Atomistry » Calcium » PDB 4qn5-4r90 » 4qwt
Atomistry »
  Calcium »
    PDB 4qn5-4r90 »
      4qwt »

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

Go back to Calcium Binding Sites List in 4qwt
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

Go back to Calcium Binding Sites List in 4qwt
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

Go back to Calcium Binding Sites List in 4qwt
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

Go back to Calcium Binding Sites List in 4qwt
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy