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Sodium in PDB 5mft: The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-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-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 5mft 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) 60.33 / 1.59
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.651, 120.651, 170.676, 90.00, 90.00, 120.00
R / Rfree (%) 11.1 / 13.9

Other elements in 5mft:

The structure of The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One also contains other interesting chemical elements:

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

Sodium binding site 1 out of 6 in 5mft

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

b:20.9
occ:1.00
 O A:HOH2357 2.3 25.7 1.0
O A:GLY335 2.3 14.6 1.0
O A:HOH2278 2.4 22.5 1.0
O A:SER332 2.4 13.4 1.0
O A:HOH2067 2.5 18.3 1.0
O A:ASP333 2.8 15.1 1.0
O A:HOH1143 3.3 27.6 0.6
HA A:ASP333 3.3 14.1 1.0
C A:ASP333 3.3 13.8 1.0
H A:ARG337 3.4 17.4 1.0
C A:GLY335 3.4 13.8 1.0
C A:SER332 3.5 12.1 1.0
CA A:ASP333 3.8 11.7 1.0
HB2 A:ARG337 3.8 16.2 1.0
H A:GLY335 3.8 14.7 1.0
N A:GLY335 3.9 12.3 1.0
N A:ARG337 4.0 14.5 1.0
HA A:SER336 4.0 17.7 1.0
N A:ASP333 4.1 12.2 1.0
C A:LEU334 4.2 14.0 1.0
CA A:GLY335 4.2 13.6 1.0
N A:LEU334 4.2 13.9 1.0
O A:HOH2941 4.2 53.3 1.0
O A:HOH1978 4.2 27.1 1.0
O A:HOH2903 4.3 52.7 1.0
O A:HOH2962 4.3 60.7 1.0
O A:HOH1143 4.4 34.6 0.5
O A:HOH2536 4.4 32.1 1.0
N A:SER336 4.4 14.1 1.0
O A:HOH1580 4.5 24.9 1.0
CA A:SER336 4.5 14.7 1.0
CB A:ARG337 4.5 13.5 1.0
C A:SER336 4.6 14.4 1.0
HB3 A:ARG337 4.6 16.2 1.0
HA A:SER332 4.6 13.9 1.0
HA2 A:GLY335 4.6 16.4 1.0
O A:LEU334 4.7 15.2 1.0
CA A:LEU334 4.7 13.1 1.0
CA A:SER332 4.7 11.6 1.0
CA A:ARG337 4.7 14.5 1.0
H A:LEU334 4.8 16.7 1.0
O A:HOH2299 4.8 53.7 1.0
HA A:ARG337 4.8 17.4 1.0
HA A:LEU334 4.9 15.7 1.0
HE A:ARG337 5.0 17.1 1.0
H A:ASP333 5.0 14.7 1.0

Sodium binding site 2 out of 6 in 5mft

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Sodium binding site 2 out of 6 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1004

b:41.1
occ:1.00
 O A:HOH1551 2.3 31.9 1.0
O A:PHE774 2.3 17.6 1.0
O A:HOH2325 2.3 48.1 1.0
O A:HOH1493 2.3 46.5 1.0
O A:HOH2270 2.3 51.5 1.0
O A:HIS771 2.6 17.0 1.0
O A:HOH2727 3.4 67.6 1.0
H A:PHE774 3.4 19.7 1.0
C A:PHE774 3.5 16.1 1.0
HA A:ARG772 3.6 21.5 1.0
C A:HIS771 3.6 17.7 1.0
HB3 A:PHE774 4.0 19.8 1.0
N A:PHE774 4.0 16.4 1.0
O A:ARG772 4.0 20.9 1.0
C A:ARG772 4.1 18.3 1.0
HB A:THR775 4.1 20.9 1.0
CA A:ARG772 4.1 17.9 1.0
CA A:PHE774 4.2 16.2 1.0
HA A:THR775 4.2 19.8 1.0
N A:ARG772 4.3 18.2 1.0
O A:GLN770 4.4 19.9 1.0
C A:GLN770 4.4 19.8 1.0
HA A:GLN770 4.5 25.2 1.0
O A:HOH2406 4.6 49.4 1.0
N A:THR775 4.6 16.5 1.0
N A:HIS771 4.6 18.1 1.0
CB A:PHE774 4.6 16.4 1.0
HD2 A:PHE774 4.6 18.6 1.0
O A:HOH2752 4.6 65.6 1.0
N A:SER773 4.6 17.5 1.0
O A:LEU769 4.7 19.4 1.0
O A:HOH2815 4.7 60.4 1.0
CA A:THR775 4.7 16.5 1.0
CA A:HIS771 4.7 17.2 1.0
CB A:THR775 4.9 17.4 1.0
H A:HIS771 4.9 21.7 1.0
C A:SER773 4.9 17.9 1.0
H A:SER773 5.0 21.0 1.0

