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Sodium in PDB 5mfs: The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One

Enzymatic activity of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-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-4-Phenyl-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-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 5mfs 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) 89.20 / 1.57
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.827, 120.827, 170.628, 90.00, 90.00, 120.00
R / Rfree (%) 11.3 / 13.9

Other elements in 5mfs:

The structure of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One (pdb code 5mfs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 5mfs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 5mfs

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Sodium binding site 1 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:20.8
occ:1.00
 O A:GLY335 2.3 15.4 1.0
O A:HOH2302 2.3 25.9 1.0
O A:SER332 2.4 13.7 1.0
O A:HOH2214 2.4 25.9 1.0
O A:HOH1927 2.5 19.7 1.0
O A:ASP333 2.8 15.9 1.0
O A:HOH1924 3.3 25.8 0.5
HA A:ASP333 3.3 15.7 1.0
C A:ASP333 3.3 13.5 1.0
C A:GLY335 3.4 14.5 1.0
H A:ARG337 3.4 17.2 1.0
C A:SER332 3.5 13.0 1.0
CA A:ASP333 3.7 13.1 1.0
HB2 A:ARG337 3.8 18.4 1.0
H A:GLY335 3.8 16.0 1.0
N A:GLY335 3.9 13.4 1.0
N A:ARG337 4.0 14.4 1.0
HA A:SER336 4.0 17.5 1.0
N A:ASP333 4.1 13.1 1.0
O A:HOH1861 4.2 26.5 1.0
N A:LEU334 4.2 13.8 1.0
O A:HOH2818 4.2 56.1 1.0
CA A:GLY335 4.2 14.1 1.0
C A:LEU334 4.2 13.6 1.0
O A:HOH2852 4.3 57.0 1.0
N A:SER336 4.3 14.2 1.0
O A:HOH2789 4.3 43.2 1.0
O A:HOH2472 4.4 36.1 1.0
O A:HOH1924 4.5 35.0 0.6
CA A:SER336 4.5 14.6 1.0
O A:HOH1789 4.5 28.6 1.0
CB A:ARG337 4.5 15.3 1.0
C A:SER336 4.6 15.2 1.0
HA A:SER332 4.6 15.1 1.0
HA2 A:GLY335 4.7 16.9 1.0
HB3 A:ARG337 4.7 18.4 1.0
O A:HOH2256 4.7 45.8 1.0
CA A:ARG337 4.7 14.4 1.0
CA A:LEU334 4.7 14.2 1.0
O A:LEU334 4.7 14.5 1.0
CA A:SER332 4.7 12.6 1.0
H A:LEU334 4.8 16.6 1.0
HA A:ARG337 4.8 17.3 1.0
HA A:LEU334 4.9 17.0 1.0
HE A:ARG337 4.9 17.5 1.0
H A:ASP333 4.9 15.7 1.0

Sodium binding site 2 out of 9 in 5mfs

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Sodium binding site 2 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1004

b:43.7
occ:1.00
 O A:HOH1559 2.2 35.1 1.0
O A:HOH2291 2.3 53.4 1.0
O A:HOH2247 2.3 53.4 1.0
O A:PHE774 2.4 18.4 1.0
O A:HOH1322 2.5 47.9 1.0
O A:HIS771 2.6 17.9 1.0
O A:HOH2587 3.2 63.2 1.0
H A:PHE774 3.5 20.5 1.0
C A:PHE774 3.5 17.1 1.0
HA A:ARG772 3.6 23.6 1.0
C A:HIS771 3.7 18.3 1.0
HB3 A:PHE774 3.9 18.9 1.0
N A:PHE774 4.0 17.1 1.0
O A:ARG772 4.1 21.5 1.0
HB A:THR775 4.1 19.9 1.0
C A:ARG772 4.1 19.3 1.0
CA A:ARG772 4.2 19.7 1.0
HA A:THR775 4.2 18.9 1.0
CA A:PHE774 4.3 16.8 1.0
N A:ARG772 4.4 19.8 1.0
O A:GLN770 4.4 19.8 1.0
HA A:GLN770 4.4 23.4 1.0
C A:GLN770 4.4 18.9 1.0
O A:HOH2704 4.5 65.7 1.0
O A:HOH2336 4.5 44.2 1.0
HD2 A:PHE774 4.5 19.1 1.0
N A:HIS771 4.6 17.4 1.0
O A:HOH2665 4.6 66.6 1.0
N A:THR775 4.6 16.6 1.0
CB A:PHE774 4.6 15.8 1.0
O A:LEU769 4.7 18.0 1.0
N A:SER773 4.7 16.9 1.0
CA A:THR775 4.7 15.8 1.0
CA A:HIS771 4.8 16.8 1.0
H A:HIS771 4.9 20.9 1.0
O A:HOH1565 4.9 57.7 1.0
CB A:THR775 4.9 16.6 1.0
C A:SER773 5.0 17.2 1.0
CA A:GLN770 5.0 19.5 1.0

Sodium binding site 3 out of 9 in 5mfs

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Sodium binding site 3 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:50.1
occ:1.00
 O A:HOH2145 2.3 40.5 1.0
O A:HOH1882 2.4 31.4 1.0
O A:HOH2806 2.4 62.5 1.0
OG A:SER508 2.4 21.5 1.0
O A:HOH2060 2.5 31.9 1.0
O A:HOH2340 2.7 58.2 1.0
H A:SER508 3.3 23.1 1.0
HB3 A:SER508 3.4 23.8 1.0
CB A:SER508 3.5 19.8 1.0
O A:HOH1796 3.9 53.5 1.0
N A:SER508 4.1 19.2 1.0
HB2 A:SER508 4.2 23.8 1.0
O A:HOH2288 4.2 57.8 1.0
O A:HOH1214 4.2 36.5 1.0
CA A:SER508 4.3 18.6 1.0
HG23 A:VAL509 4.4 22.5 1.0
OD1 A:ASN507 4.4 22.9 1.0
H A:VAL509 4.6 20.3 1.0
O A:HOH2593 4.7 62.6 1.0
O A:HOH1962 4.8 34.3 1.0
O A:HOH1855 4.9 33.0 1.0
HA A:ASN507 4.9 25.6 1.0
O A:HOH1371 4.9 30.6 1.0
C A:SER508 5.0 17.5 1.0
CG A:ASN507 5.0 23.9 1.0

Sodium binding site 4 out of 9 in 5mfs

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Sodium binding site 4 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:30.0
occ:1.00
 O A:HOH1675 2.3 35.0 1.0
O A:HOH1872 2.4 34.0 1.0
OE1 A:GLU371 2.5 17.4 1.0
O A:HOH2314 2.5 36.1 1.0
O A:HOH1145 2.8 18.0 1.0
O A:HOH1497 2.9 26.6 1.0
CD A:GLU371 3.4 16.0 1.0
HA A:GLU371 3.5 14.7 1.0
OE1 A:GLU123 3.6 19.8 1.0
O A:HOH2279 3.7 37.1 1.0
OE2 A:GLU371 3.7 16.4 1.0
O A:HOH2289 3.7 51.6 1.0
O A:HOH2691 3.8 62.5 1.0
NA A:NA1008 3.9 42.4 1.0
O A:HOH2711 4.0 69.4 1.0
O A:HOH1219 4.0 38.6 1.0
O A:HOH1154 4.0 24.7 1.0
H A:MET372 4.1 13.8 1.0
O A:HOH2579 4.1 52.1 1.0
O A:ILE370 4.3 15.2 1.0
CA A:GLU371 4.4 12.2 1.0
O A:HOH1189 4.5 45.2 1.0
O A:HOH2481 4.5 45.9 1.0
HB2 A:GLU371 4.5 15.5 1.0
CG A:GLU371 4.6 13.8 1.0
CB A:GLU371 4.8 12.9 1.0
N A:MET372 4.8 11.5 1.0
CD A:GLU123 4.8 16.3 1.0
O6 A:MLI1016 4.9 58.2 0.9
HB2 A:GLU123 4.9 15.5 1.0
O A:HOH1632 4.9 15.9 1.0
O A:HOH1261 5.0 46.7 1.0

