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Calcium in PDB 6xvu: Bacteriophytochrome Response Regulator From Deinococcus Radiodurans

Protein crystallography data

The structure of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans, PDB code: 6xvu was solved by H.Takala, J.A.Ihalainen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.65, 87.65, 181.21, 90, 90, 90
R / Rfree (%) 18.1 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans (pdb code 6xvu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans, PDB code: 6xvu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6xvu

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Calcium binding site 1 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:52.1
occ:1.00
 O A:HOH367 2.2 50.0 1.0
O A:HOH304 2.2 41.0 1.0
OD2 A:ASP66 2.3 51.2 1.0
O A:ASN68 2.3 47.8 0.5
O A:ASN68 2.3 46.4 0.5
OD1 A:ASP16 2.4 47.6 1.0
O A:HOH311 2.5 62.3 1.0
CG A:ASP16 3.1 48.6 1.0
OD2 A:ASP16 3.2 55.2 1.0
CG A:ASP66 3.4 48.4 1.0
C A:ASN68 3.6 45.7 0.5
C A:ASN68 3.6 44.3 0.5
OE2 A:GLU15 3.9 45.1 1.0
OD1 A:ASP66 4.0 49.5 1.0
CB A:ASN68 4.2 50.9 0.5
O A:HOH351 4.3 59.4 1.0
CA A:ASN68 4.3 46.5 0.5
CA A:ASN68 4.4 44.1 0.5
CB A:ASN68 4.4 46.6 0.5
O A:HOH302 4.5 48.2 1.0
CB A:ASP66 4.5 45.2 1.0
CG A:MET69 4.5 44.9 1.0
N A:MET69 4.6 44.1 1.0
CB A:ASP16 4.6 47.2 1.0
N A:ASN68 4.6 44.9 0.5
N A:ASN68 4.6 43.4 0.5
CA A:MET69 4.7 43.9 1.0
CD A:GLU15 4.9 43.9 1.0
N A:ASP16 4.9 42.7 1.0

Calcium binding site 2 out of 9 in 6xvu

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Calcium binding site 2 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:34.7
occ:0.50
 O A:HOH347 2.1 55.8 1.0
O A:GLN111 2.4 41.1 1.0
OE1 B:GLN111 2.4 56.8 1.0
O A:HOH363 2.5 44.8 1.0
O A:HOH340 2.5 46.5 1.0
OD1 A:ASN113 2.5 40.1 1.0
O B:HOH324 2.7 48.2 1.0
CG A:ASN113 3.2 39.7 1.0
ND2 A:ASN113 3.6 35.3 1.0
C A:GLN111 3.6 42.5 1.0
CD B:GLN111 3.6 52.5 1.0
N A:ASN113 3.9 39.6 1.0
C A:ALA112 4.2 38.1 1.0
NE2 B:GLN111 4.3 54.9 1.0
CB A:GLN111 4.3 49.8 1.0
CA A:ASN113 4.4 37.6 1.0
CB A:ASN113 4.4 39.0 1.0
O B:ALA112 4.5 36.5 1.0
CA A:GLN111 4.5 44.9 1.0
O A:HOH335 4.5 46.2 1.0
CA B:GLN111 4.5 43.5 1.0
O A:ALA88 4.5 51.1 1.0
N A:ALA112 4.5 42.1 1.0
CA A:ALA112 4.5 40.9 1.0
O A:HOH338 4.6 56.8 1.0
O A:LEU90 4.6 43.2 0.5
O A:LEU90 4.6 40.2 0.5
O A:ALA112 4.6 39.0 1.0
O B:TYR108 4.7 49.9 1.0
CB B:GLN111 4.8 47.4 1.0
CA B:CA202 4.8 49.6 0.5
CG B:GLN111 4.8 50.2 1.0