Sodium binding site 3 out of 6 in 5mft

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Sodium binding site 3 out of 6 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1005

b:45.7
occ:1.00
 O A:HOH2223 2.3 44.2 1.0
OG A:SER508 2.4 21.8 1.0
O A:HOH2172 2.5 27.6 1.0
O A:HOH2008 2.5 28.9 1.0
O A:HOH2933 2.5 59.8 1.0
O A:HOH2410 2.6 58.8 1.0
HB3 A:SER508 3.3 24.2 1.0
H A:SER508 3.4 22.5 1.0
CB A:SER508 3.5 20.2 1.0
O A:HOH1782 3.9 44.2 1.0
O A:HOH2358 4.0 61.0 1.0
N A:SER508 4.1 18.8 1.0
HB2 A:SER508 4.1 24.2 1.0
O A:HOH1157 4.3 33.7 1.0
CA A:SER508 4.4 18.5 1.0
O A:HOH2880 4.5 64.7 1.0
O A:HOH2633 4.5 59.9 1.0
HG23 A:VAL509 4.5 20.1 1.0
OD1 A:ASN507 4.5 21.3 1.0
O A:HOH1739 4.7 29.2 1.0
H A:VAL509 4.7 19.6 1.0
O A:HOH1969 4.8 30.5 1.0
O A:HOH1505 4.9 28.4 1.0
HA A:ASN507 5.0 24.6 1.0

Sodium binding site 4 out of 6 in 5mft

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Sodium binding site 4 out of 6 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1006

b:61.7
occ:0.78
 O A:HOH2842 2.2 58.7 1.0
O A:HOH2344 2.3 52.8 1.0
O A:HOH1268 2.3 46.1 1.0
O A:ASP452 2.3 19.5 1.0
O A:HOH1379 2.5 35.5 1.0
O A:HOH2336 2.7 55.5 1.0
H A:ASP452 3.3 23.5 1.0
HZ1 A:LYS451 3.5 46.1 0.6
C A:ASP452 3.5 19.3 1.0
OD1 A:ASP452 3.8 21.7 1.0
N A:ASP452 3.9 19.6 1.0
HB3 A:LYS451 4.0 28.2 0.4
HB3 A:LYS451 4.0 28.9 0.6
HA A:ASP453 4.1 23.2 1.0
O A:HOH2461 4.2 35.4 1.0
NZ A:LYS451 4.3 38.4 0.6
HZ2 A:LYS451 4.3 46.1 0.6
CA A:ASP452 4.3 19.1 1.0
HZ3 A:LYS451 4.4 46.1 0.6
HB2 A:ASP453 4.5 29.0 1.0
O A:HOH2781 4.5 51.7 1.0
N A:ASP453 4.6 18.5 1.0
O A:HOH2405 4.6 45.9 1.0
CA A:ASP453 4.7 19.4 1.0
HE2 A:LYS451 4.8 42.1 0.4
O A:HOH1508 4.8 41.7 1.0
CB A:LYS451 4.8 23.5 0.4
HA A:LYS451 4.8 25.4 0.6
CG A:ASP452 4.8 20.5 1.0
CB A:LYS451 4.9 24.1 0.6
HA A:LYS451 4.9 25.1 0.4
C A:LYS451 4.9 19.7 1.0

