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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:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

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

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