Sodium binding site 5 out of 9 in 5mfs

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Sodium binding site 5 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:61.8
occ:1.00
 O A:HOH2508 2.2 70.4 1.0
O A:HOH2295 2.4 42.1 1.0
O A:HOH1555 2.4 31.7 1.0
HH A:TYR544 2.8 22.4 1.0
OH A:TYR544 2.8 18.6 1.0
OD1 A:ASP452 2.9 22.4 1.0
O A:HOH2330 3.0 48.1 1.0
O A:HOH1293 3.5 48.3 1.0
HE22 A:GLN550 3.5 29.6 1.0
CZ A:TYR544 3.5 18.0 1.0
O A:HOH2687 3.6 51.7 1.0
CG A:ASP452 3.7 21.8 1.0
OD2 A:ASP452 3.7 22.4 1.0
O A:HOH2674 3.9 48.0 1.0
HE1 A:TYR544 4.0 21.1 1.0
CE1 A:TYR544 4.1 17.6 1.0
O A:HOH1843 4.2 35.8 1.0
NE2 A:GLN550 4.2 24.7 1.0
CE2 A:TYR544 4.3 18.8 1.0
HE2 A:TYR544 4.3 22.6 1.0
O A:LYS545 4.4 22.0 1.0
O A:HOH2453 4.6 58.3 1.0
OE1 A:GLN550 4.7 21.2 1.0
O A:HOH2064 4.7 40.2 1.0
HE21 A:GLN550 4.8 29.6 1.0
H A:ASP452 4.8 23.2 1.0
HB3 A:LYS545 4.8 24.2 0.4
CD A:GLN550 4.9 21.2 1.0
HB2 A:LYS545 4.9 26.6 0.6

Sodium binding site 6 out of 9 in 5mfs

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Sodium binding site 6 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:42.4
occ:1.00
 O A:HOH2481 2.0 45.9 1.0
O A:HOH1154 2.0 24.7 1.0
O A:HOH1605 2.5 18.3 1.0
OE1 A:GLU371 2.7 17.4 1.0
O A:HOH1327 3.0 28.4 1.0
O A:HOH2314 3.1 36.1 1.0
O A:HOH1535 3.1 30.7 1.0
O A:HOH1219 3.2 38.6 1.0
CD A:GLU371 3.2 16.0 1.0
O A:HOH1497 3.3 26.6 1.0
HD22 A:ASN373 3.5 22.7 1.0
OE2 A:GLU371 3.5 16.4 1.0
OE1 A:GLU107 3.8 21.9 1.0
NA A:NA1006 3.9 30.0 1.0
O A:HOH2814 4.0 52.9 1.0
OD1 A:ASP860 4.0 16.6 1.0
O A:HOH1374 4.1 23.0 1.0
OE2 A:GLU107 4.2 20.4 1.0
HG2 A:GLU371 4.2 16.5 1.0
ND2 A:ASN373 4.2 18.9 1.0
OD2 A:ASP860 4.3 15.0 1.0
CG A:GLU371 4.3 13.8 1.0
HD21 A:ASN373 4.4 22.7 1.0
CD A:GLU107 4.4 21.4 1.0
O A:HOH1632 4.4 15.9 1.0
HE21 A:GLN821 4.4 26.3 1.0
CG A:ASP860 4.6 16.3 1.0
HB2 A:ASN373 4.8 18.0 1.0
HG3 A:GLU371 4.9 16.5 1.0
O A:HOH2289 4.9 51.6 1.0
O A:HOH2435 5.0 50.9 1.0

Sodium binding site 7 out of 9 in 5mfs

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Sodium binding site 7 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1009

b:58.6
occ:1.00
 O A:HOH2400 2.2 74.3 1.0
O A:HOH2262 2.4 65.8 1.0
O A:HOH2449 2.6 37.9 1.0
OG1 A:THR91 2.6 17.3 1.0
OD1 A:ASN67 2.7 20.1 1.0
O A:HOH2378 2.9 47.5 1.0
HB A:THR91 3.2 19.9 1.0
H A:THR91 3.3 18.7 1.0
CB A:THR91 3.5 16.6 1.0
CG A:ASN67 3.6 22.1 1.0
N A:THR91 3.7 15.6 1.0
HA A:ASN67 3.9 25.2 1.0
HA A:PHE90 3.9 18.8 1.0
HE22 A:GLN41 4.0 20.2 1.0
O A:HOH2303 4.1 67.6 1.0
CA A:THR91 4.2 15.3 1.0
HB3 A:ASN67 4.3 26.0 1.0
O A:HOH1455 4.3 22.8 1.0
HD21 A:ASN67 4.4 29.8 1.0
CB A:ASN67 4.4 21.6 1.0
C A:PHE90 4.4 14.8 1.0
ND2 A:ASN67 4.4 24.8 1.0
O A:HOH2396 4.5 63.5 1.0
CA A:ASN67 4.6 21.0 1.0
CA A:PHE90 4.6 15.7 1.0
NE2 A:GLN41 4.7 16.8 1.0
HG21 A:THR91 4.7 20.4 1.0
CG2 A:THR91 4.7 17.0 1.0
HA A:THR91 4.7 18.3 1.0
HE21 A:GLN41 4.8 20.2 1.0
O A:HOH2364 4.8 66.8 1.0

