Atomistry » Iodine » PDB 5enk-5kio » 5k27
Atomistry »
  Iodine »
    PDB 5enk-5kio »
      5k27 »

Iodine in PDB 5k27: Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.

Enzymatic activity of Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.

All present enzymatic activity of Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.:
2.7.1.146; 2.7.1.147;

Protein crystallography data

The structure of Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family., PDB code: 5k27 was solved by V.Castro-Fernandez, A.Herrera-Morande, R.Zamora, F.Merino, H.M.Pereira, J.Brandao-Neto, R.Garratt, V.Guixe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.42 / 2.58
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.354, 132.354, 116.773, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. (pdb code 5k27). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family., PDB code: 5k27:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 5k27

Go back to Iodine Binding Sites List in 5k27
Iodine binding site 1 out of 5 in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.


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 Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:62.5
occ:0.96
CD2 A:LEU23 4.2 62.0 1.0
CE2 A:PHE164 4.3 50.7 1.0
CD1 A:PHE88 4.3 37.5 1.0
CE A:LYS21 4.4 61.7 1.0
CD1 A:LEU31 4.5 49.9 1.0
CB A:PHE88 4.5 44.7 1.0
CG A:LYS21 4.6 54.9 1.0
CD2 A:LEU31 4.6 40.1 1.0
CD2 A:PHE164 4.7 48.9 1.0
CA A:PHE88 4.8 43.4 1.0
CG A:LEU31 4.8 45.1 1.0
CD A:LYS21 4.8 56.1 1.0
CG A:PHE88 4.9 47.0 1.0

Iodine binding site 2 out of 5 in 5k27

Go back to Iodine Binding Sites List in 5k27
Iodine binding site 2 out of 5 in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.


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 Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:77.0
occ:0.63
CB A:ALA237 4.0 48.5 1.0
CE A:LYS273 4.1 56.8 1.0
CB A:GLU229 4.2 60.3 1.0
CB A:LYS269 4.3 62.9 1.0
CA A:GLU229 4.3 52.7 1.0
CD1 A:ILE270 4.4 46.0 1.0
CG A:GLU229 4.5 65.1 1.0
O A:LYS269 4.6 57.4 1.0
OE2 A:GLU229 4.6 83.5 1.0
O A:GLU229 4.7 68.4 1.0
CD A:LYS269 4.7 61.6 1.0
CG A:LYS273 4.8 48.5 1.0
CG A:LYS269 4.8 63.4 1.0
C A:LYS269 4.8 58.2 1.0
CD A:GLU229 4.9 80.4 1.0
C A:GLU229 5.0 56.8 1.0
NZ A:LYS273 5.0 75.9 1.0

Iodine binding site 3 out of 5 in 5k27

Go back to Iodine Binding Sites List in 5k27
Iodine binding site 3 out of 5 in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.


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 Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:71.9
occ:0.63
O A:HOH619 3.4 47.4 1.0
N A:ILE376 3.7 66.4 1.0
O A:HOH628 3.9 48.3 1.0
CA A:ASP375 4.1 78.3 1.0
NZ A:LYS370 4.2 73.6 1.0
CD A:LYS370 4.3 75.1 1.0
CD1 A:LEU105 4.3 39.2 1.0
CB A:ILE376 4.4 69.0 1.0
CG A:LYS370 4.4 64.3 1.0
C A:ASP375 4.4 76.1 1.0
CB A:ASP375 4.4 53.5 1.0
CG1 A:ILE376 4.5 65.5 1.0
CB A:LEU105 4.5 37.3 1.0
O A:ILE376 4.5 72.4 1.0
CA A:ILE376 4.5 66.9 1.0
CG2 A:ILE101 4.6 29.1 1.0
CD2 A:LEU105 4.7 50.4 1.0
CG A:LEU105 4.7 53.2 1.0
CE A:LYS370 4.8 77.9 1.0

Iodine binding site 4 out of 5 in 5k27

Go back to Iodine Binding Sites List in 5k27
Iodine binding site 4 out of 5 in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.


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 Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:67.1
occ:0.55
CB A:PRO193 3.7 57.7 1.0
CB A:LEU196 3.8 80.6 0.8
CB A:LYS159 3.8 52.6 1.0
CD A:LYS159 4.1 47.0 1.0
CA A:PRO193 4.1 66.5 1.0
CD1 A:LEU120 4.3 54.0 1.0
CG A:LYS159 4.4 50.6 1.0
N A:ALA197 4.5 92.5 1.0
CA A:LYS159 4.5 52.5 1.0
OE2 A:GLU78 4.6 97.9 1.0
CG A:PRO193 4.7 63.2 1.0
CB A:ALA197 4.7 60.7 1.0
CA A:LEU196 4.8 88.3 0.8
N A:PRO193 4.8 59.7 1.0
C A:LEU196 4.8 81.5 0.8
CD A:PRO193 4.9 60.7 1.0
N A:LYS159 4.9 60.3 1.0

Iodine binding site 5 out of 5 in 5k27

Go back to Iodine Binding Sites List in 5k27
Iodine binding site 5 out of 5 in the Crystal Structure of Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family.


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 Ancestral Protein Ancmt of Adp-Dependent Sugar Kinases Family. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:67.6
occ:0.65
OD1 B:ASP375 3.6 91.7 1.0
N B:ILE376 3.7 61.7 1.0
CE B:LYS370 3.7 64.9 1.0
CD1 B:LEU105 3.9 58.5 1.0
CG B:LYS370 4.0 58.5 1.0
CG1 B:ILE376 4.1 51.4 1.0
NZ B:LYS370 4.2 65.5 1.0
CB B:ILE376 4.2 52.2 1.0
CA B:ASP375 4.2 67.8 1.0
CD B:LYS370 4.3 69.1 1.0
CD2 B:LEU105 4.3 71.2 1.0
C B:ASP375 4.4 71.5 1.0
CG B:LEU105 4.4 48.4 1.0
CG2 B:ILE101 4.4 57.1 1.0
CB B:LEU105 4.5 56.1 1.0
CA B:ILE376 4.5 62.3 1.0
CG B:ASP375 4.6 88.0 1.0
CD1 B:ILE376 4.7 56.5 1.0
CG2 B:THR435 4.8 52.9 1.0
O B:ILE101 4.8 64.0 1.0
O B:ILE376 4.8 60.1 1.0
O B:GLY374 5.0 71.7 1.0
CB B:LYS370 5.0 48.0 1.0

Reference:

V.Castro-Fernandez, A.Herrera-Morande, R.Zamora, F.Merino, F.Gonzalez-Ordenes, F.Padilla-Salinas, H.M.Pereira, J.Brandao-Neto, R.C.Garratt, V.Guixe. Reconstructed Ancestral Enzymes Reveal That Negative Selection Drove the Evolution of Substrate Specificity in Adp-Dependent Kinases. J. Biol. Chem. V. 292 21218 2017.
ISSN: ESSN 1083-351X
PubMed: 29273585
DOI: 10.1074/JBC.AAC117.001147
Page generated: Sun Aug 11 21:13:53 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