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Chlorine in PDB 5mfr: The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One

Enzymatic activity of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One

All present enzymatic activity of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One:
3.4.11.2;

Protein crystallography data

The structure of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 5mfr was solved by G.Peng, V.Olieric, A.G.Mcewen, C.Schmitt, S.Albrecht, J.Cavarelli, C.Tarnus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.38 / 1.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.755, 120.755, 170.695, 90.00, 90.00, 120.00
R / Rfree (%) 10.4 / 12.7

Other elements in 5mfr:

The structure of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One (pdb code 5mfr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 5mfr:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5mfr

Go back to Chlorine Binding Sites List in 5mfr
Chlorine binding site 1 out of 3 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1027

b:47.8
occ:1.00
 H A:ASP216 2.3 22.0 0.3
H A:ASP216 2.3 22.0 0.7
O A:HOH1661 2.5 29.3 1.0
HB3 A:ALA254 3.0 16.4 1.0
HD22 A:ASN219 3.0 44.0 1.0
HD11 A:LEU277 3.1 21.7 1.0
N A:ASP216 3.2 18.4 1.0
HA A:VAL215 3.2 17.2 1.0
HB2 A:ASP216 3.3 27.6 0.7
HB A:VAL215 3.4 17.5 1.0
HG A:SER273 3.4 18.3 0.5
HB2 A:ASP216 3.4 25.4 0.3
O A:ALA254 3.4 16.8 1.0
HB1 A:ALA254 3.5 16.4 1.0
OG A:SER273 3.6 15.3 0.5
HD21 A:LEU277 3.6 23.2 1.0
CB A:ALA254 3.7 13.6 1.0
CG A:ASP216 3.7 23.1 0.7
HB3 A:SER273 3.7 17.1 0.5
CB A:ASP216 3.8 21.2 0.3
ND2 A:ASN219 3.8 36.7 1.0
CB A:ASP216 3.8 23.0 0.7
CA A:VAL215 3.9 14.3 1.0
OD2 A:ASP216 3.9 24.8 0.7
HD21 A:ASN219 4.0 44.0 1.0
C A:ALA254 4.0 13.2 1.0
C A:VAL215 4.0 15.9 1.0
CB A:VAL215 4.0 14.6 1.0
OD1 A:ASP216 4.1 22.3 0.7
HB2 A:SER273 4.1 17.1 0.5
CD1 A:LEU277 4.1 18.1 1.0
CA A:ASP216 4.1 20.0 0.3
CA A:ASP216 4.1 19.9 0.7
HG12 A:VAL215 4.1 18.4 1.0
HB3 A:SER273 4.3 15.0 0.5
CB A:SER273 4.4 14.3 0.5
OD1 A:ASP256 4.4 24.7 1.0
HB2 A:ALA254 4.4 16.4 1.0
O A:HOH1636 4.5 22.3 1.0
CD2 A:LEU277 4.5 19.4 1.0
CA A:ALA254 4.5 12.0 1.0
HD13 A:LEU277 4.5 21.7 1.0
HA A:VAL255 4.6 14.8 1.0
CB A:SER273 4.6 12.5 0.5
HD12 A:LEU277 4.6 21.7 1.0
HG A:LEU277 4.6 19.9 1.0
HB2 A:ASN219 4.6 32.3 1.0
CG1 A:VAL215 4.6 15.3 1.0
HA A:ASP216 4.7 24.0 0.3
HA A:ASP216 4.7 23.9 0.7
CG A:LEU277 4.7 16.6 1.0
HB3 A:ASP216 4.7 25.4 0.3
HB3 A:ASP216 4.7 27.6 0.7
N A:VAL255 4.8 12.5 1.0
CG A:ASN219 4.9 32.1 1.0
HD22 A:LEU277 4.9 23.2 1.0
HB3 A:ASN219 4.9 32.3 1.0
HG A:SER273 5.0 19.0 0.5
HA A:SER273 5.0 14.2 0.5
H A:ALA254 5.0 13.3 1.0
O A:HOH2058 5.0 54.8 1.0