Sodium binding site 8 out of 9 in 5mfs

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Sodium binding site 8 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1010

b:65.4
occ:1.00
 NE2 A:GLN517 2.4 27.2 0.4
O A:HOH2586 2.4 61.5 1.0
O A:HOH2249 2.6 61.9 1.0
O A:ASN511 2.7 18.0 1.0
O A:HOH1607 2.7 30.1 0.5
HE21 A:GLN517 2.7 32.6 0.4
OG1 A:THR513 2.9 18.6 1.0
CD A:GLN517 3.4 27.1 0.4
HG23 A:THR513 3.4 21.7 1.0
HG1 A:THR513 3.4 22.3 1.0
H A:THR513 3.5 19.1 1.0
HB2 A:ASN511 3.6 24.1 1.0
OE1 A:GLN517 3.6 26.9 0.4
C A:ASN511 3.8 17.4 1.0
HG21 A:THR513 3.8 21.7 1.0
HB3 A:ASN511 3.8 24.1 1.0
CG2 A:THR513 3.9 18.1 1.0
CB A:THR513 3.9 17.0 1.0
CB A:ASN511 4.1 20.1 1.0
N A:THR513 4.1 15.9 1.0
HG2 A:GLN514 4.2 31.6 0.6
HZ A:PHE519 4.3 27.0 1.0
HE21 A:GLN514 4.4 36.6 0.4
HA A:VAL512 4.4 19.4 1.0
HG3 A:GLN514 4.4 29.4 0.4
OE1 A:GLN517 4.4 17.0 0.6
O A:HOH1822 4.5 64.0 1.0
CA A:ASN511 4.5 17.3 1.0
HE2 A:PHE519 4.5 25.4 1.0
O A:HOH2468 4.6 47.5 1.0
O A:HOH2255 4.6 65.3 1.0
CA A:THR513 4.6 15.9 1.0
HB A:THR513 4.7 20.4 1.0
CG A:GLN517 4.7 27.2 0.4
N A:VAL512 4.8 16.6 1.0
HG22 A:THR513 4.8 21.7 1.0
O A:HOH1931 4.9 24.0 1.0
HG2 A:GLN517 4.9 32.7 0.4
HG3 A:GLN517 4.9 19.6 0.6
NE2 A:GLN514 4.9 30.5 0.4
CA A:VAL512 4.9 16.2 1.0
HG3 A:GLN517 5.0 32.7 0.4
H A:ASN511 5.0 19.7 1.0
C A:VAL512 5.0 16.7 1.0
CZ A:PHE519 5.0 22.5 1.0

Sodium binding site 9 out of 9 in 5mfs

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Sodium binding site 9 out of 9 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1011

b:78.9
occ:1.00
 O A:HOH2783 2.2 68.2 1.0
O A:HOH1293 2.2 48.3 1.0
O A:HOH2265 2.4 49.9 1.0
O A:ASP452 2.5 20.9 1.0
O A:HOH2225 2.6 61.2 1.0
O A:HOH1843 2.6 35.8 1.0
H A:ASP452 3.5 23.2 1.0
C A:ASP452 3.7 19.4 1.0
OD1 A:ASP452 3.9 22.4 1.0
HA A:ASP453 4.1 24.9 1.0
N A:ASP452 4.1 19.4 1.0
O A:HOH2508 4.2 70.4 1.0
HB3 A:LYS451 4.2 25.9 0.4
O A:HOH2745 4.2 64.5 1.0
O A:HOH2345 4.3 40.5 1.0
HB3 A:LYS451 4.3 29.2 0.6
O A:HOH2687 4.4 51.7 1.0
HD2 A:LYS451 4.4 41.8 0.6
HB2 A:ASP453 4.5 30.8 1.0
CA A:ASP452 4.5 19.1 1.0
O A:HOH2295 4.6 42.1 1.0
N A:ASP453 4.7 18.7 1.0
CA A:ASP453 4.8 20.7 1.0

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: Mon Oct 7 22:35:19 2024

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