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 Dec 13 19:39:44 2020

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