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Iodine in PDB 2noo: Crystal Structure of Mutant Nika

Enzymatic activity of Crystal Structure of Mutant Nika

All present enzymatic activity of Crystal Structure of Mutant Nika:
3.6.3.24;

Protein crystallography data

The structure of Crystal Structure of Mutant Nika, PDB code: 2noo was solved by C.Addy, M.Ohara, F.Kawai, A.Kidera, M.Ikeguchi, S.Fuchigami, M.Osawa, I.Shimada, S.Y.Park, J.R.H.Tame, J.G.Heddle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.82 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.470, 92.248, 116.383, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21

Other elements in 2noo:

The structure of Crystal Structure of Mutant Nika also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mutant Nika (pdb code 2noo). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Mutant Nika, PDB code: 2noo:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 2noo

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Iodine binding site 1 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I300

b:23.7
occ:0.50
 I1 A:TYI300 0.0 23.7 0.5
CE1 A:TYI300 2.1 21.4 1.0
CZ A:TYI300 2.9 20.4 1.0
OH A:TYI300 3.0 22.4 1.0
CD1 A:TYI300 3.1 20.7 1.0
O A:GLU444 3.3 25.4 1.0
CB A:ARG447 4.0 22.2 1.0
CB A:GLU444 4.0 27.2 1.0
CD A:GLU444 4.0 36.5 1.0
N A:GLN448 4.0 18.7 1.0
C A:GLU444 4.1 25.9 1.0
CA A:GLU444 4.1 26.2 1.0
CG A:GLU444 4.2 31.4 1.0
OE2 A:GLU444 4.2 38.5 1.0
CB A:GLN448 4.2 17.9 1.0
NE A:ARG447 4.3 31.8 1.0
CE2 A:TYI300 4.3 20.6 1.0
CG A:TYI300 4.4 18.4 1.0
OE1 A:GLU444 4.4 39.6 1.0
CA A:GLN448 4.5 17.5 1.0
CG A:ARG447 4.5 25.5 1.0
NH2 A:ARG447 4.6 32.0 1.0
C A:ARG447 4.7 20.0 1.0
CD2 A:TYI300 4.9 20.4 1.0
CZ A:ARG447 4.9 31.5 1.0
CA A:ARG447 4.9 21.6 1.0

Iodine binding site 2 out of 6 in 2noo

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Iodine binding site 2 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I300

b:24.2
occ:0.50
 I2 A:TYI300 0.0 24.2 0.5
CE2 A:TYI300 2.1 20.6 1.0
CD2 A:TYI300 3.0 20.4 1.0
CZ A:TYI300 3.1 20.4 1.0
OH A:TYI300 3.3 22.4 1.0
OE1 A:GLN131 3.7 28.7 1.0
CB A:PRO299 3.9 15.8 1.0
NE2 A:GLN131 4.0 29.0 1.0
CD A:GLN131 4.1 25.2 1.0
O A:GLY44 4.1 15.7 1.0
CG A:TYI300 4.3 18.4 1.0
CE1 A:TYI300 4.4 21.4 1.0
O A:HOH1606 4.5 36.8 1.0
CA A:GLY44 4.7 15.7 1.0
C A:GLY44 4.7 14.9 1.0
CG A:PRO299 4.8 14.8 1.0
CD1 A:TYI300 4.9 20.7 1.0
CD A:PRO404 5.0 16.5 1.0

Iodine binding site 3 out of 6 in 2noo

Go back to Iodine Binding Sites List in 2noo
Iodine binding site 3 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I382

b:27.4
occ:0.50
 I1 A:TYI382 0.0 27.4 0.5
CE1 A:TYI382 2.1 17.1 1.0
CD1 A:TYI382 3.0 18.9 1.0
CZ A:TYI382 3.0 19.2 1.0
OH A:TYI382 3.3 20.3 1.0
CG A:TYI382 4.3 15.9 1.0
CE2 A:TYI382 4.4 16.1 1.0
CD2 A:TYI382 4.9 16.7 1.0

