Atomistry » Iodine » PDB 2fwz-2noo » 2noo
Atomistry »
  Iodine »
    PDB 2fwz-2noo »
      2noo »

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

Go back to Iodine Binding Sites List in 2noo
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

Go back to Iodine Binding Sites List in 2noo
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

Go back to Iodine Binding Sites List in 2noo
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: Sun Aug 11 14:08:06 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy