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Calcium in PDB 3q08: Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5

Enzymatic activity of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5

All present enzymatic activity of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5:
1.13.11.49;

Protein crystallography data

The structure of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5, PDB code: 3q08 was solved by B.R.Goblirsch, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.91 / 3.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.704, 202.850, 247.103, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.1

Other elements in 3q08:

The structure of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 (pdb code 3q08). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5, PDB code: 3q08:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in 3q08

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Calcium binding site 1 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:16.2
occ:1.00
 OD1 D:ASP192 2.0 23.6 1.0
OE1 A:GLU70 2.3 16.3 1.0
OE2 A:GLU70 2.4 14.7 1.0
O A:THR231 2.4 10.7 1.0
CD A:GLU70 2.7 13.3 1.0
CG D:ASP192 3.0 15.7 1.0
OD2 D:ASP192 3.4 16.5 1.0
C A:THR231 3.6 9.6 1.0
CG A:GLU70 4.2 12.3 1.0
CB D:ASP192 4.2 12.7 1.0
CA D:ASP192 4.2 12.3 1.0
OD2 D:ASP193 4.3 13.0 1.0
CA A:THR232 4.3 10.4 1.0
N A:THR232 4.4 9.9 1.0
O D:LEU191 4.4 12.9 1.0
CB A:THR231 4.6 9.0 1.0
N A:LEU233 4.6 11.8 1.0
CA A:THR231 4.6 8.9 1.0
O A:LEU69 4.7 13.3 1.0
N D:ASP193 4.8 11.1 1.0
N A:THR231 4.9 8.8 1.0
C A:THR232 5.0 10.9 1.0

Calcium binding site 2 out of 20 in 3q08

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Calcium binding site 2 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:14.6
occ:1.00
 OD1 C:ASP192 2.0 22.7 1.0
OE2 B:GLU70 2.3 15.7 1.0
O B:THR231 2.4 9.4 1.0
OE1 B:GLU70 2.5 19.7 1.0
CD B:GLU70 2.7 15.0 1.0
CG C:ASP192 2.9 15.5 1.0
OD2 C:ASP192 3.3 17.6 1.0
C B:THR231 3.7 8.3 1.0
CB C:ASP192 4.2 11.5 1.0
CG B:GLU70 4.2 10.9 1.0
OD2 C:ASP193 4.3 12.9 1.0
CA C:ASP192 4.3 12.0 1.0
CA B:THR232 4.4 9.3 1.0
N B:THR232 4.5 8.6 1.0
CB B:THR231 4.5 8.5 1.0
CA B:THR231 4.6 8.3 1.0
N B:LEU233 4.6 10.1 1.0
O B:LEU69 4.7 10.9 1.0
O C:LEU191 4.7 13.4 1.0
N C:ASP193 4.7 11.4 1.0
N B:THR231 4.8 8.8 1.0

Calcium binding site 3 out of 20 in 3q08

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Calcium binding site 3 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:17.3
occ:1.00
 OD1 E:ASP192 2.1 22.7 1.0
O C:THR231 2.4 9.2 1.0
OE2 C:GLU70 2.5 15.5 1.0
OE1 C:GLU70 2.5 18.2 1.0
CD C:GLU70 2.9 14.7 1.0
CG E:ASP192 3.0 14.8 1.0
OD2 E:ASP192 3.5 17.2 1.0
C C:THR231 3.6 8.0 1.0
CB E:ASP192 4.2 10.2 1.0
CA E:ASP192 4.2 10.3 1.0
CG C:GLU70 4.4 12.1 1.0
OD2 E:ASP193 4.4 13.5 1.0
N C:THR232 4.5 8.3 1.0
CA C:THR232 4.5 9.0 1.0
CA C:THR231 4.5 7.5 1.0
CB C:THR231 4.5 7.5 1.0
N E:ASP193 4.6 9.8 1.0
O E:LEU191 4.6 11.7 1.0
O C:LEU69 4.7 11.8 1.0
N C:THR231 4.7 7.6 1.0
N C:LEU233 4.7 9.7 1.0
C E:ASP192 4.9 9.9 1.0

