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Calcium in PDB 2fnq: Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality

Enzymatic activity of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality

All present enzymatic activity of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality:
1.13.11.40;

Protein crystallography data

The structure of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality, PDB code: 2fnq was solved by M.L.Oldham, A.R.Brash, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.00 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.554, 78.023, 176.490, 90.00, 96.66, 90.00
R / Rfree (%) 25.4 / 29.6

Other elements in 2fnq:

The structure of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality (pdb code 2fnq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality, PDB code: 2fnq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2fnq

Go back to Calcium Binding Sites List in 2fnq
Calcium binding site 1 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2200

b:41.1
occ:1.00
 OD1 A:ASP391 2.3 45.2 1.0
OD1 A:ASN416 2.3 50.2 1.0
OE2 A:GLU419 2.4 48.9 1.0
O A:ASP417 2.4 49.8 1.0
O A:THR390 2.5 51.4 1.0
CG A:ASP391 3.2 45.2 1.0
CD A:GLU419 3.3 48.9 1.0
CG A:ASN416 3.4 50.2 1.0
CG A:GLU419 3.6 48.9 1.0
C A:ASP417 3.6 49.8 1.0
C A:THR390 3.6 51.4 1.0
O A:PHE418 3.7 61.8 1.0
CA A:ASP391 3.8 35.9 1.0
OD2 A:ASP391 3.9 45.2 1.0
ND2 A:ASN416 4.0 50.2 1.0
C A:PHE418 4.0 61.8 1.0
CB A:ASP391 4.1 45.2 1.0
N A:ASP417 4.2 49.8 1.0
N A:ASP391 4.2 35.9 1.0
C A:ASN416 4.2 50.1 1.0
N A:GLU419 4.4 47.6 1.0
CA A:ASP417 4.5 49.8 1.0
OE1 A:GLU419 4.5 48.9 1.0
O A:ASN416 4.5 50.1 1.0
CA A:GLU419 4.5 47.6 1.0
CB A:ASN416 4.6 50.2 1.0
CB A:GLU419 4.6 48.9 1.0
N A:PHE418 4.6 61.8 1.0
CA A:ASN416 4.7 50.1 1.0
CA A:PHE418 4.7 61.8 1.0
N A:THR390 4.9 51.4 1.0
CA A:THR390 4.9 51.4 1.0
CB A:PHE418 4.9 31.4 1.0

Calcium binding site 2 out of 6 in 2fnq

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Calcium binding site 2 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2300

b:41.1
occ:1.00
 OD1 A:ASP417 2.2 63.0 1.0
OD1 A:ASP411 2.2 46.0 1.0
O A:HIS415 2.2 38.1 1.0
O A:LYS412 2.6 44.2 1.0
CG A:ASP417 3.4 63.0 1.0
CG A:ASP411 3.4 46.0 1.0
C A:HIS415 3.4 38.1 1.0
C A:LYS412 3.7 44.2 1.0
N A:HIS415 4.0 38.1 1.0
OD2 A:ASP411 4.0 46.0 1.0
OD2 A:ASP417 4.0 63.0 1.0
CA A:HIS415 4.1 38.1 1.0
N A:ASP417 4.2 49.8 1.0
N A:LYS412 4.3 44.2 1.0
CB A:HIS415 4.4 49.8 1.0
N A:ASN416 4.4 50.1 1.0
CB A:ASP417 4.5 63.0 1.0
CB A:ASP411 4.5 46.0 1.0
N A:TRP413 4.6 51.6 1.0
CA A:ASN416 4.6 50.1 1.0
CA A:TRP413 4.6 51.6 1.0
C A:ASP411 4.6 41.4 1.0
CA A:LYS412 4.6 44.2 1.0
C A:TRP413 4.7 51.6 1.0
CD2 A:HIS415 4.8 49.8 1.0
N A:PHE414 4.9 34.9 1.0
C A:ASN416 4.9 50.1 1.0
CG A:HIS415 4.9 49.8 1.0
CA A:ASP411 4.9 41.4 1.0
CA A:ASP417 5.0 49.8 1.0

