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Iodine in PDB 3gt4: Structure of Proteinase K with the Magic Triangle I3C

Enzymatic activity of Structure of Proteinase K with the Magic Triangle I3C

All present enzymatic activity of Structure of Proteinase K with the Magic Triangle I3C:
3.4.21.64;

Protein crystallography data

The structure of Structure of Proteinase K with the Magic Triangle I3C, PDB code: 3gt4 was solved by T.Beck, T.Gruene, G.M.Sheldrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 1.76
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.784, 67.784, 101.845, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 19.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Proteinase K with the Magic Triangle I3C (pdb code 3gt4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Structure of Proteinase K with the Magic Triangle I3C, PDB code: 3gt4:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 3gt4

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Iodine binding site 1 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:15.8
occ:0.74
 I3 A:I3C301 0.0 15.8 0.7
C6 A:I3C301 2.1 15.8 1.0
C1 A:I3C301 3.1 15.8 1.0
C5 A:I3C301 3.1 15.8 1.0
C7 A:I3C301 3.2 15.8 1.0
N13 A:I3C301 3.3 15.8 1.0
O8 A:I3C301 3.5 15.8 1.0
O9 A:I3C301 3.6 15.8 1.0
N A:GLY259 3.6 6.3 1.0
CA A:GLY259 3.8 9.6 1.0
O A:HOH607 3.8 20.6 1.0
O A:HOH539 3.9 11.3 1.0
O A:HOH694 4.1 26.3 1.0
O A:ASN270 4.1 7.0 1.0
CB A:LYS258 4.1 12.2 1.0
C A:LYS258 4.1 9.6 1.0
O A:HOH601 4.2 27.6 1.0
C2 A:I3C301 4.4 15.8 1.0
C4 A:I3C301 4.4 15.8 1.0
CB A:ASN270 4.5 3.2 1.0
CA A:LYS258 4.5 9.5 1.0
O A:HOH656 4.5 33.1 1.0
O A:LYS258 4.8 8.4 1.0
C3 A:I3C301 4.9 15.8 1.0
C A:ASN270 5.0 7.3 1.0

Iodine binding site 2 out of 9 in 3gt4

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Iodine binding site 2 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:15.8
occ:0.83
 I2 A:I3C301 0.0 15.8 0.8
C4 A:I3C301 2.1 15.8 1.0
C3 A:I3C301 3.0 15.8 1.0
C5 A:I3C301 3.1 15.8 1.0
C10 A:I3C301 3.2 15.8 1.0
N13 A:I3C301 3.2 15.8 1.0
O12 A:I3C301 3.3 15.8 1.0
O11 A:I3C301 3.9 15.8 1.0
C2 A:I3C301 4.3 15.8 1.0
C6 A:I3C301 4.4 15.8 1.0
O A:HOH514 4.4 30.7 1.0
C1 A:I3C301 4.9 15.8 1.0

Iodine binding site 3 out of 9 in 3gt4

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Iodine binding site 3 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:15.8
occ:0.82
 I1 A:I3C301 0.0 15.8 0.8
C2 A:I3C301 2.1 15.8 1.0
C3 A:I3C301 3.0 15.8 1.0
C1 A:I3C301 3.1 15.8 1.0
C10 A:I3C301 3.2 15.8 1.0
C7 A:I3C301 3.4 15.8 1.0
O11 A:I3C301 3.4 15.8 1.0
O8 A:I3C301 3.7 15.8 1.0
O9 A:I3C301 3.9 15.8 1.0
O12 A:I3C301 3.9 15.8 1.0
C4 A:I3C301 4.3 15.8 1.0
C6 A:I3C301 4.4 15.8 1.0
O A:HOH694 4.4 26.3 1.0
O A:HOH603 4.5 18.1 1.0
C5 A:I3C301 4.9 15.8 1.0
O A:HOH703 4.9 31.2 1.0

