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Chlorine 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:

Iodine (I) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5, PDB code: 3vic:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in 3vic

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Chlorine binding site 1 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl227

b:29.1
occ:1.00
 N A:GLY155 3.4 30.3 1.0
N A:GLY154 3.6 28.8 1.0
O A:HOH703 3.8 35.5 1.0
CG A:MET189 3.9 31.3 1.0
N A:ARG153 4.0 26.9 1.0
C A:ARG153 4.0 27.6 1.0
CB A:ALA152 4.1 28.0 1.0
CA A:ARG153 4.1 27.2 1.0
CA A:GLY155 4.2 31.3 1.0
CA A:GLY154 4.2 30.3 1.0
C A:ALA152 4.3 28.7 1.0
C A:GLY154 4.3 31.9 1.0
CE A:MET189 4.3 28.8 1.0
O A:ALA152 4.6 27.4 1.0
CB A:MET189 4.6 30.8 1.0
SD A:MET189 4.8 33.5 1.0
O A:ARG153 4.8 27.1 1.0
CA A:ALA152 4.8 29.1 1.0

Chlorine binding site 2 out of 16 in 3vic

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Chlorine binding site 2 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl228

b:44.4
occ:1.00
 ND2 A:ASN128 3.1 26.3 0.5
O A:HOH1233 3.5 30.3 1.0
NZ C:LYS182 3.6 27.1 1.0
CA A:ASN128 3.7 25.0 0.5
O A:PHE129 3.7 28.2 1.0
C A:ASN128 3.7 24.5 0.5
CA A:ASN128 3.8 24.9 0.5
C A:ASN128 3.8 24.8 0.5
O A:ASN128 3.9 24.5 0.5
CE C:LYS182 4.0 27.1 1.0
C A:PHE129 4.0 25.5 1.0
O A:ASN128 4.1 24.3 0.5
CA A:PRO130 4.1 28.3 1.0
CG A:ASN128 4.1 29.8 0.5
N A:PRO130 4.2 26.0 1.0
CD A:PRO131 4.2 31.6 1.0
SD C:MET156 4.2 30.8 1.0
CB A:ASN128 4.4 24.9 0.5
N A:PHE129 4.4 24.4 1.0
CE C:MET156 4.5 34.5 1.0
ND2 A:ASN128 4.5 26.5 0.5
CB A:ASN128 4.6 24.7 0.5
OE1 C:GLU94 4.6 25.9 1.0
O A:HOH745 4.6 30.3 1.0
N A:ASN128 4.8 24.8 0.5
CG2 C:THR180 4.8 23.5 1.0
N A:ASN128 4.8 24.8 0.5
CG A:ASN128 4.8 25.7 0.5
CA A:PHE129 4.9 26.5 1.0

Chlorine binding site 3 out of 16 in 3vic

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Chlorine binding site 3 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl227

b:28.2
occ:1.00
 O B:HOH841 3.2 40.2 1.0
N B:GLY155 3.4 27.0 1.0
N B:GLY154 3.7 26.8 1.0
O B:HOH624 3.9 30.7 1.0
CG B:MET189 4.1 28.6 1.0
C B:ARG153 4.1 26.0 1.0
N B:ARG153 4.1 25.1 1.0
CB B:ALA152 4.1 26.2 1.0
CA B:ARG153 4.2 26.1 1.0
CA B:GLY154 4.3 29.4 1.0
CA B:GLY155 4.3 29.2 1.0
CE B:MET189 4.3 27.3 1.0
C B:GLY154 4.3 29.9 1.0
C B:ALA152 4.3 27.6 1.0
O B:ALA152 4.7 28.7 1.0
CB B:MET189 4.7 29.0 1.0
SD B:MET189 4.8 30.5 1.0
CA B:ALA152 4.8 27.5 1.0
O B:ARG153 4.9 24.7 1.0

Chlorine binding site 4 out of 16 in 3vic

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Chlorine binding site 4 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl228

