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Calcium in PDB 3dhg: Crystal Structure of Toluene 4-Monoxygenase Hydroxylase

Protein crystallography data

The structure of Crystal Structure of Toluene 4-Monoxygenase Hydroxylase, PDB code: 3dhg was solved by L.J.Bailey, J.G.Mccoy, G.N.Phillips Jr., B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.45 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.822, 181.481, 89.917, 90.00, 107.62, 90.00
R / Rfree (%) 16.4 / 21.4

Other elements in 3dhg:

The structure of Crystal Structure of Toluene 4-Monoxygenase Hydroxylase also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase (pdb code 3dhg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase, PDB code: 3dhg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3dhg

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Calcium binding site 1 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:31.4
occ:1.00
 O E:HOH339 2.4 25.8 1.0
O B:HOH947 2.4 31.7 1.0
OE1 B:GLU184 2.5 32.1 1.0
O B:HOH542 2.5 29.8 1.0
O B:HOH382 2.5 28.6 1.0
O E:HOH1423 2.5 44.0 1.0
CD B:GLU184 3.6 30.2 1.0
OE2 B:GLU184 4.2 28.3 1.0
O B:HOH435 4.3 27.1 1.0
CD2 E:LEU175 4.3 22.6 1.0
O B:HOH451 4.3 30.4 1.0
O B:GLU184 4.5 22.5 1.0
O B:HOH1424 4.6 46.7 1.0
CG B:GLU184 4.7 25.4 1.0
O B:HOH927 4.7 46.5 1.0
O B:HOH348 4.7 26.9 1.0
O B:HOH1419 4.8 31.0 1.0
CB E:PRO178 4.8 22.7 1.0
O E:SER174 4.8 21.3 1.0
CB B:GLU184 4.8 23.9 1.0
CA E:LEU175 4.9 22.1 1.0

Calcium binding site 2 out of 9 in 3dhg

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Calcium binding site 2 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:24.7
occ:1.00
 O A:HOH559 2.4 29.5 1.0
O B:HOH1149 2.4 27.0 1.0
O B:HOH353 2.5 25.0 1.0
O B:HOH381 2.5 29.1 1.0
O E:HOH349 2.5 26.4 1.0
O B:HOH340 2.6 24.7 1.0
O B:HOH388 2.6 27.7 1.0
O B:HOH351 4.3 25.3 1.0
ND1 B:HIS171 4.4 19.4 1.0
O B:HOH376 4.4 30.4 1.0
OE2 B:GLU184 4.4 28.3 1.0
O B:HOH357 4.4 33.5 1.0
OE1 E:GLU184 4.5 29.7 1.0
O A:HOH685 4.5 23.8 1.0
O E:HOH1045 4.5 32.4 1.0
O A:HOH1281 4.7 23.5 1.0
O B:GLY183 4.7 22.3 1.0
O E:HOH378 4.7 32.2 1.0
O B:LEU182 4.9 22.6 1.0
CE1 B:HIS171 4.9 18.8 1.0
CD E:GLU184 5.0 25.6 1.0
CG E:GLU184 5.0 23.7 1.0

Calcium binding site 3 out of 9 in 3dhg

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Calcium binding site 3 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:39.9
occ:1.00
 O B:GLN108 2.2 32.1 1.0
O B:HOH1445 2.5 30.7 1.0
O B:HOH1447 2.8 52.2 1.0
C B:GLN108 3.4 30.3 1.0
CA B:GLN108 4.2 29.7 1.0
N B:MET109 4.3 30.6 1.0
CA B:MET109 4.4 30.5 1.0
CB B:GLN108 4.5 30.1 1.0
O B:VAL110 4.7 27.7 1.0
C B:MET109 4.9 29.4 1.0
OH B:TYR177 5.0 23.7 1.0

