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Zinc 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:

Chlorine (Cl) 3 atoms
Sodium (Na) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 in 5mfr

Go back to Zinc Binding Sites List in 5mfr
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn1001

b:11.0
occ:1.00
H13 A:7MK1002 1.8 9.7 0.7
O2 A:GOL1011 1.9 15.6 0.1
O2 A:7MK1002 1.9 8.1 0.7
OE1 A:GLU320 2.0 10.3 1.0
NE2 A:HIS301 2.0 9.2 1.0
NE2 A:HIS297 2.0 9.9 1.0
CD A:GLU320 2.7 10.6 1.0
C2 A:GOL1011 2.8 17.1 0.1
O1 A:7MK1002 2.8 11.3 0.7
OE2 A:GLU320 2.9 11.0 1.0
H16 A:7MK1002 2.9 13.1 0.7
CE1 A:HIS301 2.9 11.6 1.0
C9 A:7MK1002 3.0 11.8 0.7
H12 A:7MK1002 3.0 13.6 0.7
CE1 A:HIS297 3.0 10.7 1.0
CD2 A:HIS297 3.0 9.9 1.0
CD2 A:HIS301 3.1 10.5 1.0
HE1 A:HIS301 3.1 13.9 1.0
HE2 A:TYR381 3.2 12.8 1.0
HD2 A:HIS297 3.2 11.8 1.0
HH A:TYR381 3.2 14.9 1.0
HE1 A:HIS297 3.2 12.9 1.0
HD2 A:HIS301 3.3 12.7 1.0
N1 A:7MK1002 3.7 10.9 0.7
O1 A:GOL1011 3.7 17.4 0.1
O A:HOH1358 3.7 15.7 0.1
O3 A:GOL1011 3.7 16.0 0.1
H15 A:7MK1002 3.8 13.1 0.7
C1 A:GOL1011 3.8 18.8 0.1
C3 A:GOL1011 3.9 16.6 0.1
CE2 A:TYR381 3.9 10.6 1.0
OH A:TYR381 3.9 12.4 1.0
HA A:GLU320 3.9 11.0 1.0
H5 A:7MK1002 4.0 15.5 0.7
C11 A:7MK1002 4.0 12.2 0.7
HB A:THR323 4.0 11.3 1.0
HG21 A:THR323 4.0 11.9 1.0
C7 A:7MK1002 4.0 12.9 0.7
ND1 A:HIS301 4.1 10.2 1.0
ND1 A:HIS297 4.1 10.8 1.0
CG A:HIS297 4.2 9.6 1.0
CG A:HIS301 4.2 9.2 1.0
CG A:GLU320 4.2 10.6 1.0
CZ A:TYR381 4.3 10.6 1.0
O A:HOH2536 4.4 13.8 0.1
OE1 A:GLU264 4.4 10.8 1.0
HZ1 A:LYS319 4.4 13.9 1.0
HG22 A:THR323 4.5 11.9 1.0
H14 A:7MK1002 4.5 13.1 0.7
HG3 A:GLU320 4.6 12.7 1.0
HB3 A:GLU320 4.6 11.5 1.0
CG2 A:THR323 4.6 10.0 1.0
H10 A:7MK1002 4.6 14.2 0.7
H31 A:GOL1011 4.7 19.9 0.1
H11 A:GOL1011 4.7 22.6 0.1
C4 A:7MK1002 4.7 11.3 0.7
H11 A:7MK1002 4.7 14.7 0.7
H1 A:7MK1002 4.7 15.4 0.7
CB A:THR323 4.7 9.4 1.0
CB A:GLU320 4.8 9.6 1.0
HG2 A:GLU320 4.8 12.7 1.0
CA A:GLU320 4.8 9.2 1.0
HZ2 A:LYS319 4.8 13.9 1.0
HD1 A:HIS301 4.9 12.2 1.0
OE2 A:GLU264 4.9 11.3 1.0
CD2 A:TYR381 4.9 10.2 1.0
CD A:GLU264 4.9 10.2 1.0
OE2 A:GLU298 4.9 13.1 1.0
HD1 A:HIS297 4.9 13.0 1.0
OE1 A:GLU298 4.9 15.1 1.0
H6 A:7MK1002 4.9 15.5 0.7
C10 A:7MK1002 4.9 11.8 0.7
HG3 A:LYS319 4.9 12.3 1.0
HD2 A:TYR381 5.0 12.2 1.0
C1 A:7MK1002 5.0 12.8 0.7

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: Wed Dec 16 06:33:00 2020

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