b:37.5
occ:1.00
 ND2 B:ASN128 3.4 25.2 0.5
NZ D:LYS182 3.5 25.8 1.0
O B:PHE129 3.6 26.7 1.0
O B:HOH747 3.7 30.7 1.0
CA B:ASN128 3.8 23.8 0.5
C B:ASN128 3.8 23.9 0.5
CA B:ASN128 3.9 23.8 0.5
C B:ASN128 3.9 23.4 0.5
O B:ASN128 4.0 23.6 0.5
C B:PHE129 4.0 25.0 1.0
CE D:LYS182 4.0 27.6 1.0
CD B:PRO131 4.1 31.1 1.0
CA B:PRO130 4.1 28.9 1.0
SD D:MET156 4.2 29.5 1.0
CE D:MET156 4.2 28.7 1.0
N B:PRO130 4.3 27.1 1.0
O B:ASN128 4.3 23.3 0.5
N B:PHE129 4.3 23.4 1.0
OD1 B:ASN128 4.5 25.2 0.5
O B:HOH672 4.5 30.9 1.0
CB B:ASN128 4.5 23.7 0.5
CG B:ASN128 4.5 26.5 0.5
OE1 D:GLU94 4.6 23.4 1.0
CG2 D:THR180 4.8 21.3 1.0
N B:ASN128 4.8 23.6 0.5
N B:ASN128 4.8 23.6 0.5
CB B:ASN128 4.8 23.5 0.5
CG B:ASN128 4.8 24.5 0.5
CA B:PHE129 4.9 25.2 1.0

Chlorine binding site 5 out of 16 in 3vic

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Chlorine binding site 5 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl228

b:32.6
occ:1.00
 N C:GLY155 3.6 31.9 1.0
N C:GLY154 3.8 31.6 1.0
O C:HOH751 3.9 42.4 1.0
CG C:MET189 4.0 34.1 1.0
CB C:ALA152 4.0 30.2 1.0
O C:HOH898 4.0 38.5 1.0
N C:ARG153 4.1 29.7 1.0
C C:ARG153 4.1 28.9 1.0
CA C:GLY155 4.2 32.8 1.0
CA C:ARG153 4.2 30.0 1.0
CE C:MET189 4.3 29.1 1.0
C C:ALA152 4.3 31.7 1.0
CA C:GLY154 4.5 31.8 1.0
C C:GLY154 4.5 34.8 1.0
CB C:MET189 4.6 31.8 1.0
O C:ALA152 4.7 30.7 1.0
SD C:MET189 4.7 33.9 1.0
CA C:ALA152 4.8 29.3 1.0
O C:ARG153 4.9 28.8 1.0

Chlorine binding site 6 out of 16 in 3vic

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Chlorine binding site 6 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl229

b:33.4
occ:1.00
 ND2 C:ASN128 3.0 28.4 0.5
NZ A:LYS182 3.5 30.7 1.0
O C:HOH664 3.6 26.9 1.0
O C:PHE129 3.6 26.3 1.0
C C:ASN128 3.8 24.1 0.5
O C:ASN128 3.8 24.1 0.5
CA C:ASN128 3.8 24.5 0.5
CA C:ASN128 3.8 24.9 0.5
C C:ASN128 3.9 24.3 0.5
CE A:LYS182 4.0 29.7 1.0
C C:PHE129 4.0 25.6 1.0
CA C:PRO130 4.1 28.8 1.0
N C:PRO130 4.1 26.2 1.0
CG C:ASN128 4.2 25.0 0.5
CD C:PRO131 4.2 30.6 1.0
O C:ASN128 4.2 23.8 0.5
SD A:MET156 4.2 31.5 1.0
N C:PHE129 4.3 24.0 1.0
CE A:MET156 4.4 33.9 1.0
O C:HOH340 4.5 27.0 1.0
CB C:ASN128 4.6 24.2 0.5
CB C:ASN128 4.6 24.1 0.5
OE1 A:GLU94 4.7 24.4 1.0
OD1 C:ASN128 4.8 25.6 0.5
CG2 A:THR180 4.8 25.2 1.0
CA C:PHE129 4.9 25.1 1.0
N C:ASN128 4.9 24.2 0.5
N C:ASN128 4.9 24.2 0.5
N C:PRO131 4.9 30.8 1.0
CG C:ASN128 4.9 25.0 0.5
C C:PRO130 5.0 29.5 1.0

Chlorine binding site 7 out of 16 in 3vic

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Chlorine binding site 7 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl228

b:26.1
occ:1.00
 N D:GLY155 3.4 27.5 1.0
N D:GLY154 3.6 25.5 1.0
CG D:MET189 3.9 31.6 1.0
O D:HOH723 4.0 31.7 1.0
C D:ARG153 4.1 25.4 1.0
N D:ARG153 4.1 24.3 1.0
CB D:ALA152 4.1 25.2 1.0
CA D:GLY155 4.2 29.4 1.0
CA D:ARG153 4.2 25.6 1.0
CA D:GLY154 4.3 28.5 1.0
C D:GLY154 4.3 30.8 1.0
C D:ALA152 4.3 25.1 1.0
CE D:MET189 4.3 25.1 1.0
O D:ALA152 4.6 27.3 1.0
CB D:MET189 4.6 27.3 1.0
SD D:MET189 4.8 28.9 1.0
O D:ARG153 4.8 25.2 1.0
CA D:ALA152 4.9 24.5 1.0