Calcium binding site 4 out of 9 in 3dhg

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Calcium binding site 4 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:28.4
occ:1.00
 O B:HOH383 2.8 31.1 1.0
N B:SER146 3.1 15.5 1.0
N B:HIS33 3.5 17.2 1.0
CA B:LYS31 3.5 18.2 1.0
O B:HOH1426 3.5 19.1 1.0
OG B:SER146 3.5 15.2 1.0
N B:LEU32 3.5 16.7 1.0
CA B:ALA145 3.6 16.0 1.0
CB B:HIS33 3.8 17.7 1.0
C B:LYS31 3.8 17.8 1.0
C B:ALA145 3.9 16.1 1.0
CB B:ASP70 4.0 21.9 1.0
N B:LYS31 4.0 17.9 1.0
CB B:SER146 4.1 16.0 1.0
CA B:HIS33 4.1 17.2 1.0
CA B:SER146 4.2 14.9 1.0
CG B:HIS33 4.2 17.9 1.0
CB B:ALA145 4.2 16.2 1.0
CD B:LYS31 4.4 28.1 1.0
O B:HIS33 4.4 16.4 1.0
C B:LEU32 4.4 17.1 1.0
O B:PRO144 4.5 18.1 1.0
CA B:ASP70 4.5 21.2 1.0
CD2 B:HIS33 4.5 19.2 1.0
CA B:LEU32 4.5 16.6 1.0
O B:HOH1157 4.6 24.5 1.0
C B:HIS33 4.7 17.8 1.0
CB B:LYS31 4.7 19.8 1.0
N B:ALA145 4.7 14.9 1.0
O B:LYS31 4.9 17.4 1.0

Calcium binding site 5 out of 9 in 3dhg

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Calcium binding site 5 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca511

b:49.8
occ:1.00
 O E:HOH875 2.4 44.8 1.0
O E:HOH759 2.5 38.6 1.0
OD1 B:ASP179 2.5 29.5 1.0
O E:ASP179 2.6 24.7 1.0
O B:HOH369 2.7 28.7 1.0
O B:HOH845 2.9 50.9 1.0
CG B:ASP179 3.5 30.2 1.0
C E:ASP179 3.6 23.7 1.0
CB B:ASP179 4.1 26.6 1.0
CA B:ASP179 4.3 26.3 1.0
O E:HOH458 4.4 38.2 1.0
OD2 B:ASP179 4.4 35.0 1.0
CA E:ASP179 4.4 23.9 1.0
N E:ALA180 4.5 22.9 1.0
O B:PRO178 4.5 24.2 1.0
CB E:ASP179 4.5 24.2 1.0
CA E:ALA180 4.6 22.3 1.0
O B:HOH1379 4.6 53.1 1.0
O E:HOH344 4.8 24.5 1.0
C E:ALA180 4.9 21.2 1.0
O B:HOH470 5.0 30.0 1.0
N E:GLY181 5.0 20.7 1.0

Calcium binding site 6 out of 9 in 3dhg

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Calcium binding site 6 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca506

b:38.2
occ:1.00
 O C:HOH1348 2.1 37.6 1.0
O C:HOH1417 2.2 35.6 1.0
O C:HOH1418 2.4 41.5 1.0
O C:HOH188 2.5 30.9 1.0
O C:HOH1347 2.5 39.0 1.0
O C:ALA68 2.5 33.9 1.0
C C:ALA68 3.6 33.6 1.0
CA C:ALA68 4.1 33.1 1.0
N C:GLY71 4.3 31.7 1.0
CA C:GLY71 4.4 31.7 1.0
O C:LEU72 4.5 30.6 1.0
O C:ILE67 4.5 32.1 1.0
O C:HOH816 4.6 41.2 1.0
O C:HOH1382 4.7 34.7 1.0
N C:GLU69 4.8 34.4 1.0
C C:GLY71 4.9 31.4 1.0
CB C:ALA68 5.0 33.0 1.0

Calcium binding site 7 out of 9 in 3dhg

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Calcium binding site 7 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca509

b:33.5
occ:1.00
 O E:HOH505 2.4 26.9 1.0
OD2 E:ASP88 2.4 22.1 1.0
O D:HOH732 2.4 29.0 1.0
O E:HOH449 2.5 26.0 1.0
O E:HOH1449 2.5 36.3 1.0
O D:HOH610 2.5 26.0 1.0
OD1 E:ASP88 2.6 20.7 1.0
OG D:SER60 2.6 23.0 1.0
CG E:ASP88 2.8 21.4 1.0
CB D:SER60 3.5 17.6 1.0
CA D:SER60 4.0 17.6 1.0
OG E:SER92 4.0 25.8 1.0
CB E:ASP88 4.3 18.6 1.0
O D:HOH553 4.4 26.6 1.0
O D:SER60 4.6 17.0 1.0
C D:SER60 4.7 17.6 1.0
NH1 D:ARG63 4.7 24.5 1.0
O D:HOH1102 4.9 25.4 1.0
O E:ASP88 5.0 17.8 1.0
CD D:ARG63 5.0 22.1 1.0

