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Zinc in PDB 4qir: Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe

Enzymatic activity of Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe

All present enzymatic activity of Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe, PDB code: 4qir was solved by B.Nocek, A.Joachimiak, L.Berlicki, S.Vassiliou, A.Mucha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.76 / 1.70
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 223.813, 223.813, 57.958, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe (pdb code 4qir). 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 Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe, PDB code: 4qir:

Zinc binding site 1 out of 1 in 4qir

Go back to Zinc Binding Sites List in 4qir
Zinc binding site 1 out of 1 in the Crystal Structure of Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe


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 Aminopeptidase N in Complex with the Phosphinic Dipeptide Analogue Ll-(R,S)-2-(Pyridin-3-Yl)Ethylglyp[CH2]Phe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn909

b:10.7
occ:0.73
 OE1 A:GLU316 1.9 9.7 1.0
NE2 A:HIS297 2.0 14.8 1.0
NE2 A:HIS293 2.1 11.0 1.0
O13 A:379901 2.2 10.1 1.0
O12 A:379901 2.4 15.4 1.0
OE2 A:GLU316 2.6 11.7 1.0
CD A:GLU316 2.6 10.8 1.0
P11 A:379901 2.7 11.7 1.0
CD2 A:HIS293 2.9 9.7 1.0
H13 A:379901 2.9 9.4 1.0
CD2 A:HIS297 3.0 13.1 1.0
HD2 A:HIS293 3.0 11.6 1.0
CE1 A:HIS297 3.0 12.5 1.0
CE1 A:HIS293 3.1 11.3 1.0
HD2 A:HIS297 3.2 15.7 1.0
HE1 A:HIS297 3.2 15.0 1.0
HE2 A:TYR377 3.4 13.4 1.0
HE1 A:HIS293 3.4 13.5 1.0
HH A:TYR377 3.4 16.3 1.0
N10 A:379901 3.7 7.8 1.0
HA A:GLU316 3.9 12.5 1.0
C3 A:379901 3.9 8.5 1.0
HB A:THR319 4.0 12.2 1.0
CG A:GLU316 4.1 9.0 1.0
C11 A:379901 4.1 12.9 1.0
CE2 A:TYR377 4.1 11.2 1.0
OH A:TYR377 4.1 13.6 1.0
CG A:HIS293 4.1 9.0 1.0
H17 A:379901 4.1 15.4 1.0
ND1 A:HIS297 4.1 11.6 1.0
HG21 A:THR319 4.2 14.3 1.0
CG A:HIS297 4.2 9.4 1.0
ND1 A:HIS293 4.2 11.1 1.0
H18 A:379901 4.2 30.6 1.0
H11 A:379901 4.2 9.4 1.0
OE1 A:GLU260 4.3 8.8 1.0
HZ2 A:LYS315 4.4 13.8 1.0
HG3 A:GLU316 4.5 10.8 1.0
CZ A:TYR377 4.5 11.1 1.0
HG2 A:GLU316 4.6 10.8 1.0
H12 A:379901 4.6 10.2 1.0
HB3 A:GLU316 4.6 15.1 1.0
OE1 A:GLU294 4.6 10.9 1.0
H1 A:379901 4.7 10.5 1.0
HZ3 A:LYS315 4.7 13.8 1.0
HG22 A:THR319 4.7 14.3 1.0
C13 A:379901 4.7 25.5 1.0
CB A:GLU316 4.7 12.6 1.0
CG2 A:THR319 4.7 11.9 1.0
CA A:GLU316 4.8 10.4 1.0
CB A:THR319 4.8 10.2 1.0
CD A:GLU260 4.8 10.9 1.0
OE2 A:GLU260 4.8 11.3 1.0
H16 A:379901 4.9 15.4 1.0
OE2 A:GLU294 4.9 14.7 1.0
HG3 A:LYS315 4.9 13.3 1.0
C1 A:379901 4.9 8.8 1.0
HD1 A:HIS297 4.9 13.9 1.0
NZ A:LYS315 5.0 11.5 1.0
HD1 A:HIS293 5.0 13.3 1.0

Reference:

S.Vassiliou, E.Weglarz-Tomczak, L.Berlicki, M.Paweczak, B.Nocek, R.Mulligan, A.Joachimiak, A.Mucha. Structure-Guided, Single-Point Modifications in the Phosphinic Dipeptide Structure Yield Highly Potent and Selective Inhibitors of Neutral Aminopeptidases. J.Med.Chem. V. 57 8140 2014.
ISSN: ISSN 0022-2623
PubMed: 25192493
DOI: 10.1021/JM501071F
Page generated: Wed Aug 20 21:49:09 2025

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