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Iodine in PDB 4z48: Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution

Protein crystallography data

The structure of Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution, PDB code: 4z48 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.55 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.400, 56.340, 65.560, 100.71, 97.04, 109.01
R / Rfree (%) 21 / 24.8

Other elements in 4z48:

The structure of Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution (pdb code 4z48). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution, PDB code: 4z48:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 1 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:23.8
occ:0.50
O A:HOH685 3.3 27.3 1.0
NH2 A:ARG68 3.5 25.3 1.0
CD A:ARG139 3.8 18.8 1.0
CG A:ARG139 3.8 16.7 1.0
CA A:MSE138 4.0 15.4 1.0
C A:MSE138 4.1 18.5 1.0
SE A:MSE138 4.1 27.6 0.8
CE A:MSE138 4.4 22.6 1.0
O A:MSE138 4.4 20.0 1.0
O A:HOH689 4.4 42.6 1.0
O A:HOH443 4.4 32.0 1.0
N A:ARG139 4.5 18.0 1.0
CZ A:ARG68 4.6 30.4 1.0
CB A:MSE138 4.6 16.5 1.0
O A:HOH582 4.7 26.9 1.0
O A:HOH690 4.7 27.3 1.0
CB A:ARG139 4.8 17.1 1.0
O A:HOH511 4.8 26.2 1.0
CG1 A:VAL96 4.9 21.5 1.0
NE A:ARG68 4.9 23.0 1.0
O A:HOH569 5.0 22.9 1.0

Iodine binding site 2 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 2 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:42.4
occ:0.50
O A:HOH411 3.4 37.5 1.0
N A:LYS208 3.8 29.2 1.0
CB A:LYS208 3.9 34.2 1.0
NH2 A:ARG211 3.9 50.1 1.0
CG A:ASP207 4.0 33.1 1.0
OD2 A:ASP207 4.0 34.0 1.0
N A:LYS209 4.1 31.2 1.0
CB A:ASP207 4.1 25.5 1.0
CG A:LYS209 4.1 57.5 1.0
CA A:LYS208 4.2 30.3 1.0
O A:HOH547 4.3 34.8 1.0
CD A:LYS209 4.3 71.7 1.0
CE A:LYS209 4.3 80.0 1.0
C A:LYS208 4.4 36.0 1.0
CG A:LYS208 4.5 40.2 1.0
OD1 A:ASP207 4.5 33.5 1.0
CB A:LYS209 4.5 34.7 1.0
C A:ASP207 4.8 29.4 1.0
CA A:LYS209 4.9 31.3 1.0
CA A:ASP207 5.0 23.2 1.0

Iodine binding site 3 out of 7 in 4z48

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Iodine binding site 3 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:30.3
occ:0.40
NH1 A:ARG92 3.6 40.3 1.0
CA A:ALA94 3.9 20.2 1.0
CA B:GLY181 3.9 41.6 1.0
CG A:ASN97 4.0 30.0 1.0
CB A:ASN97 4.0 15.5 1.0
ND2 A:ASN97 4.1 28.4 1.0
O A:ASP91 4.1 21.6 1.0
O A:HOH638 4.1 34.4 1.0
CB A:ALA94 4.2 21.2 1.0
CD A:ARG92 4.3 40.5 1.0
OD1 A:ASN97 4.4 31.9 1.0
N A:ALA94 4.4 20.9 1.0
O A:HOH527 4.7 37.4 1.0
O B:GLY181 4.7 43.4 1.0
CZ A:ARG92 4.7 55.5 1.0
C B:GLY181 4.8 42.9 1.0
N B:GLY181 4.9 42.3 1.0
O A:ALA94 5.0 21.3 1.0
NE A:ARG92 5.0 46.4 1.0