Iodine binding site 4 out of 9 in 3gt4

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Iodine binding site 4 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:15.8
occ:0.12
 I3 A:I3C302 0.0 15.8 0.1
C6 A:I3C302 2.1 15.8 0.4
C5 A:I3C302 3.0 15.8 0.4
C1 A:I3C302 3.0 15.8 0.4
C7 A:I3C302 3.2 15.8 0.4
N13 A:I3C302 3.2 15.8 0.4
O9 A:I3C302 3.3 15.8 0.4
O8 A:I3C302 3.8 15.8 0.4
C4 A:I3C302 4.3 15.8 0.4
C2 A:I3C302 4.4 15.8 0.4
O A:HOH731 4.7 42.0 1.0
O A:HOH645 4.8 17.1 1.0
C3 A:I3C302 4.9 15.8 0.4

Iodine binding site 5 out of 9 in 3gt4

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Iodine binding site 5 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:15.8
occ:0.19
 I2 A:I3C302 0.0 15.8 0.2
C4 A:I3C302 2.1 15.8 0.4
C5 A:I3C302 3.0 15.8 0.4
N13 A:I3C302 3.1 15.8 0.4
C3 A:I3C302 3.1 15.8 0.4
C10 A:I3C302 3.4 15.8 0.4
O11 A:I3C302 3.6 15.8 0.4
O A:HOH645 3.7 17.1 1.0
CB A:ALA158 4.0 6.4 1.0
OG A:SER224 4.0 10.5 1.0
C A:LEU133 4.0 6.6 1.0
O12 A:I3C302 4.1 15.8 0.4
OG1 A:THR223 4.1 6.8 1.0
CA A:LEU133 4.1 4.6 1.0
CA A:GLY160 4.2 6.1 1.0
N A:LEU133 4.2 10.6 1.0
C6 A:I3C302 4.3 15.8 0.4
O A:LEU133 4.3 5.6 1.0
N A:GLY134 4.3 13.4 1.0
C2 A:I3C302 4.4 15.8 0.4
O A:HOH584 4.5 9.0 1.0
C A:SER132 4.5 9.0 1.0
O A:SER132 4.6 8.6 1.0
O A:HOH687 4.6 25.5 1.0
O A:HOH631 4.6 29.6 1.0
N A:GLY160 4.7 5.8 1.0
O A:HOH303 4.8 12.7 0.6
C1 A:I3C302 4.9 15.8 0.4
N A:ASN161 4.9 5.9 1.0
C A:GLY160 5.0 6.9 1.0

Iodine binding site 6 out of 9 in 3gt4

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Iodine binding site 6 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:15.8
occ:0.11
 I1 A:I3C302 0.0 15.8 0.1
C2 A:I3C302 2.1 15.8 0.4
O A:HOH628 2.9 32.4 1.0
C3 A:I3C302 3.0 15.8 0.4
C1 A:I3C302 3.1 15.8 0.4
O A:HOH304 3.1 28.7 0.6
C10 A:I3C302 3.1 15.8 0.4
O12 A:I3C302 3.4 15.8 0.4
C7 A:I3C302 3.4 15.8 0.4
O8 A:I3C302 3.4 15.8 0.4
O A:HOH716 3.6 45.0 1.0
O11 A:I3C302 3.7 15.8 0.4
O A:SER221 3.8 8.0 1.0
O A:HOH621 3.9 39.1 1.0
CB A:ASN161 3.9 20.6 1.0
CA A:GLY222 4.1 4.6 1.0
O9 A:I3C302 4.2 15.8 0.4
O A:HOH303 4.3 12.7 0.6
C4 A:I3C302 4.4 15.8 0.4
C6 A:I3C302 4.4 15.8 0.4
C A:SER221 4.7 11.2 1.0
C5 A:I3C302 4.9 15.8 0.4
N A:GLY222 4.9 8.1 1.0