Chlorine binding site 2 out of 3 in 5mfr

Go back to Chlorine Binding Sites List in 5mfr
Chlorine binding site 2 out of 3 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1028

b:50.5
occ:1.00
 H A:ASP561 2.1 22.9 1.0
HA A:ASN560 2.8 22.8 0.8
HA A:ASN560 2.8 22.3 0.2
N A:ASP561 2.9 19.1 1.0
O A:HOH2466 3.0 37.6 1.0
HB2 A:ASP561 3.1 25.2 1.0
CG A:ASP561 3.5 26.0 1.0
OD1 A:ASP561 3.5 29.0 1.0
CA A:ASN560 3.6 19.0 0.8
CB A:ASP561 3.6 21.0 1.0
CA A:ASN560 3.6 18.6 0.2
OD1 A:ASN560 3.7 19.7 0.8
CG A:ASN560 3.7 22.7 0.8
C A:ASN560 3.7 17.4 1.0
HD22 A:ASN560 3.7 27.4 0.2
CA A:ASP561 3.9 17.7 1.0
O A:HOH2358 3.9 51.7 0.8
ND2 A:ASN560 4.0 26.5 0.8
O A:ARG559 4.0 24.2 1.0
HB3 A:ASN560 4.0 24.6 0.2
OD2 A:ASP561 4.1 29.2 1.0
HD21 A:ASN560 4.1 31.8 0.8
O A:HOH2076 4.2 56.8 1.0
CB A:ASN560 4.3 21.5 0.8
O A:HOH2815 4.3 56.2 1.0
HD22 A:ASN560 4.3 31.8 0.8
H A:PHE562 4.3 19.2 1.0
O A:HOH1382 4.3 30.5 1.0
HB2 A:ALA338 4.4 22.4 1.0
CB A:ASN560 4.4 20.5 0.2
HA A:ASP561 4.4 21.3 1.0
HB3 A:ASP561 4.5 25.2 1.0
ND2 A:ASN560 4.6 22.9 0.2
O A:HOH1235 4.6 49.1 1.0
N A:ASN560 4.7 18.2 1.0
HB2 A:ASN560 4.8 25.8 0.8
C A:ARG559 4.8 21.2 1.0
O A:HOH1155 4.9 34.6 1.0
N A:PHE562 4.9 16.0 1.0
O A:ASN560 5.0 17.4 1.0
C A:ASP561 5.0 16.1 1.0

Chlorine binding site 3 out of 3 in 5mfr

Go back to Chlorine Binding Sites List in 5mfr
Chlorine binding site 3 out of 3 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1029

b:61.1
occ:1.00
 H A:GLN32 2.4 20.6 1.0
H A:ALA31 2.9 19.4 1.0
O A:HOH2039 2.9 24.6 1.0
HG2 A:GLN32 3.0 33.8 1.0
HB3 A:ALA31 3.1 23.9 1.0
O A:HOH1434 3.1 21.7 1.0
N A:GLN32 3.2 17.1 1.0
N A:ALA31 3.4 16.2 1.0
O A:HOH1891 3.4 44.6 0.5
HB2 A:GLN32 3.4 26.5 1.0
O A:HOH2233 3.5 51.3 1.0
CG A:GLN32 3.8 28.1 1.0
CB A:ALA31 3.9 19.9 1.0
CB A:ASP30 3.9 32.0 1.0
CA A:ALA31 3.9 16.2 1.0
CB A:GLN32 3.9 22.1 1.0
C A:ALA31 4.1 16.5 1.0
HA A:ASP30 4.1 21.2 1.0
C A:ASP30 4.1 16.4 1.0
HG3 A:GLN32 4.1 33.8 1.0
O A:HOH2682 4.2 28.4 1.0
CA A:GLN32 4.2 19.1 1.0
H A:LYS33 4.2 19.9 1.0
HB2 A:ALA31 4.3 23.9 1.0
CA A:ASP30 4.3 17.6 1.0
HZ2 A:LYS151 4.5 39.5 0.4
HE21 A:GLN32 4.6 46.9 1.0
HB1 A:ALA31 4.6 23.9 1.0
O A:HOH2523 4.7 47.4 1.0
HA A:GLN32 4.9 22.9 1.0
HB3 A:GLN32 4.9 26.5 1.0
HA A:ALA31 4.9 19.4 1.0
N A:LYS33 4.9 16.6 1.0
HZ3 A:LYS151 5.0 39.5 0.4

Reference:

G.Peng, A.G.Mcewen, V.Olieric, C.Schmitt, S.Albrecht, J.Cavarelli, C.Tarnus. Insight Into the Remarkable Affinity and Selectivity of the Aminobenzosuberone Scaffold For the M1 Aminopeptidases Family Based on Structure Analysis. Proteins V. 85 1413 2017.
ISSN: ESSN 1097-0134
PubMed: 28383176
DOI: 10.1002/PROT.25301
Page generated: Sat Jul 12 05:27:32 2025

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