Calcium binding site 3 out of 9 in 6xvu

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Calcium binding site 3 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:43.6
occ:1.00
 O A:ARG71 2.3 44.6 1.0
O C:HOH350 2.3 40.2 1.0
O C:ARG71 2.4 48.4 1.0
O A:HOH344 2.5 41.8 1.0
OE1 C:GLU76 2.5 42.2 1.0
OE2 A:GLU76 2.5 45.5 1.0
OE2 C:GLU76 2.6 44.8 1.0
OE1 A:GLU76 2.6 40.4 1.0
CD C:GLU76 2.9 41.8 1.0
CD A:GLU76 3.0 42.9 1.0
C A:ARG71 3.5 43.2 1.0
C C:ARG71 3.6 47.2 1.0
O C:HOH308 4.1 59.7 1.0
O A:HOH313 4.3 67.9 1.0
CA A:VAL72 4.4 40.9 1.0
N A:VAL72 4.4 42.2 1.0
CG C:GLU76 4.4 42.3 1.0
CA A:ARG71 4.4 45.7 1.0
N C:VAL72 4.5 43.9 1.0
CA C:VAL72 4.5 43.4 1.0
CG A:GLU76 4.5 42.5 1.0
CA C:ARG71 4.5 50.9 1.0
O C:HOH347 4.5 52.8 1.0
O A:HOH318 4.6 46.6 1.0
OD2 C:ASP73 4.6 48.9 1.0
OD2 A:ASP73 4.7 49.8 1.0
N C:ASP73 4.7 43.7 1.0
N A:ASP73 4.8 39.8 1.0
O A:HOH339 5.0 62.2 1.0

Calcium binding site 4 out of 9 in 6xvu

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Calcium binding site 4 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:58.4
occ:1.00
 O B:HOH355 2.2 55.1 1.0
OE2 B:GLU15 2.4 52.7 1.0
O B:HOH305 2.4 56.4 1.0
OD2 B:ASP20 2.5 51.4 1.0
O B:HOH340 2.5 59.5 1.0
OE1 B:GLU15 2.5 50.4 1.0
O B:HOH329 2.5 61.0 1.0
CD B:GLU15 2.7 48.1 1.0
OD2 B:ASP66 3.4 62.9 1.0
CG B:ASP20 3.6 46.1 1.0
NZ B:LYS118 4.2 68.0 1.0
CG B:GLU15 4.2 45.6 1.0
CB B:ASN17 4.3 51.7 1.0
CB B:ASP20 4.3 42.4 1.0
OD1 B:ASP20 4.3 49.2 1.0
CG B:ASP66 4.3 56.8 1.0
O B:HOH343 4.3 66.7 1.0
OD1 B:ASP16 4.4 76.7 1.0
CB B:ASP66 4.4 53.1 1.0
O B:HOH317 4.6 53.9 1.0
CE B:LYS118 4.8 63.1 1.0
O B:HOH312 4.9 50.6 1.0

Calcium binding site 5 out of 9 in 6xvu

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Calcium binding site 5 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:49.6
occ:0.50
 NH2 B:ARG82 2.2 65.0 1.0
O A:HOH310 2.5 51.6 1.0
O A:HOH363 2.6 44.8 1.0
O B:GLN111 2.7 40.4 1.0
OE1 A:GLN111 2.7 62.4 1.0
O B:HOH303 2.8 49.8 0.5
OD1 B:ASN113 3.0 38.4 1.0
CZ B:ARG82 3.1 65.9 1.0
CG B:ASN113 3.4 40.0 1.0
NE B:ARG82 3.4 70.7 1.0
ND2 B:ASN113 3.4 34.4 1.0
C B:GLN111 3.7 40.5 1.0
CD A:GLN111 3.9 55.8 1.0
CA A:GLN111 4.0 44.9 1.0
O A:ALA112 4.0 39.0 1.0
NH1 B:ARG82 4.1 66.3 1.0
N B:ASN113 4.1 38.3 1.0
CB B:GLN111 4.2 47.4 1.0
C B:ALA112 4.3 38.8 1.0
CA B:GLN111 4.4 43.5 1.0
CB A:GLN111 4.4 49.8 1.0
C A:GLN111 4.4 42.5 1.0
CA B:ASN113 4.4 37.9 1.0
O A:GLN111 4.4 41.1 1.0
O B:ALA112 4.5 36.5 1.0
CB B:ASN113 4.5 39.3 1.0
O A:TYR108 4.5 47.4 1.0
O B:ALA88 4.7 55.0 1.0
CD B:ARG82 4.7 71.1 1.0
CG A:GLN111 4.7 55.3 1.0
N B:ALA112 4.7 41.9 1.0
NE2 A:GLN111 4.8 55.2 1.0
CA A:CA202 4.8 34.7 0.5
OE1 B:GLN111 4.8 56.8 1.0
C A:ALA112 4.8 38.1 1.0
CA B:ALA112 4.8 41.1 1.0