Calcium binding site 3 out of 6 in 2fnq

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Calcium binding site 3 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2400

b:41.1
occ:1.00
 O A:ASP452 2.0 46.9 1.0
O A:HIS387 2.2 42.9 1.0
O A:GLY389 2.4 53.8 1.0
CB A:ASP452 2.9 18.0 1.0
O A:ASP454 3.0 43.8 1.0
C A:ASP452 3.0 46.9 1.0
C A:HIS387 3.2 42.9 1.0
CA A:HIS387 3.5 42.9 1.0
CA A:ASP452 3.5 46.9 1.0
CB A:HIS387 3.6 52.9 1.0
C A:GLY389 3.6 53.8 1.0
N A:ASP454 3.9 43.8 1.0
C A:ASP454 4.0 43.8 1.0
N A:PRO453 4.2 42.2 1.0
N A:GLY389 4.2 53.8 1.0
N A:ALA388 4.4 49.1 1.0
N A:ASP452 4.4 46.9 1.0
CA A:ASP454 4.4 43.8 1.0
CA A:GLY389 4.5 53.8 1.0
N A:THR390 4.6 51.4 1.0
C A:ALA388 4.6 49.1 1.0
CG A:HIS387 4.6 52.9 1.0
ND1 A:HIS387 4.6 52.9 1.0
CA A:THR390 4.7 51.4 1.0
C A:PRO453 4.7 42.2 1.0
CA A:PRO453 4.7 42.2 1.0
CB A:ASP454 4.7 73.8 1.0
CZ3 A:TRP478 4.8 48.9 1.0
CG2 A:THR390 4.8 45.1 1.0
N A:HIS387 4.9 42.9 1.0
CA A:ALA388 5.0 49.1 1.0

Calcium binding site 4 out of 6 in 2fnq

Go back to Calcium Binding Sites List in 2fnq
Calcium binding site 4 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2201

b:41.1
occ:1.00
 OD1 B:ASP391 2.3 45.2 1.0
OD1 B:ASN416 2.3 50.2 1.0
OE2 B:GLU419 2.4 48.9 1.0
O B:ASP417 2.4 49.8 1.0
O B:THR390 2.5 51.4 1.0
CG B:ASP391 3.2 45.2 1.0
CD B:GLU419 3.3 48.9 1.0
CG B:ASN416 3.4 50.2 1.0
CG B:GLU419 3.6 48.9 1.0
C B:ASP417 3.6 49.8 1.0
C B:THR390 3.6 51.4 1.0
O B:PHE418 3.7 61.8 1.0
CA B:ASP391 3.8 35.9 1.0
OD2 B:ASP391 3.9 45.2 1.0
ND2 B:ASN416 4.0 50.2 1.0
C B:PHE418 4.0 61.8 1.0
CB B:ASP391 4.1 45.2 1.0
N B:ASP417 4.2 49.8 1.0
N B:ASP391 4.2 35.9 1.0
C B:ASN416 4.2 50.1 1.0
N B:GLU419 4.4 47.6 1.0
CA B:ASP417 4.5 49.8 1.0
OE1 B:GLU419 4.5 48.9 1.0
O B:ASN416 4.5 50.1 1.0
CA B:GLU419 4.5 47.6 1.0
CB B:ASN416 4.6 50.2 1.0
CB B:GLU419 4.6 48.9 1.0
N B:PHE418 4.6 61.8 1.0
CA B:ASN416 4.7 50.1 1.0
CA B:PHE418 4.7 61.8 1.0
N B:THR390 4.9 51.4 1.0
CA B:THR390 4.9 51.4 1.0
CB B:PHE418 4.9 31.4 1.0

