Atomistry » Iodine » PDB 5kkg-5nfi » 5kss
Atomistry »
  Iodine »
    PDB 5kkg-5nfi »
      5kss »

Iodine in PDB 5kss: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller):
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller), PDB code: 5kss was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, A.M.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.941, 80.118, 71.511, 90.00, 95.51, 90.00
R / Rfree (%) 27.2 / 32.9

Other elements in 5kss:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) (pdb code 5kss). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller), PDB code: 5kss:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5kss

Go back to Iodine Binding Sites List in 5kss
Iodine binding site 1 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:0.2
occ:0.54
 ND2 A:ASN44 3.5 42.6 1.0
N A:ASN44 3.6 53.4 1.0
CG A:ASN44 3.8 44.8 1.0
ND2 B:ASN44 3.8 46.8 1.0
N B:ASN44 4.0 61.4 1.0
CB A:ASN44 4.0 49.0 1.0
CA A:SER43 4.1 57.6 1.0
CG B:ASN44 4.1 66.5 1.0
C A:SER43 4.3 55.9 1.0
O A:TYR103 4.3 46.0 1.0
CA B:SER43 4.3 63.0 1.0
O B:TYR103 4.3 58.7 1.0
OD1 A:ASN44 4.4 45.8 1.0
CB B:ASN44 4.4 66.4 1.0
CA A:ASN44 4.5 51.5 1.0
O A:HOH608 4.5 51.4 1.0
OG A:SER43 4.5 58.9 1.0
CB B:TYR103 4.5 72.5 1.0
O A:ALA42 4.5 63.3 1.0
C B:SER43 4.6 60.3 1.0
CA B:TYR103 4.6 64.8 1.0
OG B:SER43 4.7 67.2 1.0
CA A:TYR103 4.7 46.8 1.0
CB A:TYR103 4.7 47.1 1.0
O B:ALA42 4.7 68.9 1.0
OD1 B:ASN44 4.7 46.7 1.0
CD1 B:TYR103 4.7 77.7 1.0
CA B:ASN44 4.8 62.0 1.0
CB A:SER43 4.8 59.0 1.0
C A:TYR103 4.9 47.5 1.0
C B:TYR103 4.9 59.8 1.0
CD1 A:TYR103 5.0 54.5 1.0
CG B:TYR103 5.0 77.6 1.0

Iodine binding site 2 out of 3 in 5kss

Go back to Iodine Binding Sites List in 5kss
Iodine binding site 2 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:75.3
occ:0.41
 NE2 B:HIS235 3.3 71.6 1.0
N A:TYR241 3.5 74.0 1.0
CE1 B:HIS235 3.7 71.1 1.0
CB A:TYR241 3.9 75.4 1.0
CD1 A:TYR241 4.0 69.1 1.0
NE2 B:GLN242 4.1 77.8 0.0
O A:THR239 4.1 69.6 1.0
N A:GLN242 4.1 73.1 1.0
CA A:TYR241 4.1 75.5 1.0
C A:ARG240 4.3 74.8 1.0
CA A:ARG240 4.4 69.4 1.0
CG A:GLN242 4.4 68.0 0.0
CG A:TYR241 4.4 73.4 1.0
I A:IOD505 4.5 71.2 0.5
CE1 A:HIS235 4.5 73.9 1.0
NE2 A:GLN242 4.6 66.0 0.0
CD2 B:HIS235 4.6 68.6 1.0
C A:TYR241 4.6 78.3 1.0
CD A:GLN242 4.8 67.8 0.0
CB A:GLN242 4.9 70.4 1.0
ND1 B:HIS235 5.0 68.5 1.0
NE2 A:HIS235 5.0 73.5 1.0

Iodine binding site 3 out of 3 in 5kss

Go back to Iodine Binding Sites List in 5kss
Iodine binding site 3 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:71.2
occ:0.48
 NE2 A:HIS235 3.0 73.5 1.0
CE1 A:HIS235 3.2 73.9 1.0
N B:TYR241 3.5 65.3 1.0
CG B:GLN242 3.9 78.2 1.0
N B:GLN242 3.9 79.8 1.0
NE2 B:GLN242 4.0 77.8 0.0
CA B:ARG240 4.1 78.4 1.0
C B:ARG240 4.2 79.7 1.0
CB B:TYR241 4.2 66.6 1.0
O B:THR239 4.2 80.3 1.0
CA B:TYR241 4.2 66.9 1.0
CD2 A:HIS235 4.3 69.9 1.0
CD B:GLN242 4.3 79.7 0.0
CD1 B:TYR241 4.4 62.3 1.0
NE2 A:GLN242 4.5 66.0 0.0
I A:IOD503 4.5 75.3 0.4
ND1 A:HIS235 4.5 71.2 1.0
CB B:GLN242 4.6 80.8 1.0
C B:TYR241 4.6 81.0 1.0
CG B:ARG240 4.6 95.6 1.0
CE1 B:HIS235 4.6 71.1 1.0
CG B:TYR241 4.8 75.8 1.0
NE2 B:HIS235 4.9 71.6 1.0
CA B:GLN242 4.9 80.3 1.0
CB B:ARG240 5.0 64.5 1.0

Reference:

A.T.P.Machado, E.M.B.Fonseca, M.A.D.Reis, A.M.Saraiva, C.A.D.Santos, M.A.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek. Conformational Variability of the Stationary Phase Survival Protein E From Xylella Fastidiosa Revealed By X-Ray Crystallography, Small-Angle X-Ray Scattering Studies, and Normal Mode Analysis. Proteins V. 85 1931 2017.
ISSN: ESSN 1097-0134
PubMed: 28677327
DOI: 10.1002/PROT.25347
Page generated: Sun Aug 11 21:20:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy