Atomistry » Chlorine » PDB 6sa4-6sio » 6saw
Atomistry »
  Chlorine »
    PDB 6sa4-6sio »
      6saw »

Chlorine in PDB 6saw: Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).

Protein crystallography data

The structure of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State)., PDB code: 6saw 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) 55.02 / 3.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 344.650, 344.650, 92.440, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.9

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 1 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:62.5
occ:1.00
NH1 A:ARG291 2.7 56.3 1.0
NH1 A:ARG295 3.2 49.9 1.0
NH1 A:ARG294 3.2 57.9 1.0
CG A:ARG291 3.8 48.1 1.0
CD2 A:LEU105 3.8 50.5 1.0
CD A:ARG294 4.0 51.9 1.0
CZ A:ARG291 4.0 51.6 1.0
NH2 A:ARG295 4.0 66.7 1.0
CZ A:ARG295 4.0 58.3 1.0
CD A:ARG291 4.1 50.1 1.0
CG1 A:VAL244 4.2 54.2 1.0
CZ A:ARG294 4.3 56.8 1.0
NE A:ARG291 4.5 52.4 1.0
CG2 A:VAL244 4.5 61.7 1.0
CB A:ARG291 4.5 44.8 1.0
NE A:ARG294 4.6 52.7 1.0
CD1 A:LEU105 4.8 49.3 1.0
CG A:LEU105 4.8 43.4 1.0
CA A:ARG291 4.9 47.5 1.0
OE2 A:GLU118 5.0 71.1 1.0

Chlorine binding site 2 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 2 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:60.4
occ:1.00
NH1 B:ARG291 2.8 59.8 1.0
NH1 B:ARG295 2.9 60.5 1.0
NH1 B:ARG294 3.1 54.4 1.0
CG B:ARG291 3.6 52.5 1.0
CD B:ARG294 3.6 52.2 1.0
CZ B:ARG295 3.8 62.7 1.0
NH2 B:ARG295 4.0 65.3 1.0
CZ B:ARG291 4.0 55.9 1.0
CD B:ARG291 4.1 50.1 1.0
CD2 B:LEU105 4.1 51.8 1.0
CZ B:ARG294 4.2 56.3 1.0
CG1 B:VAL244 4.2 48.1 1.0
CB B:ARG291 4.3 54.8 1.0
NE B:ARG294 4.3 56.3 1.0
NE B:ARG291 4.5 51.4 1.0
CA B:ARG291 4.6 55.1 1.0
CG2 B:VAL244 4.6 50.6 1.0
CB B:ARG294 4.8 54.1 1.0
CG B:ARG294 4.8 52.4 1.0

Chlorine binding site 3 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 3 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:67.3
occ:1.00
NH1 C:ARG295 2.9 60.0 1.0
NH1 C:ARG291 3.1 63.6 1.0
NH1 C:ARG294 3.4 61.6 1.0
CZ C:ARG295 3.8 62.4 1.0
NH2 C:ARG295 3.8 64.6 1.0
CG1 C:VAL244 3.9 58.9 1.0
CD C:ARG294 3.9 54.9 1.0
CD2 C:LEU105 4.0 53.0 1.0
CG C:ARG291 4.2 57.8 1.0
CZ C:ARG291 4.4 61.6 1.0
CZ C:ARG294 4.5 59.2 1.0
CD C:ARG291 4.5 53.5 1.0
CG2 C:VAL244 4.6 60.9 1.0
NE C:ARG294 4.7 55.0 1.0
CB C:ARG291 4.8 51.5 1.0
CB C:VAL244 4.9 58.0 1.0
NE C:ARG291 4.9 53.0 1.0

Chlorine binding site 4 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 4 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:76.3
occ:1.00
NH1 D:ARG295 2.7 60.6 1.0
NH1 D:ARG291 3.0 61.0 1.0
NH1 D:ARG294 3.3 54.8 1.0
CZ D:ARG295 3.6 66.2 1.0
NH2 D:ARG295 3.7 68.7 1.0
CG D:ARG291 3.9 54.2 1.0
CD D:ARG294 4.0 48.0 1.0
CZ D:ARG291 4.2 54.7 1.0
CD D:ARG291 4.3 53.8 1.0
CD2 D:LEU105 4.3 64.5 1.0
CG1 D:VAL244 4.4 56.0 1.0
CZ D:ARG294 4.4 54.0 1.0
CB D:ARG291 4.6 51.2 1.0
NE D:ARG294 4.7 52.5 1.0
NE D:ARG291 4.7 48.7 1.0
NE D:ARG295 4.8 66.3 1.0
CG2 D:VAL244 4.8 57.6 1.0
CA D:ARG291 4.8 54.2 1.0

Chlorine binding site 5 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 5 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:68.1
occ:1.00
NH1 E:ARG295 2.9 55.7 1.0
NH1 E:ARG291 3.0 59.2 1.0
NH1 E:ARG294 3.5 60.6 1.0
CZ E:ARG295 3.8 65.5 1.0
NH2 E:ARG295 3.9 64.3 1.0
CG E:ARG291 4.0 55.8 1.0
CD2 E:LEU105 4.0 50.3 1.0
CD E:ARG294 4.1 46.9 1.0
CG1 E:VAL244 4.1 59.9 1.0
CZ E:ARG291 4.3 56.2 1.0
CD E:ARG291 4.3 53.8 1.0
CG2 E:VAL244 4.4 64.0 1.0
CZ E:ARG294 4.6 56.7 1.0
CB E:ARG291 4.6 54.2 1.0
NE E:ARG291 4.7 55.2 1.0
NE E:ARG294 4.8 52.8 1.0
CD1 E:LEU105 4.9 54.2 1.0
CB E:VAL244 4.9 62.7 1.0
CA E:ARG291 5.0 50.8 1.0

Chlorine binding site 6 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 6 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl402

b:66.5
occ:1.00
NH1 F:ARG295 2.8 62.4 1.0
NH1 F:ARG291 2.9 59.5 1.0
NH1 F:ARG294 3.4 55.5 1.0
NH2 F:ARG295 3.5 69.6 1.0
CZ F:ARG295 3.5 71.2 1.0
CG F:ARG291 3.7 55.2 1.0
CD F:ARG294 3.7 51.5 1.0
CZ F:ARG291 4.1 56.2 1.0
CD F:ARG291 4.1 53.6 1.0
CB F:ARG291 4.3 56.0 1.0
CD2 F:LEU105 4.4 63.5 1.0
CZ F:ARG294 4.4 56.0 1.0
NE F:ARG294 4.5 54.0 1.0
NE F:ARG291 4.5 54.4 1.0
CG1 F:VAL244 4.6 61.3 1.0
CG2 F:VAL244 4.6 64.6 1.0
CA F:ARG291 4.6 53.6 1.0
CB F:ARG294 4.8 52.2 1.0
NE F:ARG295 4.8 66.7 1.0
CG F:ARG294 4.9 50.8 1.0

Chlorine binding site 7 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 7 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl402

b:65.0
occ:1.00
NH1 G:ARG291 3.0 68.2 1.0
NH1 G:ARG294 3.2 70.2 1.0
NH1 G:ARG295 3.3 55.2 1.0
CD2 G:LEU105 3.8 55.7 1.0
CD G:ARG294 3.9 57.5 1.0
CG1 G:VAL244 3.9 61.7 1.0
CG G:ARG291 4.1 62.6 1.0
CZ G:ARG295 4.2 63.8 1.0
CG2 G:VAL244 4.2 60.7 1.0
CZ G:ARG291 4.2 62.9 1.0
CZ G:ARG294 4.3 64.6 1.0
NH2 G:ARG295 4.3 62.7 1.0
CD G:ARG291 4.5 64.6 1.0
NE G:ARG294 4.6 58.5 1.0
CB G:VAL244 4.7 63.4 1.0
NE G:ARG291 4.8 62.5 1.0
CB G:ARG291 4.9 61.2 1.0
CG G:LEU105 4.9 57.7 1.0

Chlorine binding site 8 out of 8 in 6saw

Go back to Chlorine Binding Sites List in 6saw
Chlorine binding site 8 out of 8 in the Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State).


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Chromophore Binding Domain of Bacteriophytochrome Linked Diguanylyl Cyclase From Idiomarina Species A28L (Dimeric Pfr-Like State). within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl402

b:67.2
occ:1.00
NH1 H:ARG295 2.9 65.9 1.0
NH1 H:ARG291 3.2 59.8 1.0
NH1 H:ARG294 3.3 66.8 1.0
CD H:ARG294 3.7 59.6 1.0
CZ H:ARG295 3.8 72.6 1.0
NH2 H:ARG295 3.8 74.7 1.0
CD2 H:LEU105 3.9 58.4 1.0
CG1 H:VAL244 4.0 69.0 1.0
CG H:ARG291 4.0 60.0 1.0
CZ H:ARG294 4.3 64.8 1.0
CG2 H:VAL244 4.4 71.4 1.0
CZ H:ARG291 4.4 60.9 1.0
NE H:ARG294 4.5 62.2 1.0
CD H:ARG291 4.5 56.0 1.0
CB H:ARG291 4.7 55.0 1.0
CB H:ARG294 4.8 57.4 1.0
CB H:VAL244 4.8 71.6 1.0
CA H:ARG291 4.8 55.3 1.0
CG H:ARG294 4.9 54.1 1.0
NE H:ARG291 4.9 60.2 1.0

Reference:

D.Buhrke, G.Gourinchas, M.Muller, N.Michael, P.Hildebrandt, A.Winkler. Distinct Chromophore-Protein Environments Enable Asymmetric Activation of A Bacteriophytochrome Activated Diguanylate Cyclase. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31801828
DOI: 10.1074/JBC.RA119.011915
Page generated: Mon Jul 29 14:52:46 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy