Atomistry » Sodium » PDB 5m1y-5mfs » 5mfr
Atomistry »
  Sodium »
    PDB 5m1y-5mfs »
      5mfr »

Sodium 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
Chlorine (Cl) 3 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One (pdb code 5mfr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 1 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1013

b:19.9
occ:1.00
 O A:GLY335 2.3 15.8 1.0
O A:HOH2332 2.3 27.3 1.0
O A:SER332 2.4 13.6 1.0
O A:HOH2209 2.4 24.7 1.0
O A:HOH1970 2.5 19.7 1.0
O A:ASP333 2.8 15.8 1.0
HA A:ASP333 3.3 15.4 1.0
O A:HOH1123 3.3 44.5 1.0
C A:ASP333 3.3 14.0 1.0
C A:GLY335 3.4 14.2 1.0
H A:ARG337 3.5 17.5 1.0
C A:SER332 3.5 12.3 1.0
CA A:ASP333 3.7 12.9 1.0
H A:GLY335 3.8 15.9 1.0
HB2 A:ARG337 3.8 17.5 1.0
N A:GLY335 3.9 13.3 1.0
N A:ARG337 4.0 14.6 1.0
HA A:SER336 4.0 17.5 1.0
N A:ASP333 4.1 12.3 1.0
CA A:GLY335 4.2 14.4 1.0
C A:LEU334 4.2 13.2 1.0
N A:LEU334 4.2 13.3 1.0
O A:HOH2879 4.2 65.1 1.0
O A:HOH1954 4.2 26.6 1.0
O A:HOH2849 4.3 52.6 1.0
O A:HOH2798 4.3 47.4 1.0
N A:SER336 4.3 14.4 1.0
O A:HOH2507 4.4 32.7 1.0
O A:HOH1731 4.5 25.7 1.0
O A:HOH2031 4.5 56.5 1.0
CA A:SER336 4.5 14.6 1.0
CB A:ARG337 4.5 14.6 1.0
C A:SER336 4.6 14.4 1.0
HA A:SER332 4.6 13.8 1.0
HA2 A:GLY335 4.6 17.3 1.0
HB3 A:ARG337 4.6 17.5 1.0
O A:LEU334 4.7 15.5 1.0
CA A:LEU334 4.7 12.7 1.0
CA A:SER332 4.7 11.5 1.0
O A:HOH2325 4.8 51.8 1.0
CA A:ARG337 4.8 14.5 1.0
H A:LEU334 4.8 15.9 1.0
HA A:ARG337 4.9 17.4 1.0
HA A:LEU334 4.9 15.2 1.0
HE A:ARG337 4.9 17.3 1.0
H A:ASP333 4.9 14.8 1.0
HA3 A:GLY335 5.0 17.3 1.0

Sodium binding site 2 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 2 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1014

b:39.7
occ:1.00
 O A:HOH1633 2.3 35.5 1.0
O A:HOH2222 2.3 54.1 1.0
O A:HOH2196 2.3 50.0 1.0
O A:PHE774 2.3 18.8 1.0
O A:HOH1400 2.4 49.5 1.0
O A:HIS771 2.5 18.0 1.0
H A:PHE774 3.4 20.1 1.0
O A:HOH2429 3.4 62.9 1.0
C A:PHE774 3.5 16.0 1.0
C A:HIS771 3.6 17.2 1.0
HA A:ARG772 3.6 21.7 1.0
HB3 A:PHE774 3.9 19.7 1.0
N A:PHE774 3.9 16.8 1.0
O A:ARG772 4.0 22.0 1.0
C A:ARG772 4.0 19.4 1.0
CA A:ARG772 4.1 18.1 1.0
HB A:THR775 4.2 21.7 1.0
CA A:PHE774 4.2 16.0 1.0
HA A:THR775 4.2 20.0 1.0
N A:ARG772 4.3 19.0 1.0
O A:GLN770 4.3 21.0 1.0
C A:GLN770 4.4 19.6 1.0
HA A:GLN770 4.5 22.9 1.0
O A:HOH2383 4.5 50.7 1.0
N A:HIS771 4.5 17.8 1.0
N A:THR775 4.6 15.3 1.0
CB A:PHE774 4.6 16.4 1.0
HD2 A:PHE774 4.6 19.4 1.0
O A:HOH2703 4.6 65.3 1.0
N A:SER773 4.6 17.1 1.0
CA A:HIS771 4.7 17.1 1.0
O A:HOH1417 4.7 55.3 1.0
O A:LEU769 4.7 18.9 1.0
CA A:THR775 4.8 16.6 1.0
H A:HIS771 4.8 21.4 1.0
O A:HOH2683 4.8 56.8 1.0
C A:SER773 4.9 18.1 1.0
CB A:THR775 4.9 18.1 1.0
H A:SER773 5.0 20.6 1.0
CA A:GLN770 5.0 19.1 1.0