Iodine binding site 7 out of 9 in 3gt4

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Iodine binding site 7 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:15.8
occ:0.21
 I3 A:I3C305 0.0 15.8 0.2
C6 A:I3C305 2.1 15.8 0.4
C5 A:I3C305 3.0 15.8 0.4
C1 A:I3C305 3.1 15.8 0.4
N13 A:I3C305 3.2 15.8 0.4
C7 A:I3C305 3.3 15.8 0.4
O8 A:I3C305 3.4 15.8 0.4
OH A:TYR195 3.7 20.1 1.0
CZ A:TYR195 3.8 13.5 1.0
CE2 A:TYR195 3.9 9.5 1.0
O9 A:I3C305 4.1 15.8 0.4
O A:HOH633 4.1 32.5 1.0
NH2 A:ARG189 4.2 11.4 1.0
CG A:PRO265 4.2 19.7 1.0
C4 A:I3C305 4.3 15.8 0.4
CE1 A:TYR195 4.4 10.7 1.0
C2 A:I3C305 4.4 15.8 0.4
CB A:PRO265 4.5 14.8 1.0
CD2 A:TYR195 4.6 6.4 1.0
OD1 A:ASN163 4.9 9.0 1.0
C3 A:I3C305 4.9 15.8 0.4

Iodine binding site 8 out of 9 in 3gt4

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Iodine binding site 8 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:15.8
occ:0.17
 I2 A:I3C305 0.0 15.8 0.2
C4 A:I3C305 2.1 15.8 0.4
O A:HOH308 2.3 14.9 0.6
O A:HOH635 2.8 40.0 1.0
C5 A:I3C305 3.0 15.8 0.4
C3 A:I3C305 3.0 15.8 0.4
N13 A:I3C305 3.1 15.8 0.4
C10 A:I3C305 3.3 15.8 0.4
O11 A:I3C305 3.6 15.8 0.4
O12 A:I3C305 3.8 15.8 0.4
O A:HOH723 4.1 34.2 1.0
C6 A:I3C305 4.3 15.8 0.4
C2 A:I3C305 4.3 15.8 0.4
CB A:PHE266 4.4 13.4 1.0
N A:PHE266 4.5 9.6 1.0
C1 A:I3C305 4.8 15.8 0.4
O A:PHE266 4.9 13.0 1.0
CB A:PRO265 4.9 14.8 1.0

Iodine binding site 9 out of 9 in 3gt4

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Iodine binding site 9 out of 9 in the Structure of Proteinase K with the Magic Triangle I3C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:15.8
occ:0.18
 I1 A:I3C305 0.0 15.8 0.2
O A:HOH306 2.1 14.1 0.6
C2 A:I3C305 2.1 15.8 0.4
O A:HOH307 2.4 18.8 0.6
C3 A:I3C305 3.1 15.8 0.4
C1 A:I3C305 3.1 15.8 0.4
C7 A:I3C305 3.2 15.8 0.4
C10 A:I3C305 3.3 15.8 0.4
O9 A:I3C305 3.3 15.8 0.4
ND2 A:ASN263 3.6 5.6 1.0
O12 A:I3C305 3.6 15.8 0.4
O11 A:I3C305 3.8 15.8 0.4
O8 A:I3C305 3.8 15.8 0.4
O A:ILE264 4.1 5.4 1.0
CA A:PRO265 4.2 9.2 1.0
C4 A:I3C305 4.4 15.8 0.4
C A:ILE264 4.4 7.5 1.0
C6 A:I3C305 4.4 15.8 0.4
CA A:ASN263 4.5 9.4 1.0
N A:PRO265 4.5 6.3 1.0
C A:ASN263 4.5 2.6 1.0
CG A:ASN263 4.6 7.1 1.0
N A:ILE264 4.7 5.8 1.0
O A:ASN263 4.8 6.9 1.0
CB A:PRO265 4.9 14.8 1.0
C5 A:I3C305 4.9 15.8 0.4

Reference:

T.Beck, T.Gruene, G.M.Sheldrick. The Magic Triangle Goes Mad: Experimental Phasing with A Bromine Derivative Acta Crystallogr.,Sect.D V. 66 374 2010.
ISSN: ISSN 0907-4449
PubMed: 20382990
DOI: 10.1107/S0907444909051609
Page generated: Sun Dec 13 19:27:33 2020

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