Atomistry » Iodine » PDB 5myq-5r4c » 5ncw
Atomistry »
  Iodine »
    PDB 5myq-5r4c »
      5ncw »

Iodine in PDB 5ncw: Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant).

Protein crystallography data

The structure of Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant)., PDB code: 5ncw 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) 55.75 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.600, 74.280, 84.380, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.3

Other elements in 5ncw:

The structure of Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 2 atoms
Chlorine (Cl) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). (pdb code 5ncw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant)., PDB code: 5ncw:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 5ncw

Go back to Iodine Binding Sites List in 5ncw
Iodine binding site 1 out of 4 in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant).


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 Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:22.8
occ:0.44
O A:HOH795 3.5 20.8 0.5
NZ A:LYS52 3.6 28.8 1.0
O A:HOH934 3.7 44.1 1.0
O A:TYR60 3.9 19.7 1.0
C A:TYR60 4.2 19.9 1.0
CA A:THR61 4.2 17.6 1.0
CG2 A:THR61 4.4 20.3 1.0
N A:THR61 4.4 17.4 1.0
CB A:THR61 4.9 21.1 1.0
C A:GLY59 4.9 24.9 1.0
N A:TYR60 4.9 19.9 1.0

Iodine binding site 2 out of 4 in 5ncw

Go back to Iodine Binding Sites List in 5ncw
Iodine binding site 2 out of 4 in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant).


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 Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:17.3
occ:0.39
O A:HOH657 3.3 33.3 1.0
N A:ILE148 3.7 18.7 1.0
O A:ILE148 4.2 21.0 1.0
CA A:TYR147 4.2 18.0 1.0
O A:HOH874 4.4 44.7 1.0
CD2 A:LEU126 4.4 24.4 1.0
C A:TYR147 4.5 20.6 1.0
O A:HOH844 4.5 18.5 0.5
CB A:ILE148 4.5 20.3 1.0
CA A:ILE148 4.5 17.3 1.0
CB A:TYR147 4.6 20.4 1.0
O A:HOH612 4.7 33.7 1.0
O A:HOH658 4.8 17.5 1.0
C A:ILE148 4.8 19.5 1.0
O A:HOH951 4.9 24.4 1.0
CG1 A:ILE148 4.9 21.5 1.0

Iodine binding site 3 out of 4 in 5ncw

Go back to Iodine Binding Sites List in 5ncw
Iodine binding site 3 out of 4 in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant).


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 Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:24.8
occ:0.44
O A:HOH674 3.2 25.7 1.0
O A:HOH995 3.8 34.8 1.0
ND2 B:ASN382 3.9 29.6 1.0
CB A:ARG259 4.1 17.3 1.0
CE A:MET192 4.1 16.9 1.0
CG A:ARG259 4.2 24.0 1.0
CB B:ASN382 4.3 17.9 1.0
CG A:MET192 4.3 17.5 1.0
CB B:HIS380 4.4 19.6 1.0
CG B:ASN382 4.6 24.1 1.0
ND1 B:HIS380 4.6 26.3 1.0
SD A:MET192 4.6 18.4 1.0
CG B:HIS380 4.7 23.5 1.0
CB A:ALA178 4.8 19.9 1.0
CD A:ARG259 4.8 32.8 1.0

Iodine binding site 4 out of 4 in 5ncw

Go back to Iodine Binding Sites List in 5ncw
Iodine binding site 4 out of 4 in the Structure of the Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant).


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 Trypsin Induced Serpin-Type Proteinase Inhibitor, Miropin (V367K/K368A Mutant). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I507

b:19.6
occ:0.28
SD A:MET34 3.2 19.6 0.3
OG A:SER69 3.4 16.8 0.3
OG A:SER69 3.5 14.5 0.7
CG A:MET34 3.6 15.6 0.3
OG A:SER33 3.6 16.3 0.7
OG A:SER33 3.7 20.3 0.3
OD1 A:ASN37 3.7 16.7 1.0
CE A:MET34 3.9 15.2 0.7
CB A:SER69 4.1 15.1 0.3
N A:MET34 4.1 12.2 1.0
CA A:MET34 4.1 11.3 0.7
CB A:SER33 4.1 13.1 0.3
CA A:MET34 4.1 11.3 0.3
CB A:SER69 4.1 14.2 0.7
CB A:MET34 4.3 12.3 0.7
C A:SER33 4.3 14.2 1.0
CD1 A:LEU30 4.4 21.3 1.0
CB A:SER33 4.4 16.7 0.7
CB A:MET34 4.5 12.9 0.3
CA A:SER69 4.5 13.8 0.7
O A:SER33 4.5 12.8 1.0
CA A:SER69 4.6 13.5 0.3
CD2 A:LEU72 4.6 23.1 1.0
O A:LEU30 4.7 13.8 1.0
CG A:MET34 4.7 14.0 0.7
CG A:ASN37 4.8 14.2 1.0
O A:HOH834 4.9 36.4 1.0
CA A:SER33 4.9 11.6 0.3
CE A:MET34 5.0 17.5 0.3

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 Dec 13 19:40:38 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy