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Iodine in PDB 3ehg: Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp

Enzymatic activity of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp

All present enzymatic activity of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp, PDB code: 3ehg was solved by F.Trajtenberg, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.03 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.379, 49.078, 81.436, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.5

Other elements in 3ehg:

The structure of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp (pdb code 3ehg). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp, PDB code: 3ehg:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 1 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2

b:19.6
occ:0.70
 NH2 A:ARG341 3.6 29.0 1.0
N A:ILE353 3.8 19.1 1.0
CA A:HIS352 3.9 18.1 1.0
CD2 A:HIS352 3.9 20.8 1.0
CB A:HIS352 4.1 18.1 1.0
O A:ILE353 4.1 24.1 1.0
CG A:HIS352 4.3 17.4 1.0
O A:HOH80 4.3 44.2 1.0
C A:HIS352 4.4 17.5 1.0
CG2 A:ILE353 4.4 23.4 1.0
O A:HOH100 4.7 46.1 1.0
O A:HOH78 4.7 50.0 1.0
O A:LEU351 4.7 18.4 1.0
CA A:ILE353 4.8 20.2 1.0
CZ A:ARG341 4.8 29.5 1.0
C A:ILE353 4.8 22.0 1.0
O A:HOH82 4.9 43.7 1.0

Iodine binding site 2 out of 12 in 3ehg

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Iodine binding site 2 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I3

b:24.1
occ:0.66
 OG A:SER319 3.5 21.1 0.5
CG A:ARG304 3.7 19.9 0.5
CD A:ARG304 3.8 22.4 0.5
C A:ASP320 3.9 19.1 1.0
CA A:ASP320 3.9 18.7 1.0
N A:ASP321 4.0 19.7 1.0
O A:SER319 4.0 18.4 1.0
C A:SER319 4.1 18.1 1.0
N A:ASP320 4.1 16.7 1.0
CB A:SER319 4.1 19.1 0.5
O A:THR302 4.2 19.9 1.0
CB A:ASP321 4.2 22.4 1.0
CB A:SER319 4.3 19.3 0.5
O A:ASP320 4.3 20.4 1.0
N A:ARG304 4.4 16.4 0.5
N A:ARG304 4.4 16.8 0.5
CB A:ARG304 4.4 18.1 0.5
CB A:ARG304 4.4 19.4 0.5
CG2 A:THR302 4.5 23.8 1.0
CB A:THR302 4.5 22.4 1.0
CA A:ASP321 4.5 22.2 1.0
C A:THR302 4.6 19.1 1.0
CA A:SER319 4.8 18.1 0.5
CA A:SER319 4.8 18.1 0.5
CG A:ASP321 4.9 24.0 1.0
CA A:CYS303 4.9 16.8 1.0
N A:CYS303 4.9 18.5 1.0
O A:HOH127 5.0 44.5 1.0
C A:CYS303 5.0 16.8 1.0

Iodine binding site 3 out of 12 in 3ehg

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Iodine binding site 3 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I4

b:27.8
occ:0.40
 O A:HOH163 3.8 64.3 1.0
CB A:GLN299 4.2 22.3 1.0
NE2 A:GLN299 4.3 23.6 1.0
O A:HOH76 4.3 40.6 1.0
CD A:GLN299 4.4 21.8 1.0
CG A:GLN299 4.7 21.1 1.0
O A:GLN299 4.8 20.7 1.0
OE1 A:GLN299 4.8 25.9 1.0
NZ A:LYS301 4.9 30.0 1.0
O A:HOH40 4.9 31.8 1.0

Iodine binding site 4 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 4 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:28.5
occ:0.27
 O A:HOH109 2.9 42.5 1.0
O A:GLY243 3.0 41.0 1.0
C A:GLY243 3.4 36.2 1.0
O A:HOH67 3.5 41.4 1.0
OD1 A:ASN281 3.5 25.9 1.0
O A:HOH41 3.7 37.2 1.0
CA A:GLY243 3.8 38.3 1.0
O A:HOH107 3.8 35.9 1.0
CD A:ARG245 3.8 25.4 1.0
CD1 A:LEU277 4.0 33.4 1.0
N A:ILE244 4.0 31.7 1.0
ND2 A:ASN281 4.1 19.9 1.0
CG A:ASN281 4.3 25.4 1.0
N A:ARG245 4.3 22.7 1.0
C A:ILE244 4.4 24.9 1.0
CA A:ILE244 4.5 29.4 1.0
CG A:ARG245 4.5 25.9 1.0
CD2 A:LEU277 4.6 32.5 1.0
CG A:LEU277 4.7 29.3 1.0
O A:ILE244 4.8 24.3 1.0
O A:HOH31 5.0 32.2 1.0
CA A:ARG245 5.0 20.9 1.0
N A:GLY243 5.0 37.4 1.0

