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Chlorine in PDB 5lly: Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L

Protein crystallography data

The structure of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L, PDB code: 5lly was solved by G.Gourinchas, A.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.13 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.500, 129.000, 122.010, 90.00, 96.34, 90.00
R / Rfree (%) 17.7 / 23

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (pdb code 5lly). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L, PDB code: 5lly:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5lly

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Chlorine binding site 1 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl602

b:52.6
occ:1.00
 O D:HOH792 3.3 41.6 1.0
NH1 D:ARG292 3.4 39.6 1.0
N D:ARG292 3.4 42.9 1.0
CD D:ARG292 3.4 39.0 1.0
CG D:ARG292 3.4 40.8 1.0
CB D:ARG292 3.7 37.8 1.0
N D:ARG291 3.7 47.0 1.0
CE1 D:TYR120 4.0 49.4 1.0
CD1 D:TYR120 4.1 36.2 1.0
CA D:ARG292 4.2 41.4 1.0
CB D:ARG291 4.2 40.6 1.0
CA D:ARG291 4.3 44.1 1.0
CZ D:ARG292 4.3 40.1 1.0
C D:ARG291 4.3 44.6 1.0
NE D:ARG292 4.3 39.9 1.0
C D:GLY290 4.5 41.0 1.0
OE2 D:GLU98 4.5 50.9 1.0
CA D:GLY290 4.6 39.1 1.0
CZ2 D:TRP96 4.9 41.9 1.0

Chlorine binding site 2 out of 8 in 5lly

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Chlorine binding site 2 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl603

b:37.4
occ:1.00
 NH1 D:ARG295 3.0 59.3 1.0
NH1 D:ARG291 3.1 41.3 1.0
NH1 D:ARG294 3.2 37.1 1.0
O D:HOH785 3.5 40.1 1.0
NH2 D:ARG295 3.7 58.6 1.0
CD D:ARG291 3.8 40.3 1.0
CG D:ARG291 3.8 37.8 1.0
CZ D:ARG295 3.8 56.1 1.0
CD D:ARG294 3.9 43.6 1.0
CZ D:ARG291 4.2 40.1 1.0
CB D:ARG291 4.2 40.6 1.0
CG1 D:VAL244 4.2 36.8 1.0
CZ D:ARG294 4.3 45.3 1.0
CD2 D:LEU105 4.4 37.7 1.0
CA D:ARG291 4.4 44.1 1.0
NE D:ARG291 4.4 40.8 1.0
NE D:ARG294 4.5 43.9 1.0
CG2 D:VAL244 4.6 30.4 1.0
CB D:ARG294 4.8 35.8 1.0
CG D:ARG294 5.0 35.8 1.0

Chlorine binding site 3 out of 8 in 5lly

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Chlorine binding site 3 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:42.4
occ:1.00
 NH1 A:ARG291 3.1 49.2 1.0
NH1 A:ARG295 3.2 44.8 1.0
NH1 A:ARG294 3.2 44.5 1.0
CD A:ARG294 3.8 40.8 1.0
CD A:ARG291 3.9 44.5 1.0
NH2 A:ARG295 3.9 51.2 1.0
CZ A:ARG295 4.0 47.0 1.0
CG1 A:VAL244 4.0 42.9 1.0
CD2 A:LEU105 4.1 43.4 1.0
CG A:ARG291 4.1 44.7 1.0
CZ A:ARG291 4.2 50.9 1.0
CZ A:ARG294 4.2 45.0 1.0
CB A:ARG291 4.4 44.5 1.0
NE A:ARG294 4.5 46.4 1.0
NE A:ARG291 4.5 46.4 1.0
CA A:ARG291 4.5 48.6 1.0
CB A:ARG294 4.9 36.2 1.0
CG A:ARG294 5.0 37.7 1.0
CG2 A:VAL244 5.0 45.5 1.0

Chlorine binding site 4 out of 8 in 5lly

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Chlorine binding site 4 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:91.0
occ:1.00
 NH1 A:ARG292 3.4 38.7 1.0
N A:ARG292 3.5 35.5 1.0
O A:HOH710 3.5 43.0 1.0
N A:ARG291 3.7 46.0 1.0
CG A:ARG292 3.7 36.4 1.0
CD A:ARG292 3.8 37.3 1.0
CB A:ARG292 3.9 35.7 1.0
C A:GLY290 4.2 48.0 1.0
CB A:ARG291 4.2 44.5 1.0
CA A:ARG291 4.3 48.6 1.0
CA A:GLY290 4.3 47.7 1.0
CA A:ARG292 4.3 40.4 1.0
C A:ARG291 4.4 54.4 1.0
CZ A:ARG292 4.4 41.5 1.0
CE1 A:TYR120 4.5 79.1 1.0
NE A:ARG292 4.6 39.5 1.0
CD1 A:TYR120 4.6 76.8 1.0
CG A:ARG291 4.9 44.7 1.0
OE2 A:GLU98 4.9 65.7 1.0
O A:HIS121 4.9 90.0 1.0

