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Calcium in PDB 4qwt: Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate

Enzymatic activity of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate

All present enzymatic activity of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate:
1.13.11.40;

Protein crystallography data

The structure of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate, PDB code: 4qwt was solved by D.B.Neau, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.42 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.030, 170.670, 104.720, 90.00, 95.36, 90.00
R / Rfree (%) 16.2 / 21.5

Other elements in 4qwt:

The structure of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate (pdb code 4qwt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate, PDB code: 4qwt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4qwt

Go back to Calcium Binding Sites List in 4qwt
Calcium binding site 1 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:25.3
occ:1.00
 O A:HIS17 2.3 23.1 0.9
O A:ASP81 2.3 23.7 1.0
O A:GLY19 2.3 25.4 1.0
O A:HOH877 2.4 26.3 1.0
OD2 A:ASP79 2.4 28.4 0.9
O A:ASP79 2.4 26.9 1.0
CG A:ASP79 3.3 31.1 0.6
C A:HIS17 3.4 21.8 1.0
C A:ASP79 3.5 29.6 1.0
C A:ASP81 3.5 20.9 1.0
C A:GLY19 3.6 25.4 1.0
CB A:ASP79 3.6 27.8 1.0
N A:GLY19 4.0 26.5 1.0
CA A:HIS17 4.0 24.9 0.8
N A:ASP81 4.1 26.2 1.0
C A:ALA18 4.1 25.3 1.0
CB A:HIS17 4.1 26.4 1.0
CA A:ASP79 4.2 29.7 0.9
C A:PRO80 4.2 28.2 1.0
CA A:ASP81 4.3 25.0 1.0
N A:ALA18 4.4 22.2 1.0
O A:ALA18 4.4 23.4 1.0
OD1 A:ASP79 4.4 30.4 0.9
CA A:GLY19 4.4 24.2 1.0
O A:PRO80 4.4 24.5 1.0
N A:PRO80 4.5 30.5 1.0
N A:THR20 4.5 22.5 1.0
CZ3 A:TRP105 4.5 23.8 1.0
CA A:THR20 4.5 24.2 1.0
N A:TRP82 4.5 25.1 0.9
CA A:ALA18 4.6 27.3 1.0
CB A:ASP81 4.7 25.0 1.0
CA A:PRO80 4.8 24.9 1.0
CH3 A:ACT720 4.8 41.1 0.9
CA A:TRP82 4.8 22.3 1.0
CB A:THR20 4.9 20.9 1.0
ND1 A:HIS17 4.9 39.8 0.8
CG A:HIS17 5.0 30.6 0.6
O A:HOH891 5.0 29.4 1.0

Calcium binding site 2 out of 8 in 4qwt

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Calcium binding site 2 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:24.5
occ:1.00
 OE2 A:GLU51 2.4 23.9 1.0
O B:HOH801 2.4 24.3 1.0
O A:HOH806 2.4 21.5 1.0
O A:HOH846 2.4 23.4 1.0
OD1 B:ASN655 2.4 20.7 1.0
O B:HOH803 2.5 20.9 1.0
O A:HOH802 2.6 24.3 1.0
CD A:GLU51 3.3 24.4 1.0
CG B:ASN655 3.5 20.4 1.0
ND2 B:ASN655 3.8 21.6 1.0
OE1 A:GLU51 3.9 24.1 0.8
O A:HOH884 4.1 29.7 1.0
CB A:GLU51 4.1 22.7 1.0
CG A:GLU51 4.2 19.9 1.0
O A:HOH871 4.2 29.8 1.0
O A:HOH1002 4.3 28.1 1.0
O A:LYS42 4.3 30.4 1.0
CA A:GLU51 4.5 26.0 1.0
OE1 B:GLN658 4.6 24.5 1.0
N A:GLN52 4.7 23.8 1.0
O B:LEU651 4.7 22.6 1.0
CA A:GLY43 4.7 28.7 0.9
CB B:ASN655 4.8 20.7 1.0
O A:SER44 4.8 23.1 1.0
O A:GLN52 4.8 25.0 1.0
OH A:TYR53 4.9 27.4 0.9
O A:HOH936 4.9 32.5 1.0

Calcium binding site 3 out of 8 in 4qwt

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Calcium binding site 3 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca715

b:23.7
occ:1.00
 OE2 B:GLU51 2.4 22.5 0.8
OD1 A:ASN655 2.4 18.9 1.0
O A:HOH801 2.4 18.7 1.0
O A:HOH813 2.5 26.6 1.0
O B:HOH805 2.5 22.6 1.0
O B:HOH802 2.5 23.0 1.0
O B:HOH821 2.5 20.9 1.0
CD B:GLU51 3.3 23.3 0.8
CG A:ASN655 3.5 24.5 0.8
OE1 B:GLU51 3.9 21.5 1.0
ND2 A:ASN655 3.9 23.0 1.0
CB B:GLU51 4.2 21.6 1.0
O B:HOH918 4.2 28.3 0.8
CG B:GLU51 4.2 20.8 1.0
O B:LYS42 4.3 24.7 0.8
O B:HOH833 4.3 30.0 1.0
O B:HOH842 4.4 31.7 1.0
OE1 A:GLN658 4.5 23.5 1.0
CA B:GLU51 4.6 19.3 1.0
N B:GLN52 4.6 22.1 1.0
O A:LEU651 4.6 22.4 1.0
CA B:GLY43 4.7 22.3 1.0
CB A:ASN655 4.8 20.4 1.0
O B:GLN52 4.8 24.5 1.0
O B:SER44 4.9 24.3 1.0
OH B:TYR53 4.9 26.4 0.7
CA A:ASN655 5.0 21.5 1.0

Calcium binding site 4 out of 8 in 4qwt

Go back to Calcium Binding Sites List in 4qwt
Calcium binding site 4 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:25.4
occ:1.00
 O B:GLY19 2.2 23.4 1.0
OD2 B:ASP79 2.3 29.8 1.0
O B:ASP81 2.4 23.6 1.0
O B:ASP79 2.4 28.7 1.0
O B:HOH1093 2.4 25.4 1.0
O B:HIS17 2.4 26.3 1.0
CG B:ASP79 3.3 33.5 0.9
C B:HIS17 3.4 24.9 1.0
C B:GLY19 3.5 22.5 0.8
C B:ASP79 3.5 27.1 0.8
C B:ASP81 3.6 25.0 0.7
CB B:ASP79 3.7 28.4 1.0
CA B:HIS17 4.1 27.6 1.0
C B:ALA18 4.1 22.2 1.0
N B:GLY19 4.1 23.9 1.0
N B:ASP81 4.1 28.6 1.0
CB B:HIS17 4.2 26.4 1.0
O B:ALA18 4.2 21.6 0.9
CA B:ASP79 4.2 30.0 1.0
C B:PRO80 4.3 30.0 1.0
CA B:ASP81 4.3 27.2 0.9
CA B:GLY19 4.4 21.9 1.0
N B:THR20 4.4 22.5 1.0
N B:ALA18 4.4 21.8 1.0
OD1 B:ASP79 4.4 32.5 0.7
CA B:THR20 4.4 22.0 1.0
CZ3 B:TRP105 4.5 25.7 1.0
N B:PRO80 4.5 25.7 1.0
N B:TRP82 4.6 24.1 1.0
CA B:ALA18 4.6 23.0 1.0
O B:PRO80 4.6 26.4 1.0
CA B:PRO80 4.7 28.3 0.7
CA B:TRP82 4.7 21.5 1.0
O B:HOH828 4.8 32.4 0.7
CB B:ASP81 4.8 25.4 1.0
CB B:THR20 4.8 25.9 1.0
O B:HOH1137 4.9 33.2 0.8

Calcium binding site 5 out of 8 in 4qwt

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Calcium binding site 5 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:26.7
occ:1.00
 O C:GLY19 2.3 25.4 1.0
O C:ASP81 2.3 25.0 1.0
OD2 C:ASP79 2.3 30.8 1.0
O C:HIS17 2.3 27.2 1.0
O C:ASP79 2.4 31.2 1.0
O C:HOH931 2.4 28.9 0.8
CG C:ASP79 3.3 33.8 0.8
C C:HIS17 3.4 23.0 1.0
C C:ASP79 3.5 31.4 0.9
C C:ASP81 3.5 26.2 0.9
C C:GLY19 3.5 24.9 0.7
CB C:ASP79 3.7 32.4 1.0
N C:ASP81 4.0 25.9 1.0
N C:GLY19 4.1 25.4 0.9
CA C:HIS17 4.1 23.3 1.0
C C:ALA18 4.1 27.5 1.0
CB C:HIS17 4.2 30.3 1.0
C C:PRO80 4.2 36.5 1.0
CA C:ASP79 4.2 34.4 0.8
CA C:ASP81 4.3 28.9 1.0
O C:ALA18 4.3 25.0 1.0
CA C:GLY19 4.4 28.8 1.0
OD1 C:ASP79 4.4 35.0 0.7
N C:ALA18 4.4 21.4 1.0
N C:THR20 4.4 25.1 1.0
CA C:THR20 4.5 23.3 1.0
N C:PRO80 4.5 31.6 1.0
O C:PRO80 4.5 33.8 1.0
N C:TRP82 4.5 25.9 1.0
CA C:ALA18 4.6 21.3 1.0
CZ3 C:TRP105 4.6 24.8 0.9
CA C:PRO80 4.7 30.7 1.0
CB C:ASP81 4.7 32.4 1.0
CA C:TRP82 4.7 25.3 0.9
CB C:THR20 4.8 21.6 1.0
O C:HOH1294 4.9 42.6 1.0
O C:HOH885 4.9 27.7 1.0
CG C:HIS17 5.0 35.6 1.0
CD2 C:HIS17 5.0 37.5 1.0

Calcium binding site 6 out of 8 in 4qwt

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Calcium binding site 6 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:23.8
occ:1.00
 OD1 D:ASN655 2.4 22.6 1.0
O C:HOH807 2.4 22.3 1.0
OE2 C:GLU51 2.4 23.0 1.0
O C:HOH801 2.5 22.6 1.0
O D:HOH808 2.5 23.4 1.0
O C:HOH1301 2.6 25.7 1.0
O D:HOH1176 2.6 26.4 1.0
CD C:GLU51 3.3 24.3 0.8
CG D:ASN655 3.4 23.5 1.0
ND2 D:ASN655 3.8 24.0 1.0
OE1 C:GLU51 3.9 22.1 1.0
O C:LYS42 4.1 28.9 1.0
CB C:GLU51 4.1 24.5 1.0
O C:HOH983 4.2 33.0 1.0
CG C:GLU51 4.2 22.7 1.0
O D:HOH1153 4.2 26.4 1.0
O C:HOH918 4.3 32.0 1.0
CA C:GLU51 4.5 20.5 1.0
OE1 D:GLN658 4.5 20.5 1.0
CA C:GLY43 4.5 27.4 1.0
N C:GLN52 4.6 26.0 1.0
O D:LEU651 4.7 22.8 1.0
CB D:ASN655 4.7 20.9 1.0
O C:GLN52 4.8 21.0 1.0
O C:SER44 4.8 25.3 1.0
OH C:TYR53 4.9 29.8 1.0