Calcium binding site 5 out of 6 in 2fnq

Go back to Calcium Binding Sites List in 2fnq
Calcium binding site 5 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2301

b:41.1
occ:1.00
 OD1 B:ASP417 2.2 63.0 1.0
OD1 B:ASP411 2.2 46.0 1.0
O B:HIS415 2.2 38.1 1.0
O B:LYS412 2.6 44.2 1.0
CG B:ASP417 3.4 63.0 1.0
CG B:ASP411 3.4 46.0 1.0
C B:HIS415 3.4 38.1 1.0
C B:LYS412 3.7 44.2 1.0
N B:HIS415 4.0 38.1 1.0
OD2 B:ASP411 4.0 46.0 1.0
OD2 B:ASP417 4.0 63.0 1.0
CA B:HIS415 4.1 38.1 1.0
N B:ASP417 4.2 49.8 1.0
N B:LYS412 4.3 44.2 1.0
CB B:HIS415 4.4 49.8 1.0
N B:ASN416 4.4 50.1 1.0
CB B:ASP417 4.5 63.0 1.0
CB B:ASP411 4.5 46.0 1.0
CA B:ASN416 4.6 50.1 1.0
N B:TRP413 4.6 51.6 1.0
CA B:TRP413 4.6 51.6 1.0
C B:ASP411 4.6 41.4 1.0
CA B:LYS412 4.6 44.2 1.0
C B:TRP413 4.7 51.6 1.0
CD2 B:HIS415 4.8 49.8 1.0
N B:PHE414 4.9 34.9 1.0
C B:ASN416 4.9 50.1 1.0
CG B:HIS415 4.9 49.8 1.0
CA B:ASP411 4.9 41.4 1.0
CA B:ASP417 5.0 49.8 1.0

Calcium binding site 6 out of 6 in 2fnq

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Calcium binding site 6 out of 6 in the Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Insights From the X-Ray Crystal Structure of Coral 8R- Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2401

b:41.1
occ:1.00
 O B:ASP452 2.0 46.9 1.0
O B:HIS387 2.2 42.9 1.0
O B:GLY389 2.4 53.8 1.0
CB B:ASP452 2.9 18.0 1.0
O B:ASP454 3.0 43.8 1.0
C B:ASP452 3.0 46.9 1.0
C B:HIS387 3.2 42.9 1.0
CA B:HIS387 3.5 42.9 1.0
CA B:ASP452 3.5 46.9 1.0
C B:GLY389 3.6 53.8 1.0
CB B:HIS387 3.6 52.9 1.0
N B:ASP454 3.9 43.8 1.0
C B:ASP454 4.0 43.8 1.0
N B:PRO453 4.2 42.2 1.0
N B:GLY389 4.2 53.8 1.0
N B:ALA388 4.4 49.1 1.0
N B:ASP452 4.4 46.9 1.0
CA B:ASP454 4.4 43.8 1.0
CA B:GLY389 4.5 53.8 1.0
N B:THR390 4.6 51.4 1.0
C B:ALA388 4.6 49.1 1.0
CG B:HIS387 4.6 52.9 1.0
ND1 B:HIS387 4.6 52.9 1.0
CA B:THR390 4.7 51.4 1.0
C B:PRO453 4.7 42.2 1.0
CA B:PRO453 4.7 42.2 1.0
CB B:ASP454 4.7 73.8 1.0
CZ3 B:TRP478 4.8 48.9 1.0
CG2 B:THR390 4.8 45.1 1.0
N B:HIS387 4.9 42.9 1.0
CA B:ALA388 5.0 49.1 1.0

Reference:

M.L.Oldham, A.R.Brash, M.E.Newcomer. Insights From the X-Ray Crystal Structure of Coral 8R-Lipoxygenase: Calcium Activation Via A C2-Like Domain and A Structural Basis of Product Chirality. J.Biol.Chem. V. 280 39545 2005.
ISSN: ISSN 0021-9258
PubMed: 16162493
DOI: 10.1074/JBC.M506675200
Page generated: Fri Jul 12 10:33:21 2024

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