Iodine binding site 5 out of 12 in 3ehg

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Iodine binding site 5 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I6

b:22.2
occ:0.16
 O A:HOH84 3.1 39.9 1.0
O A:HOH91 3.4 49.8 1.0
N A:GLU327 3.5 38.3 1.0
CG A:GLU327 3.8 48.0 1.0
OG A:SER330 3.9 34.8 1.0
CA A:GLY326 4.0 31.1 1.0
CA A:SER330 4.1 32.9 1.0
O A:HOH71 4.1 46.0 1.0
CB A:GLU327 4.1 44.7 1.0
C4' A:ATP1 4.2 17.6 1.0
CD A:GLU327 4.3 57.4 1.0
CB A:SER330 4.3 32.1 1.0
C A:GLY326 4.3 34.8 1.0
CA A:GLU327 4.4 42.6 1.0
OE2 A:GLU327 4.6 62.2 1.0
C5' A:ATP1 4.6 20.0 1.0
O A:SER330 4.6 29.5 1.0
O A:ASN329 4.7 39.5 1.0
C A:SER330 4.8 30.9 1.0
OE1 A:GLU327 4.8 62.3 1.0
O2' A:ATP1 4.8 18.5 1.0
O4' A:ATP1 4.9 16.9 1.0

Iodine binding site 6 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 6 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


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 the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I7

b:30.6
occ:0.25
 O A:HOH123 2.1 38.7 1.0
O A:HOH136 2.7 53.9 1.0
O A:HOH137 3.0 49.6 1.0
CG2 A:ILE256 3.8 21.8 1.0
CG1 A:VAL295 3.9 18.7 1.0
O A:HOH164 3.9 46.8 1.0
CB A:VAL295 4.1 16.5 1.0
O A:HOH27 4.4 29.6 1.0
CG2 A:VAL295 4.4 15.6 1.0
O A:HOH157 4.6 56.4 1.0
CA A:THR292 4.6 17.0 1.0
O A:HOH144 4.7 55.4 1.0
CG1 A:ILE256 4.7 21.6 1.0
OG1 A:THR292 4.8 20.5 1.0
CG2 A:THR292 4.8 18.9 1.0
CB A:ILE256 4.9 18.6 1.0
CD1 A:ILE256 4.9 25.4 1.0
O A:HOH161 4.9 56.6 1.0
CB A:THR292 5.0 19.6 1.0

Iodine binding site 7 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 7 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I8

b:22.4
occ:0.25
 O A:HOH18 2.9 31.9 1.0
NH1 A:ARG343 3.2 22.1 1.0
NH2 A:ARG343 3.2 25.1 1.0
CZ A:ARG343 3.7 20.9 1.0
CD2 A:LEU278 3.8 29.0 1.0
CD1 A:PHE346 3.8 25.6 1.0
CB A:ALA347 3.9 22.4 1.0
CA A:ALA347 4.1 21.8 1.0
CD1 A:ILE282 4.1 21.7 1.0
CE1 A:PHE346 4.1 28.4 1.0
CG A:LEU278 4.4 24.2 1.0
N A:ALA347 4.5 22.6 1.0
O A:HOH75 4.6 49.4 1.0
CD1 A:LEU278 4.7 25.4 1.0
O A:PHE346 4.7 25.4 1.0
C A:PHE346 4.7 22.6 1.0
CG A:PHE346 5.0 25.1 1.0
NE A:ARG343 5.0 20.3 1.0
ND2 A:ASN279 5.0 23.4 1.0

Iodine binding site 8 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 8 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9

b:31.2
occ:0.25
 O A:HOH113 3.4 37.4 1.0
O A:HOH115 3.9 49.5 1.0
OD2 A:ASP354 4.1 45.7 1.0
CB A:ASP354 4.7 29.0 1.0
CG A:ASP354 4.8 37.0 1.0
O A:HOH372 4.8 23.4 1.0
O A:HOH100 4.9 46.1 1.0

Iodine binding site 9 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 9 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I10

b:27.6
occ:0.16
 O A:HOH108 3.0 50.9 1.0
O A:HOH65 3.3 35.9 1.0
CB A:MET285 4.1 21.9 1.0
CG1 A:ILE244 4.2 31.4 1.0
CG A:MET285 4.2 28.4 1.0
CA A:MET285 4.3 20.4 1.0
CE A:MET285 4.5 36.1 1.0
N A:GLY243 4.6 37.4 1.0
SD A:MET285 4.6 39.3 1.0
N A:MET285 4.6 17.7 1.0
CB A:ILE244 5.0 28.5 1.0

Iodine binding site 10 out of 12 in 3ehg

Go back to Iodine Binding Sites List in 3ehg
Iodine binding site 10 out of 12 in the Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of the Atp-Binding Domain of Desk in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I11

b:37.2
occ:0.20
 OE2 A:GLU342 2.4 33.0 1.0
CD A:GLU342 3.5 32.1 1.0
CA A:GLY339 4.0 18.9 1.0
CB A:GLU342 4.2 20.8 1.0
CG A:GLU342 4.3 26.2 1.0
N A:GLY339 4.3 19.4 1.0
O A:LEU338 4.3 19.6 1.0
OE1 A:GLU342 4.3 36.8 1.0
C A:LEU338 4.5 19.4 1.0
CG A:LEU338 4.8 23.0 1.0
O A:GLY339 4.9 19.9 1.0

Reference:

F.Trajtenberg, M.Grana, N.Ruetalo, H.Botti, A.Buschiazzo. Structural and Enzymatic Insights Into the Atp Binding and Autophosphorylation Mechanism of A Sensor Histidine Kinase J.Biol.Chem. V. 285 24892 2010.
ISSN: ISSN 0021-9258
PubMed: 20507988
DOI: 10.1074/JBC.M110.147843
Page generated: Sun Aug 11 15:05:29 2024

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