Sodium binding site 5 out of 6 in 5mft

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Sodium binding site 5 out of 6 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1007

b:30.3
occ:1.00
 O A:HOH1693 2.3 43.6 1.0
OE1 A:GLU371 2.5 18.1 1.0
O A:HOH1682 2.5 44.0 1.0
O A:HOH2373 2.7 37.5 1.0
O A:HOH1153 2.8 16.6 1.0
O A:HOH1298 3.0 33.5 1.0
CD A:GLU371 3.3 16.3 1.0
HA A:GLU371 3.4 15.2 1.0
OE1 A:GLU123 3.6 20.9 1.0
O A:HOH1241 3.6 28.5 0.4
OE2 A:GLU371 3.6 16.0 1.0
O A:HOH2370 3.7 42.1 1.0
O A:HOH2743 3.7 61.7 1.0
O A:HOH1614 3.8 33.6 1.0
O A:HOH2738 3.9 63.0 1.0
O A:HOH1176 4.0 29.6 1.0
O A:HOH1241 4.0 26.3 0.6
H A:MET372 4.0 14.4 1.0
O A:ILE370 4.3 16.5 1.0
CA A:GLU371 4.3 12.7 1.0
HB2 A:GLU371 4.4 16.5 1.0
CG A:GLU371 4.6 14.5 1.0
CB A:GLU371 4.7 13.7 1.0
O A:HOH1600 4.7 50.7 1.0
N A:MET372 4.7 12.0 1.0
CD A:GLU123 4.8 17.4 1.0
O A:HOH2817 4.9 65.1 1.0
O A:HOH1711 4.9 18.3 1.0
HB2 A:GLU123 4.9 15.4 1.0
O7 A:MLI1024 5.0 51.3 0.8

Sodium binding site 6 out of 6 in 5mft

Go back to Sodium Binding Sites List in 5mft
Sodium binding site 6 out of 6 in the The Crystal Structure of E. Coli Aminopeptidase N in Complex with 7- Amino-1-Bromo-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-1-Bromo-4-Phenyl-5,7,8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1008

b:56.3
occ:1.00
 O A:HOH1595 2.2 39.5 1.0
OD1 A:ASN399 2.3 16.6 0.3
O A:HOH2246 2.4 55.7 1.0
O A:HOH2035 2.4 72.0 1.0
O A:HOH1658 2.7 59.2 1.0
OD1 A:ASN399 2.7 20.8 0.7
O A:SER429 2.8 19.1 1.0
HD21 A:ASN399 3.1 25.5 0.7
CG A:ASN399 3.2 16.9 0.3
HA A:SER429 3.2 21.1 1.0
HD21 A:ASN399 3.2 21.3 0.3
HZ2 A:LYS402 3.4 50.7 0.8
CG A:ASN399 3.5 19.7 0.7
HD22 A:ASN430 3.5 33.8 0.7
ND2 A:ASN399 3.6 17.7 0.3
C A:SER429 3.6 19.9 1.0
ND2 A:ASN399 3.6 21.3 0.7
CA A:SER429 3.9 17.6 1.0
HB2 A:ASN430 4.0 28.0 0.7
O A:HOH2075 4.0 41.1 1.0
HB2 A:ASN430 4.2 27.1 0.3
NZ A:LYS402 4.2 42.2 0.8
ND2 A:ASN430 4.3 28.2 0.7
O A:HOH1247 4.3 24.5 0.3
HB2 A:SER429 4.3 20.9 1.0
HD22 A:ASN399 4.4 21.3 0.3
HZ3 A:LYS402 4.4 50.7 0.8
O A:ALA428 4.4 19.8 1.0
HD22 A:ASN399 4.4 25.5 0.7
HB3 A:ASN399 4.5 18.8 0.3
CB A:ASN399 4.5 15.6 0.3
HZ1 A:LYS402 4.5 50.7 0.8
HD2 A:LYS402 4.6 40.2 0.8
HD21 A:ASN430 4.7 33.8 0.7
N A:ASN430 4.7 19.9 1.0
HD2 A:LYS402 4.7 26.5 0.2
CB A:SER429 4.7 17.4 1.0
CB A:ASN430 4.8 23.3 0.7
O A:HOH2458 4.9 64.1 1.0
CB A:ASN399 4.9 17.2 0.7
HB2 A:ASN399 4.9 18.8 0.3
CB A:ASN430 4.9 22.6 0.3
HB3 A:ASN430 5.0 27.1 0.3
N A:SER429 5.0 16.3 1.0
CG A:ASN430 5.0 26.2 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: Mon Oct 7 22:39:53 2024

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