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Iodine in PDB 3vic: Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5

Protein crystallography data

The structure of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5, PDB code: 3vic was solved by J.M.Battad, D.A.K.Traore, E.Byres, M.Wilce, R.J.Devenish, J.Rossjohn, M.Prescott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.80 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 150.271, 186.060, 185.150, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.4

Other elements in 3vic:

The structure of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 (pdb code 3vic). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5, PDB code: 3vic:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 1 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I226

b:33.8
occ:1.00
 O A:HOH1065 3.3 46.6 1.0
OG A:SER210 3.5 41.3 1.0
ND2 E:ASN205 3.6 35.8 1.0
N A:VAL211 3.9 36.0 1.0
CB E:ASN205 3.9 36.5 1.0
C A:SER210 3.9 37.5 1.0
O A:SER210 3.9 38.1 1.0
CA A:HIS204 4.0 34.8 1.0
CB A:ASN203 4.0 37.3 1.0
N A:GLU212 4.0 34.5 1.0
C A:VAL211 4.0 33.6 1.0
CA A:VAL211 4.1 33.6 1.0
N A:HIS204 4.1 35.4 1.0
C A:ASN203 4.1 35.0 1.0
CG A:ASN203 4.2 39.1 1.0
O A:ASN203 4.3 33.5 1.0
CG E:ASN205 4.3 35.1 1.0
CB A:SER210 4.3 37.7 1.0
CB A:GLU212 4.4 36.0 1.0
C A:HIS204 4.4 36.0 1.0
OD1 A:ASN203 4.5 39.1 1.0
ND2 A:ASN203 4.6 40.8 1.0
O A:VAL211 4.6 32.4 1.0
N A:ASN205 4.7 36.0 1.0
CA A:SER210 4.7 35.6 1.0
CE A:LYS45 4.7 57.7 1.0
CA A:ASN203 4.8 35.9 1.0
CA A:GLU212 4.8 33.7 1.0
CG A:LYS45 4.8 39.9 1.0
O A:HOH1377 4.9 46.8 1.0
O A:HIS204 4.9 37.2 1.0
NZ A:LYS45 5.0 55.3 1.0

Iodine binding site 2 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 2 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I226

b:35.5
occ:1.00
 O B:HOH866 3.7 42.6 1.0
N B:HIS204 4.0 35.7 1.0
CB B:ASN203 4.0 37.5 1.0
CB B:SER210 4.0 36.6 1.0
CA B:HIS204 4.0 35.0 1.0
N B:GLU212 4.0 32.6 1.0
C B:ASN203 4.0 34.9 1.0
N B:VAL211 4.1 32.4 1.0
CG B:ASN203 4.1 42.3 1.0
C B:SER210 4.1 33.0 1.0
C B:VAL211 4.1 33.5 1.0
O B:SER210 4.1 36.3 1.0
CE B:LYS45 4.2 46.5 1.0
CD B:LYS45 4.2 45.1 1.0
CA B:VAL211 4.2 34.1 1.0
O B:ASN203 4.2 33.3 1.0
CB B:GLU212 4.4 35.7 1.0
OD1 B:ASN203 4.4 39.5 1.0
C B:HIS204 4.4 36.6 1.0
ND2 B:ASN203 4.5 41.2 1.0
CA B:ASN203 4.7 36.0 1.0
N B:ASN205 4.7 37.4 1.0
O B:VAL211 4.7 33.4 1.0
CA B:SER210 4.7 35.1 1.0
NZ B:LYS45 4.8 40.0 1.0
CA B:GLU212 4.8 32.8 1.0
OG B:SER210 4.9 39.5 1.0
O B:HIS204 4.9 37.4 1.0

Iodine binding site 3 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 3 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I226

b:34.6
occ:1.00
 O C:HOH1428 3.2 54.0 1.0
CE C:LYS45 3.7 55.9 1.0
CB C:ASN203 3.9 38.8 1.0
N C:HIS204 3.9 36.6 1.0
CA C:HIS204 4.0 35.9 1.0
CB C:SER210 4.0 37.7 1.0
C C:ASN203 4.0 36.0 1.0
O C:SER210 4.0 34.7 1.0
C C:SER210 4.0 34.7 1.0
O C:ASN203 4.1 34.7 1.0
N C:GLU212 4.1 34.9 1.0
CG C:ASN203 4.1 40.8 1.0
NZ C:LYS45 4.1 57.1 1.0
CD C:LYS45 4.1 46.8 1.0
N C:VAL211 4.1 34.7 1.0
C C:VAL211 4.2 35.3 1.0
CA C:VAL211 4.3 34.8 1.0
C C:HIS204 4.4 37.3 1.0
CB C:GLU212 4.4 36.4 1.0
OD1 C:ASN203 4.5 40.8 1.0
ND2 C:ASN203 4.5 42.5 1.0
CA C:ASN203 4.6 37.1 1.0
N C:ASN205 4.6 37.4 1.0
CA C:SER210 4.7 35.7 1.0
O C:VAL211 4.7 35.0 1.0
CA C:GLU212 4.9 35.0 1.0