Calcium binding site 7 out of 8 in 4qwt

Go back to Calcium Binding Sites List in 4qwt
Calcium binding site 7 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca714

b:23.8
occ:1.00
 OE2 D:GLU51 2.3 27.0 0.9
OD1 C:ASN655 2.4 21.5 1.0
O C:HOH818 2.4 25.5 1.0
O D:HOH803 2.4 23.7 1.0
O D:HOH804 2.5 26.7 1.0
O D:HOH805 2.5 22.0 1.0
O D:HOH827 2.5 24.1 1.0
CD D:GLU51 3.3 27.0 0.8
CG C:ASN655 3.4 24.1 0.6
ND2 C:ASN655 3.8 22.9 1.0
OE1 D:GLU51 3.9 25.4 1.0
O D:HOH1035 4.0 33.9 1.0
O D:HOH941 4.1 27.9 0.9
CG D:GLU51 4.2 26.5 1.0
CB D:GLU51 4.3 27.0 1.0
O D:LYS42 4.3 27.1 1.0
O D:HOH1154 4.4 34.3 1.0
CA D:GLU51 4.6 27.8 1.0
OE1 C:GLN658 4.6 20.5 1.0
N D:GLN52 4.6 26.2 1.0
O C:LEU651 4.7 24.1 0.8
CA D:GLY43 4.7 24.0 1.0
CB C:ASN655 4.8 22.8 1.0
O D:GLN52 4.8 21.2 0.9
O D:SER44 4.9 25.3 1.0

Calcium binding site 8 out of 8 in 4qwt

Go back to Calcium Binding Sites List in 4qwt
Calcium binding site 8 out of 8 in the Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Anaerobic Crystal Structure of DELTA413-417:Gs Lox in Complex with Arachidonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:25.1
occ:1.00
 O D:GLY19 2.2 22.8 1.0
OD2 D:ASP79 2.3 36.5 0.8
O D:ASP79 2.3 31.9 1.0
O D:HOH823 2.3 30.1 1.0
O D:ASP81 2.3 25.6 1.0
O D:HIS17 2.4 21.1 1.0
CG D:ASP79 3.2 35.5 0.7
C D:ASP79 3.4 31.5 0.8
C D:HIS17 3.5 24.7 0.9
C D:GLY19 3.5 24.6 1.0
C D:ASP81 3.5 28.5 1.0
CB D:ASP79 3.6 38.0 1.0
N D:ASP81 4.0 27.2 0.9
N D:GLY19 4.1 26.2 1.0
C D:ALA18 4.1 25.3 0.9
CA D:ASP79 4.1 34.5 0.7
CA D:HIS17 4.1 24.9 0.8
C D:PRO80 4.2 27.8 0.6
CB D:HIS17 4.2 28.8 1.0
CA D:ASP81 4.3 30.2 1.0
O D:ALA18 4.3 22.1 1.0
CA D:GLY19 4.4 23.1 1.0
OD1 D:ASP79 4.4 42.7 1.0
N D:THR20 4.4 27.0 1.0
N D:PRO80 4.4 30.6 1.0
CA D:THR20 4.4 30.7 1.0
N D:ALA18 4.5 21.7 1.0
N D:TRP82 4.5 26.3 0.9
O D:PRO80 4.6 24.2 0.7
CZ3 D:TRP105 4.6 25.4 1.0
CA D:ALA18 4.6 25.5 1.0
CA D:PRO80 4.7 30.1 0.9
CB D:ASP81 4.7 28.7 0.9
CA D:TRP82 4.8 22.9 1.0
CB D:THR20 4.8 27.4 1.0
O D:HOH830 4.9 24.8 1.0

Reference:

D.B.Neau, G.Bender, W.E.Boeglin, S.G.Bartlett, A.R.Brash, M.E.Newcomer. Crystal Structure of A Lipoxygenase in Complex with Substrate: the Arachidonic Acid Binding Site of 8R-Lipoxygenase. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25231982
DOI: 10.1074/JBC.M114.599662
Page generated: Sun Jul 14 12:33:53 2024

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