Sodium binding site 3 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 3 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1015

b:51.0
occ:1.00
 O A:HOH2163 2.3 40.8 1.0
OG A:SER508 2.4 23.3 1.0
O A:HOH2835 2.4 64.5 1.0
O A:HOH1924 2.4 30.8 1.0
O A:HOH1999 2.5 31.4 1.0
O A:HOH2359 2.6 63.0 1.0
H A:SER508 3.3 22.4 1.0
HB3 A:SER508 3.4 25.6 1.0
CB A:SER508 3.5 21.3 1.0
O A:HOH1859 4.0 51.5 1.0
N A:SER508 4.1 18.7 1.0
HB2 A:SER508 4.1 25.6 1.0
O A:HOH2365 4.2 59.9 1.0
O A:HOH1166 4.3 36.7 1.0
CA A:SER508 4.3 18.0 1.0
HG23 A:VAL509 4.4 22.2 1.0
O A:HOH2706 4.5 61.6 1.0
OD1 A:ASN507 4.5 23.4 1.0
H A:VAL509 4.7 19.2 1.0
O A:HOH1721 4.7 31.3 1.0
O A:HOH1871 4.8 32.4 1.0
O A:HOH1452 4.9 31.4 1.0

Sodium binding site 4 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 4 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1016

b:76.8
occ:1.00
 O A:HOH2692 2.1 66.0 1.0
O A:HOH2283 2.3 52.8 1.0
O A:ASP452 2.3 19.1 1.0
O A:HOH1263 2.4 49.6 1.0
O A:HOH1149 2.5 36.4 1.0
O A:HOH2265 2.7 52.2 1.0
HZ1 A:LYS451 3.0 46.8 0.5
H A:ASP452 3.3 21.6 1.0
O A:HOH2504 3.5 73.8 1.0
C A:ASP452 3.5 17.7 1.0
HZ3 A:LYS451 3.7 46.8 0.5
NZ A:LYS451 3.8 39.0 0.5
OD1 A:ASP452 3.9 22.4 1.0
N A:ASP452 3.9 18.0 1.0
HB3 A:LYS451 4.0 26.8 0.5
HB3 A:LYS451 4.0 28.9 0.5
O A:HOH2375 4.1 39.7 1.0
HA A:ASP453 4.2 23.7 1.0
HZ2 A:LYS451 4.2 46.8 0.5
CA A:ASP452 4.3 17.9 1.0
HB2 A:ASP453 4.4 29.4 1.0
O A:HOH1594 4.5 49.3 1.0
N A:ASP453 4.6 18.0 1.0
O A:HOH2340 4.6 47.1 1.0
HE3 A:LYS451 4.7 45.7 0.5
CA A:ASP453 4.7 19.7 1.0
HA A:LYS451 4.8 22.3 0.5
CE A:LYS451 4.8 38.1 0.5
HA A:LYS451 4.8 23.0 0.5
CB A:LYS451 4.9 24.1 0.5
CB A:LYS451 4.9 22.3 0.5
NA A:NA1019 4.9 52.7 1.0
C A:LYS451 4.9 18.1 1.0
CG A:ASP452 4.9 20.1 1.0

Sodium binding site 5 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 5 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1017

b:29.1
occ:1.00
 O A:HOH1418 2.2 42.2 1.0
O A:HOH1597 2.4 43.1 1.0
OE1 A:GLU371 2.5 18.7 1.0
O A:HOH2317 2.5 44.8 1.0
O A:HOH1159 2.8 17.7 1.0
O A:HOH1273 3.0 31.4 1.0
CD A:GLU371 3.3 16.6 1.0
HA A:GLU371 3.5 16.3 1.0
O A:HOH1670 3.6 25.5 0.5
OE2 A:GLU371 3.6 16.4 1.0
HZ1 A:LYS8 3.6 32.2 0.3
OE1 A:GLU123 3.6 21.5 1.0
O A:HOH2312 3.7 43.2 1.0
O A:HOH1437 3.8 21.6 0.7
O A:HOH2191 3.9 58.2 1.0
H A:MET372 4.0 15.3 1.0
O A:HOH1117 4.1 29.4 1.0
O A:HOH1670 4.1 24.9 0.5
O A:HOH2637 4.1 33.0 0.6
O A:HOH1437 4.2 12.9 0.3
O A:HOH1193 4.2 27.8 0.5
O A:ILE370 4.3 17.3 1.0
HZ3 A:LYS8 4.3 32.2 0.3
NZ A:LYS8 4.3 26.9 0.3
CA A:GLU371 4.4 13.6 1.0
HZ2 A:LYS8 4.4 32.2 0.3
HB2 A:GLU371 4.4 16.9 1.0
CG A:GLU371 4.6 14.1 1.0
CB A:GLU371 4.7 14.1 1.0
N A:MET372 4.8 12.7 1.0
O A:HOH1929 4.8 31.7 0.5
CD A:GLU123 4.9 18.1 1.0
HE3 A:LYS8 4.9 24.3 0.2
O A:HOH1680 4.9 18.2 1.0
O7 A:MLI1023 4.9 55.4 0.8
HZ3 A:LYS8 4.9 23.1 0.2
HB2 A:GLU123 5.0 15.7 1.0

Sodium binding site 6 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 6 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1018

b:59.5
occ:1.00
 O A:HOH2394 2.2 75.2 1.0
O A:HOH2409 2.4 40.3 1.0
O A:HOH2246 2.5 70.8 1.0
HG1 A:THR91 2.6 22.5 1.0
OG1 A:THR91 2.6 18.7 1.0
OD1 A:ASN67 2.7 21.1 1.0
O A:HOH2356 3.3 53.4 1.0
H A:THR91 3.3 17.6 1.0
HB A:THR91 3.3 20.1 1.0
CB A:THR91 3.5 16.7 1.0
CG A:ASN67 3.6 23.5 1.0
N A:THR91 3.7 14.7 1.0
HA A:PHE90 3.9 17.8 1.0
HA A:ASN67 3.9 25.0 1.0
HE22 A:GLN41 4.0 19.8 1.0
CA A:THR91 4.2 14.4 1.0
O A:HOH1498 4.3 25.4 1.0
HB3 A:ASN67 4.3 27.1 1.0
HD21 A:ASN67 4.4 33.6 1.0
ND2 A:ASN67 4.4 28.0 1.0
C A:PHE90 4.4 14.2 1.0
CB A:ASN67 4.4 22.6 1.0
CA A:PHE90 4.6 14.8 1.0
CA A:ASN67 4.6 20.9 1.0
NE2 A:GLN41 4.7 16.5 1.0
HG21 A:THR91 4.7 21.9 1.0
CG2 A:THR91 4.8 18.2 1.0
HE21 A:GLN41 4.8 19.8 1.0
HA A:THR91 4.8 17.2 1.0
O A:HOH1258 5.0 37.1 1.0

Sodium binding site 7 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 7 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1019

b:52.7
occ:1.00
 O A:HOH2340 2.3 47.1 1.0
O A:HOH1535 2.5 27.2 1.0
O A:HOH2504 2.6 73.8 1.0
OD1 A:ASP452 2.7 22.4 1.0
HH A:TYR544 2.7 23.0 1.0
OH A:TYR544 2.8 19.2 1.0
O A:HOH2653 3.1 65.7 1.0
O A:HOH2263 3.1 42.2 1.0
O A:HOH1263 3.4 49.6 1.0
CZ A:TYR544 3.5 16.2 1.0
CG A:ASP452 3.5 20.1 1.0
O A:HOH1594 3.6 49.3 1.0
HE22 A:GLN550 3.6 28.2 1.0
OD2 A:ASP452 3.6 21.6 1.0
HE1 A:TYR544 3.9 20.4 1.0
O A:HOH1149 3.9 36.4 1.0
CE1 A:TYR544 4.0 17.0 1.0
O A:HOH2721 4.0 37.7 1.0
CE2 A:TYR544 4.3 17.2 1.0
NE2 A:GLN550 4.4 23.5 1.0
HE2 A:TYR544 4.4 20.7 1.0
O A:LYS545 4.4 20.4 1.0
H A:ASP452 4.5 21.6 1.0
O A:HOH2118 4.8 41.0 1.0
OE1 A:GLN550 4.8 20.5 1.0
HB3 A:LYS545 4.8 26.8 0.4
NA A:NA1016 4.9 76.8 1.0
O A:HOH2455 4.9 61.1 1.0
HE21 A:GLN550 4.9 28.2 1.0
HB2 A:LYS545 4.9 25.5 0.6
CB A:ASP452 4.9 18.9 1.0