Iodine binding site 4 out of 6 in 2noo

Go back to Iodine Binding Sites List in 2noo
Iodine binding site 4 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I382

b:16.3
occ:1.00
 I2 A:TYI382 0.0 16.3 1.0
CE2 A:TYI382 2.1 16.1 1.0
CZ A:TYI382 3.0 19.2 1.0
CD2 A:TYI382 3.0 16.7 1.0
OH A:TYI382 3.1 20.3 1.0
CD A:ARG386 4.0 12.9 1.0
CG A:TYI382 4.3 15.9 1.0
CE1 A:TYI382 4.3 17.1 1.0
NE A:ARG386 4.4 11.3 1.0
NH1 A:ARG386 4.7 10.6 1.0
CZ A:ARG386 4.8 11.1 1.0
CD1 A:TYI382 4.9 18.9 1.0

Iodine binding site 5 out of 6 in 2noo

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Iodine binding site 5 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1271

b:35.0
occ:0.70
 O A:HOH1318 1.8 10.2 0.8
CE1 A:TYR271 2.2 18.7 1.0
OH A:TYR271 2.9 20.4 1.0
CZ A:TYR271 2.9 17.4 1.0
CD1 A:TYR271 3.2 18.5 1.0
O A:HOH1628 3.2 48.3 1.0
OG A:SER308 3.9 22.8 1.0
CB A:GLU267 3.9 10.0 1.0
CG A:GLU267 4.0 10.8 1.0
CD A:GLU267 4.0 13.0 1.0
CE2 A:TYR271 4.2 14.6 1.0
OE2 A:GLU267 4.3 16.4 1.0
O A:HOH1483 4.3 25.7 1.0
CD1 A:LEU318 4.4 16.6 1.0
CG A:TYR271 4.5 13.6 1.0
OE1 A:GLU267 4.5 17.0 1.0
CA A:GLU267 4.5 9.8 1.0
O A:GLU267 4.5 10.8 1.0
O A:HOH1626 4.7 43.0 1.0
CB A:SER308 4.8 20.7 1.0
C A:GLU267 4.8 10.3 1.0
CD2 A:TYR271 4.8 15.3 1.0

Iodine binding site 6 out of 6 in 2noo

Go back to Iodine Binding Sites List in 2noo
Iodine binding site 6 out of 6 in the Crystal Structure of Mutant Nika


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Mutant Nika within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1284

b:26.4
occ:0.50
 CE1 A:TYR284 2.4 25.0 1.0
CD1 A:TYR284 3.2 22.1 1.0
CZ A:TYR284 3.4 23.0 1.0
OH A:TYR284 3.5 24.0 1.0
O A:ALA282 3.7 18.4 1.0
O A:HOH1615 3.7 40.1 1.0
CB A:LEU226 4.1 24.3 1.0
N A:ASP227 4.3 23.3 1.0
OD2 A:ASP227 4.5 25.4 1.0
CG A:TYR284 4.5 19.6 1.0
CE2 A:TYR284 4.6 22.9 1.0
CB A:ASP227 4.7 23.9 1.0
N A:LEU226 4.7 23.8 1.0
C A:ALA282 4.8 17.5 1.0
CG A:ASP227 4.8 26.3 1.0
CA A:LEU226 4.8 24.1 1.0
CD1 A:LEU226 4.9 26.9 1.0
CG A:LEU226 4.9 26.6 1.0
C A:LEU226 5.0 23.4 1.0

Reference:

C.Addy, M.Ohara, F.Kawai, A.Kidera, M.Ikeguchi, S.Fuchigami, M.Osawa, I.Shimada, S.Y.Park, J.R.Tame, J.G.Heddle. Nickel Binding to Nika: An Additional Binding Site Reconciles Spectroscopy, Calorimetry and Crystallography. Acta Crystallogr.,Sect.D V. 63 221 2007.
ISSN: ISSN 0907-4449
PubMed: 17242515
DOI: 10.1107/S0907444906048712
Page generated: Fri Aug 8 13:23:28 2025

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