503 3.3 58.0 1.0 CD2 C:HIS82 3.3 19.1 1.0 OE1 C:GLU265 3.8 44.3 1.0 OE2 C:GLU266 3.8 21.9 1.0 O3 C:CO3503 3.8 51.9 1.0 CB C:ASN237 4.0 19.6 1.0 CB C:ASP307 4.1 19.0 1.0 ND1 C:HIS82 4.1 19.4 1.0 CD C:GLU265 4.2 39.7 1.0 O2 C:CO3503 4.2 57.5 1.0 CB C:ASP236 4.3 18.8 1.0 OE2 C:GLU265 4.3 49.1 1.0 CG C:ASN237 4.3 19.8 1.0 CG C:HIS82 4.3 20.2 1.0 CD C:GLU266 4.6 20.6 1.0 ND2 C:ASN237 4.6 21.2 1.0 CA C:ASP236 4.7 19.4 1.0 N C:ASN308 4.8 22.4 1.0 CA C:ASP307 4.8 19.4 1.0 OD1 C:ASN237 4.8 19.8 1.0 C C:ASP236 4.8 20.2 1.0 CA C:ASN237 4.9 18.4 1.0 OE1 C:GLU266 4.9 22.1 1.0 N C:ASN237 5.0 20.1 1.0

Zinc binding site 7 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:25.6 occ:1.00 OD2 D:ASP236 2.0 15.8 1.0 OE2 D:GLU266 2.0 20.5 1.0 O2 D:CO3503 2.1 51.4 1.0 NE2 D:HIS401 2.2 23.1 1.0 O3 D:CO3503 2.3 33.9 1.0 C D:CO3503 2.4 54.0 1.0 OE1 D:GLU266 2.4 23.5 1.0 CD D:GLU266 2.5 20.8 1.0 CG D:ASP236 2.9 16.9 1.0 CD2 D:HIS401 3.1 23.3 1.0 CE1 D:HIS401 3.2 23.8 1.0 OD1 D:ASP236 3.2 16.4 1.0 O D:HOH823 3.3 45.3 1.0 ZN D:ZN502 3.3 28.5 1.0 O1 D:CO3503 3.5 58.3 1.0 OE1 D:GLU265 4.0 45.0 1.0 CG D:GLU266 4.0 20.8 1.0 CG D:HIS401 4.3 22.3 1.0 ND1 D:HIS401 4.3 22.8 1.0 CB D:ASP236 4.3 18.3 1.0 CE1 D:HIS82 4.3 18.5 1.0 NE2 A:HIS156 4.4 33.8 1.0 NE2 D:HIS82 4.4 21.0 1.0 CD D:PRO86 4.6 19.5 1.0 CE1 A:HIS156 4.7 33.9 1.0 CG D:PRO86 4.7 18.8 1.0 SD D:MET400 4.7 29.1 1.0 CG D:MET400 4.8 22.4 1.0 O D:HOH601 4.9 22.5 1.0 CB D:GLU266 4.9 21.4 1.0 CD D:GLU265 4.9 36.6 1.0

Zinc binding site 8 out of 8 in the Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:28.5 occ:1.00 OD1 D:ASP307 2.0 22.8 1.0 OD1 D:ASP236 2.1 16.4 1.0 O3 D:CO3503 2.2 33.9 1.0 NE2 D:HIS82 2.2 21.0 1.0 O D:HOH823 2.3 45.3 1.0 OD2 D:ASP307 2.4 19.1 1.0 CG D:ASP307 2.6 21.1 1.0 CG D:ASP236 3.0 16.9 1.0 CE1 D:HIS82 3.0 18.5 1.0 CD2 D:HIS82 3.2 18.5 1.0 C D:CO3503 3.3 54.0 1.0 ZN D:ZN501 3.3 25.6 1.0 OD2 D:ASP236 3.3 15.8 1.0 O2 D:CO3503 3.8 51.4 1.0 OE2 D:GLU266 3.8 20.5 1.0 OE1 D:GLU265 3.8 45.0 1.0 CB D:ASN237 3.9 22.1 1.0 CB D:ASP307 4.1 19.9 1.0 OE2 D:GLU265 4.2 45.0 1.0 CD D:GLU265 4.2 36.6 1.0 O1 D:CO3503 4.2 58.3 1.0 ND1 D:HIS82 4.2 19.6 1.0 CG D:ASN237 4.3 22.4 1.0 CB D:ASP236 4.3 18.3 1.0 CG D:HIS82 4.3 19.9 1.0 CD D:GLU266 4.6 20.8 1.0 ND2 D:ASN237 4.6 24.5 1.0 CA D:ASP236 4.7 18.3 1.0 N D:ASN308 4.8 22.7 1.0 CA D:ASP307 4.8 20.1 1.0 OD1 D:ASN237 4.8 24.0 1.0 C D:ASP236 4.8 21.2 1.0 OE1 D:GLU266 4.9 23.5 1.0 CA D:ASN237 4.9 20.0 1.0 N D:ASN237 4.9 21.0 1.0

D.D.Nguyen, R.Pandian, D.Kim, S.C.Ha, H.J.Yoon, K.S.Kim, K.H.Yun, J.H.Kim, K.K.Kim. Structural and Kinetic Bases For the Metal Preference of the M18 Aminopeptidase From Pseudomonas Aeruginosa Biochem.Biophys.Res.Commun. V. 447 101 2014.
ISSN: ISSN 0006-291X
PubMed: 24704201
DOI: 10.1016/J.BBRC.2014.03.109