Iodine in PDB 5ncu: Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Protein crystallography data
The structure of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin., PDB code: 5ncu
was solved by
T.Goulas,
M.Ksiazek,
I.Garcia-Ferrer,
D.Mizgalska,
J.Potempa,
X.Gomis-Ruth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.89 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.000,
70.040,
90.860,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
18.4
|
Other elements in 5ncu:
The structure of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
(pdb code 5ncu). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the
Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin., PDB code: 5ncu:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
Iodine binding site 1 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 1 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I402
b:32.3
occ:0.43
|
O
|
A:HOH824
|
3.1
|
39.4
|
1.0
|
N
|
A:ASP223
|
3.8
|
23.0
|
1.0
|
CG
|
A:ASP223
|
3.8
|
31.0
|
1.0
|
CB
|
A:ALA62
|
3.9
|
30.2
|
1.0
|
OD2
|
A:ASP223
|
3.9
|
35.1
|
1.0
|
CB
|
A:ASP223
|
4.0
|
25.1
|
1.0
|
CB
|
A:LYS221
|
4.1
|
25.2
|
1.0
|
OD1
|
A:ASP223
|
4.1
|
27.1
|
1.0
|
N
|
A:ALA222
|
4.2
|
24.2
|
1.0
|
CB
|
A:ALA222
|
4.3
|
25.4
|
1.0
|
CD
|
A:LYS221
|
4.3
|
38.9
|
1.0
|
O
|
B:GLY404
|
4.4
|
24.7
|
1.0
|
CA
|
A:ASP223
|
4.5
|
23.2
|
1.0
|
CA
|
A:ALA222
|
4.6
|
25.0
|
1.0
|
C
|
A:ALA222
|
4.6
|
26.3
|
1.0
|
CB
|
B:GLU405
|
4.6
|
26.1
|
1.0
|
CG
|
A:LYS221
|
4.8
|
26.0
|
1.0
|
O
|
A:HOH863
|
4.9
|
46.6
|
1.0
|
C
|
A:LYS221
|
4.9
|
26.2
|
1.0
|
NZ
|
A:LYS221
|
5.0
|
54.6
|
1.0
|
CD
|
B:GLU405
|
5.0
|
62.3
|
1.0
|
OE1
|
B:GLU405
|
5.0
|
47.6
|
1.0
|
|
Iodine binding site 2 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 2 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I403
b:23.8
occ:0.60
|
O
|
A:HOH833
|
3.6
|
34.5
|
1.0
|
N
|
A:THR226
|
3.8
|
22.1
|
1.0
|
CB
|
A:THR225
|
4.1
|
26.6
|
1.0
|
O
|
A:THR226
|
4.2
|
26.3
|
1.0
|
CA
|
A:THR225
|
4.3
|
21.0
|
1.0
|
O
|
A:HOH608
|
4.5
|
25.8
|
1.0
|
C
|
A:THR225
|
4.6
|
24.2
|
1.0
|
CG2
|
A:THR225
|
4.6
|
27.5
|
1.0
|
CA
|
A:THR226
|
4.7
|
21.8
|
1.0
|
CB
|
A:THR226
|
4.7
|
29.3
|
1.0
|
C
|
A:THR226
|
4.9
|
26.7
|
1.0
|
|
Iodine binding site 3 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 3 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I404
b:22.9
occ:0.68
|
O
|
A:HOH868
|
3.4
|
27.3
|
1.0
|
ND2
|
A:ASN169
|
3.6
|
21.5
|
1.0
|
CA
|
A:PRO166
|
3.9
|
18.6
|
1.0
|
N
|
A:PRO166
|
4.0
|
18.9
|
1.0
|
C
|
A:LEU165
|
4.2
|
21.4
|
1.0
|
CE
|
A:LYS182
|
4.2
|
31.8
|
1.0
|
CB
|
A:ASN169
|
4.2
|
19.3
|
1.0
|
O
|
A:HOH872
|
4.2
|
29.3
|
1.0
|
O
|
A:LEU165
|
4.3
|
20.9
|
1.0
|
CG
|
A:ASN169
|
4.4
|
22.0
|
1.0
|
CD
|
A:PRO166
|
4.4
|
20.9
|
1.0
|
O
|
A:HOH716
|
4.4
|
40.1
|
1.0
|
CB
|
A:PRO166
|
4.4
|
21.6
|
1.0
|
CB
|
A:LEU165
|
4.5
|
20.7
|
1.0
|
CG
|
A:PRO166
|
4.6
|
25.8
|
1.0
|
CG
|
A:LYS182
|
4.7
|
28.9
|
1.0
|
CD
|
A:LYS182
|
4.8
|
29.6
|
1.0
|
NZ
|
A:LYS182
|
4.8
|
35.3
|
1.0
|
O
|
A:HOH654
|
4.8
|
49.6
|
1.0
|
|
Iodine binding site 4 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 4 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I405
b:21.1
occ:0.88
|
OG
|
A:SER72
|
3.4
|
20.4
|
0.3
|
OG
|
A:SER108
|
3.5
|
20.8
|
1.0
|
O1
|
A:GOL411
|
3.5
|
31.2
|
0.9
|
OG
|
A:SER72
|
3.5
|
17.1
|
0.4
|
ND2
|
A:ASN76
|
3.6
|
19.8
|
1.0
|
CB
|
A:SER108
|
3.9
|
19.1
|
1.0
|
CB
|
A:SER72
|
3.9
|
18.6
|
0.3
|
C1
|
A:GOL411
|
3.9
|
37.2
|
0.9
|
N
|
A:MET73
|
4.0
|
16.7
|
1.0
|
CB
|
A:SER72
|
4.0
|
18.2
|
0.4
|
CA
|
A:MET73
|
4.1
|
16.2
|
1.0
|
CB
|
A:SER72
|
4.1
|
18.8
|
0.3
|
CE
|
A:MET73
|
4.2
|
22.3
|
1.0
|
C
|
A:SER72
|
4.2
|
18.9
|
1.0
|
CA
|
A:SER108
|
4.4
|
17.2
|
1.0
|
CB
|
A:MET73
|
4.4
|
18.2
|
1.0
|
O
|
A:SER72
|
4.4
|
16.9
|
1.0
|
CD1
|
A:LEU69
|
4.5
|
19.4
|
1.0
|
O
|
A:LEU69
|
4.7
|
16.4
|
1.0
|
CD2
|
A:LEU111
|
4.7
|
23.6
|
1.0
|
CA
|
A:SER72
|
4.8
|
15.9
|
0.3
|
CG
|
A:MET73
|
4.8
|
21.7
|
1.0
|
CG
|
A:ASN76
|
4.8
|
21.3
|
1.0
|
CA
|
A:SER72
|
4.8
|
16.1
|
0.4
|
CA
|
A:SER72
|
4.8
|
15.9
|
0.3
|
OG
|
A:SER72
|
5.0
|
22.4
|
0.3
|
|
Iodine binding site 5 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 5 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I406
b:37.0
occ:0.30
|
O
|
A:HOH632
|
3.1
|
35.4
|
1.0
|
CA
|
A:TYR107
|
3.8
|
19.4
|
1.0
|
N
|
A:ILE41
|
3.9
|
37.5
|
1.0
|
CD1
|
A:TYR107
|
4.0
|
25.2
|
1.0
|
CB
|
A:TYR107
|
4.1
|
20.9
|
1.0
|
CA
|
A:LYS40
|
4.1
|
39.6
|
1.0
|
N
|
A:TYR107
|
4.2
|
18.6
|
1.0
|
CG
|
A:LYS40
|
4.2
|
37.3
|
1.0
|
O
|
A:HOH726
|
4.3
|
30.1
|
1.0
|
O
|
A:HOH538
|
4.4
|
42.7
|
1.0
|
C
|
A:GLU106
|
4.5
|
22.4
|
1.0
|
O
|
A:ILE41
|
4.5
|
38.0
|
1.0
|
CG
|
A:TYR107
|
4.5
|
22.1
|
1.0
|
C
|
A:LYS40
|
4.6
|
43.8
|
1.0
|
O
|
A:GLU106
|
4.6
|
21.9
|
1.0
|
CG1
|
A:ILE41
|
4.6
|
38.4
|
1.0
|
CB
|
A:LYS40
|
4.6
|
41.1
|
1.0
|
O
|
A:HOH598
|
4.8
|
45.9
|
1.0
|
O
|
A:HOH843
|
4.9
|
53.3
|
1.0
|
OG
|
A:SER110
|
4.9
|
35.4
|
1.0
|
|
Iodine binding site 6 out
of 6 in 5ncu
Go back to
Iodine Binding Sites List in 5ncu
Iodine binding site 6 out
of 6 in the Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Structure of the Subtilisin Induced Serpin-Type Proteinase Inhibitor, Miropin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I407
b:40.5
occ:0.28
|
NZ
|
B:LYS407
|
3.3
|
73.8
|
1.0
|
O
|
A:HOH679
|
3.4
|
44.6
|
1.0
|
N
|
A:ASN63
|
3.4
|
22.0
|
1.0
|
CB
|
A:ASN63
|
3.7
|
21.6
|
1.0
|
N
|
A:ALA62
|
3.8
|
28.6
|
1.0
|
CG
|
A:ASN63
|
3.8
|
25.5
|
1.0
|
ND2
|
A:ASN63
|
3.8
|
23.3
|
1.0
|
CB
|
A:GLU61
|
4.0
|
31.2
|
1.0
|
CE
|
B:LYS407
|
4.1
|
62.6
|
1.0
|
CA
|
A:ASN63
|
4.1
|
20.7
|
1.0
|
CB
|
A:ALA62
|
4.2
|
30.2
|
1.0
|
CA
|
A:ALA62
|
4.3
|
29.0
|
1.0
|
C
|
A:ALA62
|
4.3
|
28.9
|
1.0
|
CG
|
A:GLU61
|
4.4
|
39.7
|
1.0
|
OD1
|
A:ASN63
|
4.4
|
22.4
|
1.0
|
OE1
|
B:GLU405
|
4.5
|
47.6
|
1.0
|
C
|
A:GLU61
|
4.5
|
32.1
|
1.0
|
O
|
A:ASN63
|
4.6
|
23.1
|
1.0
|
CA
|
A:GLU61
|
4.6
|
30.4
|
1.0
|
C
|
A:ASN63
|
4.8
|
24.1
|
1.0
|
|
Reference:
T.Goulas,
M.Ksiazek,
I.Garcia-Ferrer,
A.M.Sochaj-Gregorczyk,
I.Waligorska,
M.Wasylewski,
J.Potempa,
F.X.Gomis-Ruth.
A Structure-Derived Snap-Trap Mechanism of A Multispecific Serpin From the Dysbiotic Human Oral Microbiome. J. Biol. Chem. V. 292 10883 2017.
ISSN: ESSN 1083-351X
PubMed: 28512127
DOI: 10.1074/JBC.M117.786533
Page generated: Sun Aug 11 21:36:28 2024
|