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:
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
Go back to
Sodium Binding Sites List in 5mfs
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
|