Calcium binding site 8 out of 9 in 3dhg

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Calcium binding site 8 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca512

b:29.6
occ:1.00
 OD1 E:ASP70 2.1 22.2 0.5
CG E:ASP70 2.9 20.3 0.5
O E:HOH409 2.9 27.9 1.0
OD2 E:ASP70 3.0 21.9 0.5
N E:SER146 3.2 14.3 1.0
N E:HIS33 3.4 16.5 1.0
OG E:SER146 3.4 16.2 1.0
CA E:LYS31 3.5 18.3 1.0
O E:HOH1331 3.5 17.9 1.0
N E:LEU32 3.5 16.2 1.0
CA E:ALA145 3.6 14.3 1.0
CB E:HIS33 3.7 17.2 1.0
C E:LYS31 3.8 17.1 1.0
C E:ALA145 3.9 13.9 1.0
N E:LYS31 4.0 17.3 1.0
CB E:ASP70 4.0 17.6 0.5
CB E:SER146 4.0 14.9 1.0
CA E:HIS33 4.1 16.4 1.0
CG E:HIS33 4.2 15.5 1.0
CA E:SER146 4.2 14.2 1.0
CB E:ASP70 4.3 18.2 0.5
CB E:ALA145 4.3 13.6 1.0
C E:LEU32 4.4 15.6 1.0
O E:HOH1250 4.4 24.2 1.0
CA E:LEU32 4.5 15.8 1.0
O E:PRO144 4.5 17.5 1.0
O E:HIS33 4.5 18.5 1.0
CD2 E:HIS33 4.5 19.3 1.0
C E:HIS33 4.6 17.4 1.0
CB E:LYS31 4.7 18.3 1.0
CA E:ASP70 4.7 18.2 0.5
CA E:ASP70 4.7 18.5 0.5
O E:LYS31 4.7 18.1 1.0
N E:ALA145 4.7 15.5 1.0
CG E:LYS31 4.9 26.5 1.0
O E:HOH463 4.9 33.7 1.0

Calcium binding site 9 out of 9 in 3dhg

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Calcium binding site 9 out of 9 in the Crystal Structure of Toluene 4-Monoxygenase Hydroxylase


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 Toluene 4-Monoxygenase Hydroxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca513

b:38.8
occ:1.00
 O F:HOH1414 2.3 32.0 1.0
O F:HOH928 2.3 27.6 1.0
O F:HOH952 2.4 33.4 1.0
O F:ALA68 2.4 34.0 1.0
O F:HOH801 2.4 39.0 1.0
O F:HOH692 2.6 34.3 1.0
O F:HOH1413 2.6 35.8 1.0
C F:ALA68 3.4 33.5 1.0
CA F:ALA68 3.9 33.0 1.0
N F:GLY71 4.3 33.0 1.0
CA F:GLY71 4.3 32.8 1.0
O F:LEU72 4.4 31.0 1.0
O F:HOH1415 4.6 35.2 1.0
O F:ILE67 4.6 32.8 1.0
N F:GLU69 4.6 34.4 1.0
CB F:ALA68 4.7 32.6 1.0
C F:GLY71 4.9 32.2 1.0
CA F:GLU69 5.0 34.8 1.0

Reference:

L.J.Bailey, J.G.Mccoy, G.N.Phillips Jr., B.G.Fox. Structural Consequences of Effector Protein Complex Formation in A Diiron Hydroxylase. Proc.Natl.Acad.Sci.Usa V. 105 19194 2008.
ISSN: ISSN 0027-8424
PubMed: 19033467
DOI: 10.1073/PNAS.0807948105
Page generated: Sat Jul 13 09:01:06 2024

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