Iodine binding site 4 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 4 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I227

b:33.6
occ:1.00
 O C:HOH622 3.5 53.2 1.0
ND2 C:ASN205 3.7 39.2 1.0
CB C:ASN205 3.9 39.7 1.0
CG C:ASN205 4.4 38.3 1.0

Iodine binding site 5 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 5 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I226

b:32.3
occ:1.00
 O D:HOH901 3.4 38.7 1.0
ND2 D:ASN205 3.6 35.8 1.0
CB D:ASN205 4.0 36.3 1.0
CG D:ASN205 4.4 35.0 1.0

Iodine binding site 6 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 6 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I227

b:32.5
occ:1.00
 O D:HOH1181 3.7 38.9 1.0
N D:HIS204 3.9 34.2 1.0
CA D:HIS204 4.0 33.7 1.0
CB D:ASN203 4.0 36.4 1.0
C D:ASN203 4.1 33.6 1.0
CG D:ASN203 4.1 39.3 1.0
CB D:SER210 4.1 34.4 1.0
O D:SER210 4.1 32.4 1.0
CE D:LYS45 4.1 44.5 1.0
N D:GLU212 4.2 31.5 1.0
C D:SER210 4.2 31.8 1.0
N D:VAL211 4.3 31.2 1.0
C D:HIS204 4.3 34.6 1.0
O D:ASN203 4.3 32.3 1.0
OD1 D:ASN203 4.3 38.0 1.0
C D:VAL211 4.4 33.5 1.0
CD D:LYS45 4.4 47.8 1.0
CA D:VAL211 4.4 32.1 1.0
CB D:GLU212 4.5 33.7 1.0
ND2 D:ASN203 4.5 39.8 1.0
N D:ASN205 4.6 34.3 1.0
CA D:ASN203 4.7 34.9 1.0
O D:HIS204 4.8 35.8 1.0
NZ D:LYS45 4.8 44.1 1.0
CA D:SER210 4.9 32.5 1.0
O D:VAL211 5.0 33.3 1.0
CA D:GLU212 5.0 32.2 1.0

Iodine binding site 7 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 7 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I226

b:33.0
occ:1.00
 ND2 A:ASN205 3.6 37.7 1.0
OG E:SER210 3.8 37.2 1.0
N E:HIS204 3.9 34.9 1.0
N E:VAL211 3.9 32.8 1.0
CA E:HIS204 3.9 33.7 1.0
N E:GLU212 4.0 31.9 1.0
C E:SER210 4.0 33.1 1.0
CB A:ASN205 4.0 38.1 1.0
C E:ASN203 4.0 33.5 1.0
O E:SER210 4.0 33.2 1.0
C E:VAL211 4.1 33.2 1.0
CA E:VAL211 4.1 33.9 1.0
CB E:ASN203 4.1 36.2 1.0
CG E:ASN203 4.1 37.9 1.0
CB E:SER210 4.1 35.4 1.0
O E:ASN203 4.2 32.2 1.0
CB E:GLU212 4.3 33.4 1.0
CG A:ASN205 4.3 36.9 1.0
ND2 E:ASN203 4.4 40.0 1.0
C E:HIS204 4.4 35.1 1.0
OD1 E:ASN203 4.4 37.9 1.0
CE E:LYS45 4.6 50.4 1.0
O E:VAL211 4.6 32.3 1.0
CA E:ASN203 4.7 36.3 1.0
CA E:SER210 4.7 32.6 1.0
N E:ASN205 4.7 34.6 1.0
CD E:LYS45 4.7 50.0 1.0
CA E:GLU212 4.8 32.4 1.0
CG E:LYS45 4.8 36.3 1.0
O E:HIS204 5.0 36.3 1.0

Iodine binding site 8 out of 8 in 3vic

Go back to Iodine Binding Sites List in 3vic
Iodine binding site 8 out of 8 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I226

b:35.9
occ:1.00
 CE H:LYS45 3.9 56.8 1.0
N H:HIS204 4.0 37.9 1.0
CA H:HIS204 4.0 37.0 1.0
N H:GLU212 4.0 38.2 1.0
N H:VAL211 4.0 36.0 1.0
C H:ASN203 4.1 37.3 1.0
CB H:SER210 4.1 38.7 1.0
C H:SER210 4.1 35.7 1.0
CD H:LYS45 4.1 56.5 1.0
CB H:ASN203 4.1 40.2 1.0
O H:SER210 4.1 36.8 1.0
O H:ASN203 4.1 35.9 1.0
C H:VAL211 4.2 38.2 1.0
CG H:ASN203 4.2 42.1 1.0
CA H:VAL211 4.2 38.5 1.0
OD1 H:ASN203 4.3 42.0 1.0
C H:HIS204 4.4 38.5 1.0
CB H:GLU212 4.4 37.6 1.0
ND2 H:ASN203 4.7 44.0 1.0
N H:ASN205 4.7 38.4 1.0
CA H:SER210 4.7 36.6 1.0
NZ H:LYS45 4.7 46.8 1.0
CA H:ASN203 4.8 38.5 1.0
O H:VAL211 4.8 37.4 1.0
CA H:GLU212 4.9 35.8 1.0
O H:HIS204 4.9 39.8 1.0

Reference:

J.M.Battad, D.A.Traore, E.Byres, J.Rossjohn, R.J.Devenish, S.Olsen, M.C.Wilce, M.Prescott. A Green Fluorescent Protein Containing A Qfg Tri-Peptide Chromophore: Optical Properties and X-Ray Crystal Structure. Plos One V. 7 47331 2012.
ISSN: ESSN 1932-6203
PubMed: 23071789
DOI: 10.1371/JOURNAL.PONE.0047331
Page generated: Sun Aug 11 17:03:32 2024

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