Calcium binding site 4 out of 20 in 3q08

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Calcium binding site 4 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1001

b:19.9
occ:1.00
 OD1 B:ASP192 2.1 24.0 1.0
OE1 D:GLU70 2.3 20.8 1.0
O D:THR231 2.3 10.4 1.0
OE2 D:GLU70 2.4 18.6 1.0
CD D:GLU70 2.7 17.6 1.0
CG B:ASP192 3.1 17.4 1.0
C D:THR231 3.5 10.1 1.0
OD2 B:ASP192 3.6 20.7 1.0
CG D:GLU70 4.2 14.0 1.0
CB B:ASP192 4.3 13.6 1.0
CA B:ASP192 4.3 14.0 1.0
N D:THR232 4.4 10.3 1.0
CA D:THR232 4.4 10.5 1.0
CA D:THR231 4.5 9.9 1.0
CB D:THR231 4.5 10.2 1.0
OD2 B:ASP193 4.5 16.9 1.0
O B:LEU191 4.6 15.3 1.0
N D:LEU233 4.7 12.2 1.0
N D:THR231 4.7 10.1 1.0
O D:LEU69 4.8 14.9 1.0
N B:ASP193 4.8 13.1 1.0

Calcium binding site 5 out of 20 in 3q08

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Calcium binding site 5 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1001

b:12.4
occ:1.00
 OD1 A:ASP192 2.2 18.5 1.0
OE2 E:GLU70 2.2 14.5 1.0
OE1 E:GLU70 2.3 16.8 1.0
O E:THR231 2.4 6.9 1.0
CD E:GLU70 2.6 13.1 1.0
CG A:ASP192 3.0 13.8 1.0
OD2 A:ASP192 3.5 16.0 1.0
C E:THR231 3.6 5.4 1.0
CG E:GLU70 4.2 9.8 1.0
CB A:ASP192 4.2 9.1 1.0
CA A:ASP192 4.2 8.7 1.0
CA E:THR232 4.3 5.6 1.0
OD2 A:ASP193 4.4 9.5 1.0
N E:THR232 4.4 5.0 1.0
CA E:THR231 4.5 5.4 1.0
CB E:THR231 4.5 5.3 1.0
O A:LEU191 4.6 8.5 1.0
N E:LEU233 4.6 6.6 1.0
O E:LEU69 4.7 9.4 1.0
N E:THR231 4.7 6.1 1.0
N A:ASP193 4.7 8.0 1.0
C E:THR232 5.0 6.2 1.0

Calcium binding site 6 out of 20 in 3q08

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Calcium binding site 6 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1001

b:25.4
occ:1.00
 OD1 G:ASP192 1.9 30.9 1.0
OE2 F:GLU70 2.2 21.9 1.0
OE1 F:GLU70 2.4 23.2 1.0
O F:THR231 2.5 17.8 1.0
CD F:GLU70 2.6 21.7 1.0
CG G:ASP192 3.0 25.1 1.0
OD2 G:ASP192 3.6 26.6 1.0
C F:THR231 3.7 17.2 1.0
CG F:GLU70 4.2 20.8 1.0
CB G:ASP192 4.2 20.9 1.0
CA G:ASP192 4.2 21.1 1.0
O G:LEU191 4.3 23.3 1.0
CA F:THR232 4.5 19.1 1.0
N F:THR232 4.5 18.1 1.0
CA F:THR231 4.6 16.6 1.0
CB F:THR231 4.6 16.4 1.0
OD2 G:ASP193 4.6 18.9 1.0
O F:LEU69 4.6 20.2 1.0
N F:LEU233 4.8 20.8 1.0
N F:THR231 4.8 16.5 1.0
N G:ASP193 4.8 19.1 1.0
CG2 F:THR231 4.9 17.7 1.0

Calcium binding site 7 out of 20 in 3q08

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Calcium binding site 7 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1001

b:18.3
occ:1.00
 OD1 H:ASP192 2.1 24.4 1.0
OE1 G:GLU70 2.4 21.8 1.0
OE2 G:GLU70 2.5 20.4 1.0
O G:THR231 2.5 13.9 1.0
CD G:GLU70 2.8 18.8 1.0
CG H:ASP192 3.0 18.6 1.0
OD2 H:ASP192 3.4 22.2 1.0
C G:THR231 3.7 13.1 1.0
CB H:ASP192 4.2 14.2 1.0
CA H:ASP192 4.2 14.4 1.0
CG G:GLU70 4.3 14.7 1.0
OD2 H:ASP193 4.4 15.5 1.0
CA G:THR232 4.5 13.9 1.0
N G:THR232 4.6 13.6 1.0
N H:ASP193 4.6 12.8 1.0
CB G:THR231 4.6 12.2 1.0
O H:LEU191 4.7 15.0 1.0
CA G:THR231 4.7 12.5 1.0
O G:LEU69 4.7 15.5 1.0
N G:LEU233 4.8 14.0 1.0
N G:THR231 4.8 12.6 1.0
C H:ASP192 5.0 14.0 1.0