Iodine binding site 4 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 4 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:46.6
occ:0.50
O B:HOH426 3.3 35.6 1.0
NH2 B:ARG211 3.6 48.8 1.0
OD2 B:ASP207 4.0 27.5 1.0
CG B:ASP207 4.0 25.3 1.0
N B:LYS208 4.1 26.9 1.0
CG B:LYS209 4.1 38.8 1.0
CB B:LYS208 4.1 31.2 1.0
N B:LYS209 4.1 31.1 1.0
CB B:ASP207 4.2 20.3 1.0
CE B:LYS209 4.3 55.5 1.0
CD B:LYS209 4.3 47.1 1.0
O B:HOH534 4.4 28.4 1.0
OD1 B:ASP207 4.4 26.5 1.0
CA B:LYS208 4.4 28.2 1.0
CB B:LYS209 4.5 33.6 1.0
C B:LYS208 4.6 35.3 1.0
CG B:LYS208 4.7 34.7 1.0
CZ B:ARG211 4.7 60.5 1.0
O B:HOH567 4.7 31.5 1.0
CA B:LYS209 5.0 30.7 1.0
C B:ASP207 5.0 29.4 1.0

Iodine binding site 5 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 5 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:25.5
occ:0.30
O B:HOH657 3.2 22.8 1.0
NH2 B:ARG68 3.3 21.3 1.0
CD B:ARG139 3.6 25.2 1.0
CG B:ARG139 3.7 19.9 1.0
CA B:MSE138 4.0 14.7 1.0
C B:MSE138 4.0 18.6 1.0
CE B:MSE138 4.1 23.4 1.0
SE B:MSE138 4.1 27.6 0.8
O B:MSE138 4.3 19.2 1.0
N B:ARG139 4.4 16.8 1.0
O B:HOH427 4.4 27.3 1.0
CZ B:ARG68 4.5 25.0 1.0
O B:HOH484 4.5 21.3 1.0
CB B:ARG139 4.6 18.1 1.0
CB B:MSE138 4.7 16.1 1.0
O B:HOH541 4.8 21.2 1.0
O B:HOH404 4.8 14.8 0.5
CG1 B:VAL96 4.8 25.5 1.0
NE B:ARG68 4.9 20.5 1.0
O B:HOH664 4.9 29.1 1.0
NE B:ARG139 5.0 24.2 1.0

Iodine binding site 6 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 6 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:30.2
occ:0.40
O A:HOH428 3.3 30.1 1.0
O B:HOH562 3.4 43.2 1.0
O A:HOH536 3.5 33.8 1.0
NE2 A:GLN232 3.6 31.3 1.0
O B:VAL125 3.8 23.6 1.0
CG1 B:VAL125 4.0 27.4 1.0
CE1 B:HIS264 4.0 38.9 1.0
CD1 B:TRP116 4.1 25.7 1.0
NE2 B:HIS264 4.1 38.5 1.0
C B:VAL125 4.2 24.5 1.0
O B:HOH470 4.3 48.1 1.0
NE1 B:TRP116 4.3 26.3 1.0
CB B:VAL125 4.4 27.2 1.0
OD1 A:ASP247 4.5 27.7 1.0
N B:ARG127 4.6 21.3 1.0
N B:ARG126 4.6 21.6 1.0
CA B:ARG126 4.7 21.8 1.0
C B:ARG126 4.8 24.7 1.0
CD A:GLN232 4.8 31.7 1.0
CA B:VAL125 5.0 22.2 1.0

Iodine binding site 7 out of 7 in 4z48

Go back to Iodine Binding Sites List in 4z48
Iodine binding site 7 out of 7 in the Crystal Structure of A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution


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 A DUF1329 Family Protein (DESPIG_00262) From Desulfovibrio Piger Atcc 29098 at 1.75 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I305

b:32.9
occ:0.30
CG B:GLU222 3.3 31.1 0.4
N B:LYS223 3.6 25.5 1.0
CA B:GLU222 4.0 23.8 0.6
CA B:GLU222 4.0 23.7 0.4
CB B:GLU222 4.1 25.1 0.6
CB B:GLU222 4.1 24.8 0.4
O B:HOH410 4.2 39.4 1.0
C B:GLU222 4.3 27.6 1.0
CD B:GLU222 4.4 34.8 0.4
O B:LYS223 4.4 30.7 1.0
CG B:GLU222 4.5 32.8 0.6
CA B:LYS223 4.6 24.9 1.0
CB B:LYS223 4.6 28.6 1.0
OE2 B:GLU222 4.6 16.2 0.4
CH2 B:TRP228 4.9 30.2 1.0
C B:LYS223 4.9 28.3 1.0
CZ3 B:TRP228 4.9 28.5 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sun Dec 13 19:38:11 2020

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