Chlorine binding site 5 out of 8 in 5lly

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Chlorine binding site 5 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl602

b:54.9
occ:1.00
 NH1 C:ARG295 2.9 61.6 1.0
NH1 C:ARG291 3.0 47.5 1.0
NH1 C:ARG294 3.1 44.5 1.0
O C:HOH781 3.3 43.2 1.0
CD C:ARG294 3.7 41.5 1.0
CG C:ARG291 3.7 41.5 1.0
CZ C:ARG295 3.8 60.4 1.0
CD C:ARG291 3.8 42.3 1.0
NH2 C:ARG295 3.9 63.5 1.0
CZ C:ARG294 4.2 46.7 1.0
CZ C:ARG291 4.2 46.9 1.0
CB C:ARG291 4.2 41.9 1.0
CG1 C:VAL244 4.3 41.4 1.0
CD2 C:LEU105 4.3 48.9 1.0
NE C:ARG294 4.4 46.1 1.0
CA C:ARG291 4.4 42.8 1.0
NE C:ARG291 4.4 44.9 1.0
CG2 C:VAL244 4.6 39.8 1.0
CB C:ARG294 4.8 37.5 1.0
CG C:ARG294 4.9 40.5 1.0

Chlorine binding site 6 out of 8 in 5lly

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Chlorine binding site 6 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl603

b:80.5
occ:1.00
 O C:HOH782 3.1 43.8 1.0
NH1 C:ARG292 3.2 46.1 1.0
CG C:ARG292 3.2 40.7 1.0
N C:ARG292 3.3 42.4 1.0
CB C:ARG292 3.4 39.6 1.0
CD C:ARG292 3.4 44.6 1.0
N C:ARG291 3.8 45.1 1.0
CA C:ARG292 4.0 43.5 1.0
CZ C:ARG292 4.2 44.8 1.0
NE C:ARG292 4.3 42.9 1.0
C C:GLY290 4.3 42.8 1.0
C C:ARG291 4.3 41.7 1.0
CA C:GLY290 4.4 41.7 1.0
CA C:ARG291 4.4 42.8 1.0
CB C:ARG291 4.5 41.9 1.0
CE1 C:TYR120 4.6 78.0 1.0
OE2 C:GLU98 4.8 62.5 1.0
O C:HIS121 4.8 87.2 1.0
CD1 C:TYR120 4.9 74.1 1.0

Chlorine binding site 7 out of 8 in 5lly

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Chlorine binding site 7 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:40.0
occ:1.00
 NH1 B:ARG295 2.9 56.1 1.0
NH1 B:ARG291 3.2 35.4 1.0
NH1 B:ARG294 3.2 34.1 1.0
NH2 B:ARG295 3.3 38.5 1.0
O B:HOH776 3.4 39.7 1.0
CZ B:ARG295 3.5 51.4 1.0
CD B:ARG294 3.7 37.8 1.0
CD B:ARG291 3.8 37.8 1.0
CG B:ARG291 3.8 34.5 1.0
CD2 B:LEU105 4.0 48.6 1.0
CG1 B:VAL244 4.0 41.9 1.0
CB B:ARG291 4.2 38.1 1.0
CZ B:ARG294 4.3 36.9 1.0
CA B:ARG291 4.3 38.8 1.0
CZ B:ARG291 4.3 41.8 1.0
NE B:ARG294 4.4 39.2 1.0
NE B:ARG291 4.5 35.5 1.0
CG2 B:VAL244 4.7 42.6 1.0
CB B:ARG294 4.7 33.4 1.0
NE B:ARG295 4.7 55.5 1.0
CG B:ARG294 4.8 33.3 1.0
O B:ARG291 5.0 41.8 1.0
CB B:VAL244 5.0 41.5 1.0

Chlorine binding site 8 out of 8 in 5lly

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Chlorine binding site 8 out of 8 in the Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Photosensory Module of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl603

b:43.5
occ:1.00
 NH1 B:ARG292 3.1 37.5 1.0
O B:HOH782 3.2 29.4 1.0
N B:ARG292 3.3 33.7 1.0
CG B:ARG292 3.4 41.4 1.0
CD B:ARG292 3.5 42.3 1.0
CB B:ARG292 3.5 34.0 1.0
O B:HOH714 3.6 36.9 1.0
N B:ARG291 3.9 37.5 1.0
CE1 B:TYR120 4.0 42.5 1.0
CA B:ARG292 4.0 37.0 1.0
CZ B:ARG292 4.1 39.2 1.0
NE B:ARG292 4.2 42.9 1.0
CB B:ARG291 4.3 38.1 1.0
C B:ARG291 4.3 40.9 1.0
CD1 B:TYR120 4.4 36.7 1.0
CA B:ARG291 4.4 38.8 1.0
C B:GLY290 4.5 35.6 1.0
OE2 B:GLU98 4.6 43.0 1.0
CA B:GLY290 4.7 31.1 1.0
CZ2 B:TRP96 5.0 37.5 1.0

Reference:

G.Gourinchas, S.Etzl, C.Gobl, U.Vide, T.Madl, A.Winkler. Long-Range Allosteric Signaling in Red Light-Regulated Diguanylyl Cyclases. Sci Adv V. 3 02498 2017.
ISSN: ESSN 2375-2548
PubMed: 28275738
DOI: 10.1126/SCIADV.1602498
Page generated: Sat Jul 12 05:00:35 2025

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