Calcium binding site 8 out of 20 in 3q08

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Calcium binding site 8 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1001

b:17.6
occ:1.00
 OD1 I:ASP192 2.2 25.2 1.0
OE1 H:GLU70 2.3 19.2 1.0
O H:THR231 2.4 11.9 1.0
OE2 H:GLU70 2.4 19.3 1.0
CD H:GLU70 2.7 17.6 1.0
CG I:ASP192 3.0 16.6 1.0
OD2 I:ASP192 3.4 17.7 1.0
C H:THR231 3.6 10.2 1.0
OD2 I:ASP193 4.2 12.9 1.0
CB I:ASP192 4.2 11.7 1.0
CG H:GLU70 4.2 14.3 1.0
CA I:ASP192 4.3 11.7 1.0
CA H:THR232 4.4 10.9 1.0
N H:THR232 4.4 10.3 1.0
CA H:THR231 4.5 9.2 1.0
CB H:THR231 4.6 8.7 1.0
N H:THR231 4.6 9.4 1.0
O H:LEU69 4.6 14.6 1.0
N H:LEU233 4.6 11.8 1.0
O I:LEU191 4.8 14.0 1.0
N I:ASP193 4.8 11.0 1.0

Calcium binding site 9 out of 20 in 3q08

Go back to Calcium Binding Sites List in 3q08
Calcium binding site 9 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1001

b:18.1
occ:1.00
 OD1 J:ASP192 2.1 26.6 1.0
O I:THR231 2.2 12.4 1.0
OE1 I:GLU70 2.4 20.6 1.0
OE2 I:GLU70 2.5 20.6 1.0
CD I:GLU70 2.8 19.2 1.0
CG J:ASP192 3.1 21.0 1.0
OD2 J:ASP192 3.5 23.6 1.0
C I:THR231 3.5 11.9 1.0
CB J:ASP192 4.3 16.9 1.0
CG I:GLU70 4.3 16.7 1.0
N I:THR232 4.4 12.0 1.0
CA J:ASP192 4.4 16.4 1.0
OD2 J:ASP193 4.4 16.7 1.0
CA I:THR232 4.4 12.5 1.0
CB I:THR231 4.5 10.8 1.0
CA I:THR231 4.5 10.7 1.0
N I:THR231 4.6 11.0 1.0
O J:LEU191 4.6 16.3 1.0
O I:LEU69 4.7 18.4 1.0
N I:LEU233 4.7 14.6 1.0
N J:ASP193 4.8 14.4 1.0

Calcium binding site 10 out of 20 in 3q08

Go back to Calcium Binding Sites List in 3q08
Calcium binding site 10 out of 20 in the Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Chlorite Dismutase From D. Aromatica at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca1001

b:26.5
occ:1.00
 OE2 J:GLU70 2.2 27.1 1.0
OE1 J:GLU70 2.4 28.6 1.0
O J:THR231 2.4 18.7 1.0
OD1 F:ASP192 2.6 32.0 1.0
CD J:GLU70 2.6 26.4 1.0
CG F:ASP192 3.2 25.1 1.0
OD2 F:ASP192 3.5 27.6 1.0
C J:THR231 3.6 17.6 1.0
CG J:GLU70 4.2 24.1 1.0
CA F:ASP192 4.2 20.7 1.0
CB F:ASP192 4.3 20.9 1.0
OD2 F:ASP193 4.4 18.3 1.0
CA J:THR232 4.5 18.9 1.0
N J:THR232 4.5 17.7 1.0
O F:LEU191 4.5 22.5 1.0
O J:LEU69 4.6 24.9 1.0
CB J:THR231 4.6 16.7 1.0
CA J:THR231 4.6 16.5 1.0
N F:ASP193 4.7 18.7 1.0
N J:THR231 4.7 16.4 1.0
N J:LEU233 4.7 20.7 1.0
C F:ASP192 4.9 19.5 1.0

Reference:

B.R.Goblirsch, B.R.Streit, J.L.Dubois, C.M.Wilmot. Structural Features Promoting Dioxygen Production By Dechloromonas Aromatica Chlorite Dismutase. J.Biol.Inorg.Chem. V. 15 879 2010.
ISSN: ISSN 0949-8257
PubMed: 20386942
DOI: 10.1007/S00775-010-0651-0
Page generated: Sat Jul 13 17:01:37 2024

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