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Iodine in PDB 3c7t: Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate

Protein crystallography data

The structure of Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate, PDB code: 3c7t was solved by Y.Chen, N.Carpino, N.Nassar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.20 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.901, 134.410, 135.188, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.1

Other elements in 3c7t:

The structure of Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 15 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate (pdb code 3c7t). 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 the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate, PDB code: 3c7t:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 1 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1

b:28.7
occ:1.00
 O B:HOH332 3.6 19.3 1.0
N B:MET215 3.6 21.6 1.0
CG B:MET215 4.0 26.4 0.5
CB B:MET215 4.0 24.8 1.0
CE B:LYS179 4.1 18.1 1.0
CG B:MET215 4.3 25.8 0.5
OD1 B:ASP214 4.3 22.7 1.0
CA B:ASP214 4.3 19.1 1.0
NZ B:LYS179 4.3 17.9 1.0
CA B:MET215 4.4 24.0 1.0
O B:VAL213 4.4 17.8 1.0
CD B:LYS179 4.4 18.8 1.0
C B:ASP214 4.5 20.2 1.0
CG B:LYS179 4.7 16.6 1.0
N B:THR216 4.7 24.1 1.0
C B:MET215 5.0 24.9 1.0
CG B:ASP214 5.0 23.3 1.0

Iodine binding site 2 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 2 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I4

b:44.8
occ:0.50
 O C:LEU274 3.7 33.1 1.0
CB C:LYS304 3.8 35.5 1.0
CD1 C:TRP306 3.9 27.4 1.0
CA C:ARG275 4.0 37.6 1.0
CA C:PRO305 4.0 33.9 1.0
C C:LEU274 4.1 32.8 1.0
CG C:ARG275 4.2 37.4 1.0
N C:ARG275 4.2 35.1 1.0
NE1 C:TRP306 4.2 26.7 1.0
N C:TRP306 4.4 31.6 1.0
CE C:LYS304 4.4 41.7 1.0
CB C:PRO305 4.5 34.1 1.0
CD C:LYS304 4.5 39.5 1.0
CB C:ARG275 4.6 37.0 1.0
CB C:LEU274 4.7 30.2 1.0
CG C:LYS304 4.7 37.8 1.0
C C:PRO305 4.8 32.9 1.0
CG C:TRP306 4.8 27.6 1.0
CA C:LYS304 4.8 35.4 1.0

Iodine binding site 3 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 3 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I5

b:34.0
occ:0.50
 CA C:GLY118 3.8 26.4 1.0
C C:GLY118 3.9 26.5 1.0
N C:ARG115 4.1 23.0 1.0
N C:LYS119 4.1 26.9 1.0
CE2 C:TYR122 4.2 19.5 1.0
O C:GLY118 4.3 26.0 1.0
O C:ALA113 4.3 21.1 1.0
O C:ARG115 4.4 23.3 1.0
CA C:HIS114 4.4 23.9 1.0
CG C:ARG115 4.4 23.2 1.0
CD2 C:TYR122 4.5 17.1 1.0
CE2 C:PHE96 4.6 24.6 1.0
CZ C:PHE96 4.6 23.7 1.0
N C:GLY118 4.7 26.1 1.0
ND1 C:HIS114 4.7 32.7 1.0
C C:HIS114 4.8 23.3 1.0
CA C:LYS119 4.8 26.7 1.0
O C:HOH399 4.9 34.3 1.0

Iodine binding site 4 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 4 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I2

b:37.9
occ:1.00
 CA D:GLY118 3.8 22.6 1.0
C D:GLY118 3.8 22.9 1.0
N D:ARG115 3.9 18.8 1.0
CE2 D:TYR122 4.1 15.6 1.0
O D:ALA113 4.1 18.1 1.0
N D:LYS119 4.2 22.9 1.0
O D:GLY118 4.2 21.1 1.0
CA D:HIS114 4.2 20.1 1.0
O D:ARG115 4.3 20.3 1.0
CG D:ARG115 4.3 20.1 1.0
CD2 D:TYR122 4.5 16.2 1.0
C D:HIS114 4.5 19.2 1.0
CE2 D:PHE96 4.6 23.1 1.0
CD2 D:HIS114 4.6 31.2 1.0
N D:GLY118 4.6 23.1 1.0
CZ D:PHE96 4.8 23.0 1.0
CA D:ARG115 4.9 19.2 1.0
C D:ALA113 4.9 18.8 1.0
N D:HIS114 5.0 19.2 1.0

Iodine binding site 5 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 5 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I3

b:27.7
occ:1.00
 O D:HOH407 3.3 25.0 1.0
N D:MET215 3.6 22.4 1.0
CB D:MET215 4.0 25.3 1.0
CE D:LYS179 4.2 17.5 1.0
OD1 D:ASP214 4.3 22.2 1.0
CA D:ASP214 4.3 18.9 1.0
CG D:MET215 4.3 25.9 0.5
NZ D:LYS179 4.3 14.9 1.0
O D:VAL213 4.3 16.5 1.0
CA D:MET215 4.4 24.3 1.0
CD D:LYS179 4.4 15.4 1.0
C D:ASP214 4.5 20.7 1.0
CG D:LYS179 4.7 13.8 1.0
N D:THR216 4.8 25.1 1.0
CG D:ASP214 4.8 21.8 1.0
C D:MET215 5.0 25.6 1.0
CG D:MET215 5.0 24.7 0.5

Iodine binding site 6 out of 6 in 3c7t

Go back to Iodine Binding Sites List in 3c7t
Iodine binding site 6 out of 6 in the Crystal Structure of the Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate


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 Ecdysone Phosphate Phosphatase, Eppase, From Bombix Mori in Complex with Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I6

b:42.9
occ:0.50
 CD1 D:TRP306 3.8 25.1 1.0
CG D:LYS304 3.8 32.1 1.0
CA D:PRO305 3.8 28.1 1.0
CA D:ARG275 3.9 35.2 1.0
O D:LEU274 3.9 31.4 1.0
CB D:LYS304 4.0 29.2 1.0
CG D:ARG275 4.1 35.2 1.0
N D:TRP306 4.1 26.6 1.0
NE1 D:TRP306 4.2 24.5 1.0
C D:LEU274 4.3 30.9 1.0
CE D:LYS304 4.3 35.2 1.0
N D:ARG275 4.3 32.6 1.0
O D:HOH394 4.4 32.8 1.0
CB D:PRO305 4.4 28.0 1.0
CB D:ARG275 4.4 34.9 1.0
C D:PRO305 4.5 27.2 1.0
CD D:LYS304 4.6 33.2 1.0
CA D:LYS304 4.7 28.7 1.0
CG D:TRP306 4.7 25.3 1.0
N D:PRO305 4.9 28.6 1.0

Reference:

Y.Chen, J.Jakoncic, J.Wang, X.Zheng, N.Carpino, N.Nassar. Structural and Functional Characterization of the C-Terminal Domain of the Ecdysteroid Phosphate Phosphatase From Bombyx Mori Reveals A New Enzymatic Activity. Biochemistry V. 47 12135 2008.
ISSN: ISSN 0006-2960
PubMed: 18937503
DOI: 10.1021/BI801318W
Page generated: Sun Aug 11 14:50:20 2024

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