Calcium binding site 6 out of 9 in 6xvu

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Calcium binding site 6 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:104.6
occ:1.00
 O C:HOH305 1.8 66.3 1.0
O C:HOH315 2.0 70.6 1.0
O C:HOH328 2.4 54.0 1.0
O C:HOH366 2.5 59.1 1.0
OE2 C:GLU15 2.6 57.7 1.0
OD1 C:ASP16 2.8 77.5 1.0
OD2 C:ASP66 3.3 56.0 1.0
CD C:GLU15 3.4 54.5 1.0
OE1 C:GLU15 3.5 55.6 1.0
CG C:ASP16 4.0 74.2 1.0
O C:ASN68 4.1 55.2 0.5
CB C:ASP66 4.1 47.4 1.0
CG C:ASP66 4.2 47.9 1.0
O C:ASN68 4.2 53.4 0.5
N C:ASP16 4.3 58.2 1.0
OD2 C:ASP16 4.5 82.0 1.0
NZ C:LYS118 4.6 65.3 1.0
CA C:GLU15 4.7 51.8 1.0
CG C:GLU15 4.7 52.1 1.0
OD2 C:ASP20 4.9 65.2 1.0
N C:ASN17 4.9 60.6 1.0

Calcium binding site 7 out of 9 in 6xvu

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Calcium binding site 7 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:36.9
occ:0.50
 NH1 C:ARG82 1.8 42.0 0.5
O C:HOH303 2.3 40.0 0.5
O C:GLN111 2.4 34.7 1.0
OE1 D:GLN111 2.5 52.4 1.0
O D:HOH339 2.6 40.2 1.0
O D:HOH312 2.6 46.0 1.0
CZ C:ARG82 2.8 44.3 0.5
OD1 C:ASN113 2.8 36.7 1.0
O C:HOH302 2.9 48.7 0.5
NE C:ARG82 3.0 44.2 0.5
CG C:ASN113 3.3 38.4 1.0
C C:GLN111 3.5 36.2 1.0
ND2 C:ASN113 3.6 37.0 1.0
CD D:GLN111 3.7 48.2 1.0
N C:ASN113 3.9 37.2 1.0
NH2 C:ARG82 4.0 44.6 0.5
C C:ALA112 4.1 38.5 1.0
CB C:GLN111 4.2 39.3 1.0
CA C:GLN111 4.3 36.2 1.0
CA D:GLN111 4.3 40.7 1.0
CA C:ASN113 4.3 37.5 1.0
O D:ALA112 4.4 38.6 1.0
O C:ALA112 4.4 35.3 1.0
CD C:ARG82 4.4 44.8 0.5
CB C:ASN113 4.4 37.1 1.0
NE2 D:GLN111 4.5 49.4 1.0
N C:ALA112 4.5 36.9 1.0
CA C:ALA112 4.5 38.3 1.0
CB D:GLN111 4.6 42.3 1.0
O C:ALA88 4.6 43.4 1.0
O D:TYR108 4.7 43.2 1.0
CG D:GLN111 4.7 47.1 1.0
C D:GLN111 4.8 40.3 1.0
O D:GLN111 4.8 40.2 1.0
CA D:CA202 4.9 34.8 0.5
O C:LEU90 4.9 41.6 0.5
O C:LEU90 4.9 43.4 0.5
O C:HOH301 4.9 35.5 0.5

