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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

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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

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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

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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

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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

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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

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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

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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

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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

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