Chlorine binding site 8 out of 16 in 3vic

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Chlorine binding site 8 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl229

b:36.3
occ:1.00
 ND2 D:ASN128 3.2 26.5 0.5
O D:HOH263 3.6 27.0 1.0
O D:PHE129 3.6 27.0 1.0
NZ B:LYS182 3.6 28.0 1.0
CA D:ASN128 3.8 23.0 0.5
C D:ASN128 3.8 24.2 0.5
CA D:ASN128 3.8 22.9 0.5
CE B:LYS182 3.9 24.9 1.0
O D:ASN128 3.9 22.8 0.5
C D:PHE129 3.9 25.2 1.0
C D:ASN128 4.0 23.6 0.5
CA D:PRO130 4.0 28.2 1.0
N D:PRO130 4.1 26.6 1.0
CG D:ASN128 4.2 27.8 0.5
SD B:MET156 4.2 29.3 1.0
CD D:PRO131 4.3 29.6 1.0
O D:ASN128 4.3 22.5 0.5
CE B:MET156 4.3 28.1 1.0
N D:PHE129 4.4 22.5 1.0
CB D:ASN128 4.5 22.9 0.5
O D:HOH746 4.6 30.5 1.0
CB D:ASN128 4.6 22.8 0.5
OD1 D:ASN128 4.6 24.1 0.5
CG2 B:THR180 4.6 22.6 1.0
OE1 B:GLU94 4.7 24.6 1.0
CG D:ASN128 4.8 23.6 0.5
N D:ASN128 4.8 22.7 0.5
N D:ASN128 4.8 22.7 0.5
CA D:PHE129 4.9 24.5 1.0
C D:PRO130 5.0 26.5 1.0
CB D:PRO130 5.0 29.4 1.0

Chlorine binding site 9 out of 16 in 3vic

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Chlorine binding site 9 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl227

b:31.1
occ:1.00
 N E:GLY155 3.4 28.9 1.0
N E:GLY154 3.7 29.4 1.0
CG E:MET189 4.0 29.9 1.0
CB E:ALA152 4.0 25.6 1.0
C E:ARG153 4.1 25.4 1.0
N E:ARG153 4.2 26.8 1.0
O E:HOH399 4.2 32.1 1.0
CA E:ARG153 4.2 26.7 1.0
CA E:GLY155 4.2 28.5 1.0
CE E:MET189 4.3 25.8 1.0
CA E:GLY154 4.3 30.3 1.0
C E:ALA152 4.3 27.7 1.0
C E:GLY154 4.4 31.1 1.0
O E:ALA152 4.7 27.1 1.0
CB E:MET189 4.7 28.8 1.0
SD E:MET189 4.7 30.0 1.0
CA E:ALA152 4.8 28.1 1.0
O E:ARG153 4.9 25.0 1.0

Chlorine binding site 10 out of 16 in 3vic

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Chlorine binding site 10 out of 16 in the Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Green-Fluorescent Variant of the Non-Fluorescent Chromoprotein RTMS5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl228

b:43.1
occ:1.00
 ND2 E:ASN128 3.3 25.9 0.5
NZ G:LYS182 3.5 25.4 1.0
O E:PHE129 3.6 26.7 1.0
O E:HOH380 3.8 35.0 1.0
CA E:ASN128 3.8 24.4 0.5
C E:ASN128 3.8 24.2 0.5
CA E:ASN128 3.8 24.3 0.5
CE G:LYS182 3.9 28.9 1.0
C E:ASN128 3.9 24.2 0.5
O E:ASN128 3.9 25.9 0.5
C E:PHE129 4.0 27.0 1.0
CA E:PRO130 4.1 27.3 1.0
CD E:PRO131 4.1 28.8 1.0
SD G:MET156 4.2 30.7 1.0
O E:ASN128 4.2 25.2 0.5
N E:PRO130 4.2 27.0 1.0
CE G:MET156 4.3 36.0 1.0
N E:PHE129 4.4 23.7 1.0
CG E:ASN128 4.4 29.1 0.5
ND2 E:ASN128 4.5 25.7 0.5
CB E:ASN128 4.6 24.3 0.5
OE1 G:GLU94 4.6 27.7 1.0
CB E:ASN128 4.7 24.2 0.5
CG2 G:THR180 4.7 22.9 1.0
O E:HOH950 4.8 35.0 1.0
N E:ASN128 4.8 24.1 0.5
N E:ASN128 4.8 24.1 0.5
CA E:PHE129 4.8 25.8 1.0
CG E:ASN128 4.9 25.1 0.5
ND2 E:ASN23 5.0 27.4 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 Jul 21 06:56:09 2024

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