Calcium binding site 8 out of 9 in 6xvu

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Calcium binding site 8 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:64.3
occ:1.00
 OD1 D:ASP16 2.2 71.2 1.0
O D:HOH337 2.2 62.4 1.0
OE2 D:GLU15 2.3 54.2 1.0
OD1 D:ASN17 2.5 55.7 1.0
O D:HOH304 2.5 59.6 1.0
OD2 D:ASP66 3.1 82.0 1.0
CD D:GLU15 3.3 48.2 1.0
CG D:ASP16 3.3 66.2 1.0
OE1 D:GLU15 3.6 50.6 1.0
CG D:ASN17 3.6 58.7 1.0
OD2 D:ASP16 3.8 72.9 1.0
N D:ASN17 4.0 55.9 1.0
N D:ASP16 4.1 56.7 1.0
CB D:ASN17 4.2 56.2 1.0
CG D:ASP66 4.2 76.4 1.0
O D:ASN68 4.3 81.9 1.0
CB D:ASP16 4.5 63.8 1.0
CG D:GLU15 4.6 49.6 1.0
NZ D:LYS118 4.6 70.2 1.0
OD1 D:ASP20 4.7 67.3 1.0
CA D:ASP16 4.7 61.5 1.0
ND2 D:ASN17 4.7 60.4 1.0
CB D:ASP66 4.7 70.6 1.0
CA D:ASN17 4.7 55.5 1.0
C D:ASP16 4.8 59.4 1.0
CA D:GLU15 5.0 53.1 1.0

Calcium binding site 9 out of 9 in 6xvu

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Calcium binding site 9 out of 9 in the Bacteriophytochrome Response Regulator From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Bacteriophytochrome Response Regulator From Deinococcus Radiodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:34.8
occ:0.50
 NH2 D:ARG82 1.8 36.2 0.5
OE1 C:GLN111 2.3 48.3 1.0
O D:HOH303 2.4 30.0 0.5
O D:GLN111 2.4 40.2 1.0
O D:HOH339 2.5 40.2 1.0
O C:HOH326 2.6 40.0 1.0
CZ D:ARG82 2.8 36.9 0.5
O D:HOH301 2.8 39.2 0.5
OD1 D:ASN113 2.8 38.4 1.0
NE D:ARG82 3.2 38.5 0.5
CG D:ASN113 3.4 36.4 1.0
CD C:GLN111 3.5 44.4 1.0
ND2 D:ASN113 3.6 31.0 1.0
C D:GLN111 3.6 40.3 1.0
NH1 D:ARG82 3.9 34.2 0.5
N D:ASN113 4.1 39.9 1.0
NE2 C:GLN111 4.1 45.7 1.0
CB D:GLN111 4.2 42.3 1.0
O C:ALA112 4.3 35.3 1.0
CA C:GLN111 4.3 36.2 1.0
C D:ALA112 4.3 39.8 1.0
CA D:GLN111 4.4 40.7 1.0
CA D:ASN113 4.5 37.6 1.0
O D:ALA88 4.5 43.7 1.0
O C:TYR108 4.5 32.9 1.0
CB C:GLN111 4.5 39.3 1.0
CD D:ARG82 4.6 43.2 0.5
CB D:ASN113 4.6 37.3 1.0
CG C:GLN111 4.6 41.4 1.0
N D:ALA112 4.6 40.9 1.0
CA D:ALA112 4.7 41.5 1.0
O D:ALA112 4.7 38.6 1.0
C C:GLN111 4.8 36.2 1.0
O D:LEU90 4.8 39.3 1.0
O C:GLN111 4.9 34.7 1.0
CA C:CA202 4.9 36.9 0.5

Reference:

E.Multamaki, R.Nanekar, D.Morozov, T.Lievonen, D.Golonka, W.Wahlgren, B.Stucki-Buchli, J.Rossi, G.Groenhof, V.Hytonen, S.Westenhoff, A.Moglich, J.A.Ihalainen, H.Takala. Activity and Interactions of Two Canonical Bacteriophytochromes To Be Published.
Page generated: Wed Jul 9 20:07:45 2025

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