Sodium binding site 8 out of 8 in 5mfr

Go back to Sodium Binding Sites List in 5mfr
Sodium binding site 8 out of 8 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 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-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1020

b:26.4
occ:0.30
 HE1 A:MET260 1.2 46.4 0.7
CE A:MET260 1.9 38.7 0.7
HE3 A:MET260 1.9 46.4 0.7
O A:HOH2146 1.9 19.4 0.3
OE1 A:GLN821 2.2 19.0 0.4
OD1 A:ASN373 2.4 16.2 0.4
O A:HOH2146 2.4 25.4 0.7
HE2 A:MET260 2.4 46.4 0.7
O A:HOH1701 2.5 15.6 0.3
OD1 A:ASN373 2.8 15.8 0.6
SD A:MET260 2.8 19.6 0.3
O A:HOH1591 2.8 24.6 0.7
HB3 A:ASN373 2.9 18.7 0.6
CG A:ASN373 3.1 14.9 0.4
CG A:ASN373 3.1 14.9 0.6
CD A:GLN821 3.2 17.9 0.4
HE22 A:GLN821 3.3 19.6 0.6
SD A:MET260 3.4 36.5 0.7
NE2 A:GLN821 3.4 16.3 0.6
HG3 A:MET260 3.4 23.4 0.3
HE2 A:MET260 3.5 28.7 0.3
CB A:ASN373 3.5 15.6 0.6
O A:HOH1701 3.5 17.7 0.7
CD A:GLN821 3.5 14.7 0.6
HE22 A:GLN821 3.5 20.1 0.4
OE1 A:GLN821 3.6 15.8 0.6
CE A:MET260 3.6 23.9 0.3
CG A:MET260 3.6 19.5 0.3
HE21 A:GLN821 3.7 19.6 0.6
HB3 A:ASN373 3.8 17.6 0.4
ND2 A:ASN373 3.8 13.6 0.4
NE2 A:GLN821 3.8 16.7 0.4
HD21 A:ASN373 3.8 16.4 0.4
HE1 A:MET260 3.8 28.7 0.3
HA A:ASN373 3.8 16.1 0.4
O A:GLU121 3.8 12.9 1.0
HG2 A:MET260 3.9 23.4 0.3
CB A:ASN373 3.9 14.7 0.4
HG2 A:GLN821 4.0 17.4 0.6
ND2 A:ASN373 4.0 16.7 0.6
H A:ALA122 4.1 13.7 1.0
HA A:ASN373 4.1 16.3 0.6
O A:HOH2270 4.2 34.0 1.0
HB2 A:ASN373 4.2 18.7 0.6
HD21 A:ASN373 4.2 20.0 0.6
CG A:GLN821 4.3 14.5 0.6
O A:HOH1371 4.3 19.8 1.0
HG2 A:GLN821 4.3 19.4 0.4
OE1 A:GLU107 4.4 20.9 0.3
CA A:ASN373 4.4 13.6 0.6
CA A:ASN373 4.4 13.4 0.4
CG A:GLN821 4.4 16.2 0.4
HD22 A:ASN373 4.5 16.4 0.4
HD22 A:ASN373 4.5 20.0 0.6
HG3 A:MET260 4.5 36.9 0.7
HE3 A:MET260 4.5 28.7 0.3
CG A:MET260 4.6 30.8 0.7
HE21 A:GLN821 4.6 20.1 0.4
C A:GLU121 4.6 11.9 1.0
N A:ALA122 4.6 11.4 1.0
HB3 A:GLN821 4.7 16.7 0.6
HB3 A:GLN821 4.7 17.4 0.4
HG2 A:MET260 4.7 36.9 0.7
O A:ASN373 4.8 14.4 0.6
O A:HOH2243 4.8 12.8 0.3
O A:HOH1483 4.8 13.9 0.3
HB2 A:ASN373 4.8 17.6 0.4
HE21 A:GLN119 4.8 15.1 1.0
H8 A:7MK1002 4.9 15.4 0.7
O A:ASN373 4.9 11.8 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: Mon Oct 7 22:35:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy