Atomistry » Calcium » PDB 3f5v-3fib » 3fg3
Atomistry »
  Calcium »
    PDB 3f5v-3fib »
      3fg3 »

Calcium in PDB 3fg3: Crystal Structure of DELTA413-417:Gs I805W Lox

Enzymatic activity of Crystal Structure of DELTA413-417:Gs I805W Lox

All present enzymatic activity of Crystal Structure of DELTA413-417:Gs I805W Lox:
1.13.11.40;

Protein crystallography data

The structure of Crystal Structure of DELTA413-417:Gs I805W Lox, PDB code: 3fg3 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) 34.54 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.704, 170.214, 104.202, 90.00, 96.13, 90.00
R / Rfree (%) 16.2 / 20.6

Other elements in 3fg3:

The structure of Crystal Structure of DELTA413-417:Gs I805W Lox 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 Crystal Structure of DELTA413-417:Gs I805W Lox (pdb code 3fg3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of DELTA413-417:Gs I805W Lox, PDB code: 3fg3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 1 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:23.4
occ:1.00
 O A:ASP452 2.3 25.5 1.0
O A:GLY389 2.3 21.4 1.0
O A:ASP454 2.3 21.0 1.0
O A:HOH1226 2.3 21.0 1.0
O A:HIS387 2.3 20.6 1.0
OD2 A:ASP452 2.4 26.6 1.0
C A:ASP452 3.4 26.2 1.0
C A:HIS387 3.4 20.2 1.0
CG A:ASP452 3.4 31.1 1.0
C A:ASP454 3.5 19.5 1.0
C A:GLY389 3.5 20.5 1.0
CB A:ASP452 3.8 28.4 1.0
N A:ASP454 4.0 21.0 1.0
CA A:HIS387 4.0 21.9 1.0
N A:GLY389 4.0 19.7 1.0
C A:ALA388 4.1 18.6 1.0
CA A:ASP452 4.2 29.0 1.0
CB A:HIS387 4.2 24.0 1.0
C A:PRO453 4.2 23.3 1.0
CA A:ASP454 4.3 21.1 1.0
O A:ALA388 4.3 19.8 1.0
CA A:GLY389 4.4 19.7 1.0
N A:PRO453 4.4 25.0 1.0
N A:ALA388 4.4 19.6 1.0
O A:PRO453 4.5 22.4 1.0
CA A:THR390 4.5 19.6 1.0
CZ3 A:TRP478 4.5 19.4 1.0
OD1 A:ASP452 4.5 30.6 1.0
N A:TRP455 4.5 19.2 1.0
N A:THR390 4.5 20.2 1.0
O A:HOH2318 4.6 44.4 1.0
CA A:ALA388 4.7 18.4 1.0
CA A:PRO453 4.7 23.9 1.0
O A:HOH2101 4.7 46.9 1.0
CA A:TRP455 4.7 19.4 1.0
CB A:ASP454 4.8 21.0 1.0
CB A:THR390 4.8 21.1 1.0
O A:HOH1358 4.9 50.7 1.0

Calcium binding site 2 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 2 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:21.6
occ:1.00
 OE2 A:GLU424 2.3 21.2 1.0
O B:HOH326 2.4 21.1 1.0
OD1 B:ASN1028 2.4 21.8 1.0
O A:HOH190 2.5 19.0 1.0
O B:HOH1143 2.5 22.6 1.0
O A:HOH1083 2.5 20.1 1.0
O A:HOH1108 2.5 21.6 1.0
CD A:GLU424 3.3 21.6 1.0
CG B:ASN1028 3.5 20.2 1.0
ND2 B:ASN1028 3.8 20.8 1.0
OE1 A:GLU424 3.9 23.1 1.0
O A:HOH1293 4.0 30.3 1.0
O A:HOH1124 4.1 26.5 1.0
CG A:GLU424 4.2 18.7 1.0
O A:LYS412 4.3 27.3 1.0
CB A:GLU424 4.3 21.1 1.0
O A:HOH1119 4.3 24.8 1.0
CA A:GLU424 4.5 21.3 1.0
OE1 B:GLN1031 4.6 20.8 1.0
O B:LEU1024 4.6 21.4 1.0
N A:GLN425 4.6 21.1 1.0
CA A:GLY413 4.6 24.1 1.0
O A:SER414 4.8 18.5 1.0
CB B:ASN1028 4.8 20.5 1.0
OH A:TYR426 4.9 25.0 1.0
O A:GLN425 4.9 20.8 1.0

Calcium binding site 3 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 3 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1067

b:22.0
occ:1.00
 OE2 B:GLU424 2.3 21.5 1.0
OD1 A:ASN1028 2.3 17.8 1.0
O A:HOH206 2.4 19.9 1.0
O B:HOH305 2.5 22.6 1.0
O A:HOH65 2.5 18.2 1.0
O B:HOH1160 2.6 20.0 1.0
O B:HOH93 2.6 20.9 1.0
CD B:GLU424 3.2 23.3 1.0
CG A:ASN1028 3.4 19.0 1.0
ND2 A:ASN1028 3.8 18.0 1.0
OE1 B:GLU424 4.0 19.4 1.0
O B:HOH1076 4.1 26.5 1.0
CB B:GLU424 4.2 20.0 1.0
CG B:GLU424 4.2 18.7 1.0
O B:HOH1188 4.3 27.3 1.0
O B:LYS412 4.3 27.2 1.0
CA B:GLU424 4.5 18.7 1.0
O A:HOH1117 4.5 35.3 1.0
OE1 A:GLN1031 4.5 19.0 1.0
N B:GLN425 4.6 21.9 1.0
O A:LEU1024 4.6 18.5 1.0
O B:GLN425 4.7 21.1 1.0
CA B:GLY413 4.7 20.9 1.0
CB A:ASN1028 4.7 17.9 1.0
OH B:TYR426 4.8 27.4 1.0
O B:SER414 5.0 21.1 1.0

Calcium binding site 4 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 4 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1501

b:23.8
occ:1.00
 O B:GLY389 2.3 22.2 1.0
O B:HOH1123 2.3 20.4 1.0
OD2 B:ASP452 2.3 26.9 1.0
O B:ASP454 2.3 22.6 1.0
O B:ASP452 2.3 24.7 1.0
O B:HIS387 2.4 20.9 1.0
CG B:ASP452 3.3 31.7 1.0
C B:ASP452 3.4 26.2 1.0
C B:HIS387 3.4 21.1 1.0
C B:GLY389 3.5 22.5 1.0
C B:ASP454 3.6 23.3 1.0
CB B:ASP452 3.6 26.6 1.0
N B:GLY389 4.0 22.0 1.0
N B:ASP454 4.0 23.2 1.0
C B:ALA388 4.1 22.0 1.0
CA B:HIS387 4.1 22.7 1.0
CA B:ASP452 4.1 28.0 1.0
CB B:HIS387 4.2 23.8 1.0
C B:PRO453 4.3 26.1 1.0
O B:ALA388 4.3 22.2 1.0
CA B:ASP454 4.3 24.2 1.0
OD1 B:ASP452 4.4 34.9 1.0
CA B:GLY389 4.4 22.1 1.0
N B:THR390 4.4 22.4 1.0
N B:ALA388 4.5 20.4 1.0
CZ3 B:TRP478 4.5 20.5 1.0
CA B:THR390 4.5 22.5 1.0
N B:PRO453 4.5 26.0 1.0
N B:TRP455 4.5 22.6 1.0
O B:HOH2320 4.6 48.4 1.0
CA B:ALA388 4.6 20.8 1.0
O B:PRO453 4.7 25.3 1.0
CA B:TRP455 4.7 22.5 1.0
CA B:PRO453 4.7 26.1 1.0
CB B:ASP454 4.8 23.8 1.0
CB B:THR390 4.9 23.4 1.0
O B:HOH1351 4.9 45.3 1.0

Calcium binding site 5 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 5 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1501

b:24.8
occ:1.00
 O C:ASP454 2.3 23.3 1.0
O C:GLY389 2.3 24.2 1.0
O C:HIS387 2.3 23.3 1.0
O C:HOH1224 2.4 30.0 1.0
OD2 C:ASP452 2.4 31.0 1.0
O C:ASP452 2.4 28.7 1.0
CG C:ASP452 3.4 34.9 1.0
C C:HIS387 3.4 22.0 1.0
C C:ASP452 3.5 31.2 1.0
C C:ASP454 3.5 23.7 1.0
C C:GLY389 3.6 23.0 1.0
CB C:ASP452 3.7 34.5 1.0
N C:GLY389 4.0 22.8 1.0
CA C:HIS387 4.0 23.4 1.0
CB C:HIS387 4.1 25.6 1.0
N C:ASP454 4.1 26.7 1.0
C C:ALA388 4.1 22.0 1.0
CA C:ASP452 4.2 34.1 1.0
C C:PRO453 4.2 28.1 1.0
CA C:ASP454 4.3 25.4 1.0
O C:ALA388 4.4 21.6 1.0
CA C:GLY389 4.4 21.8 1.0
N C:ALA388 4.4 21.2 1.0
OD1 C:ASP452 4.5 38.3 1.0
CA C:THR390 4.5 21.2 1.0
CZ3 C:TRP478 4.5 24.6 1.0
N C:THR390 4.5 23.3 1.0
N C:TRP455 4.5 23.4 1.0
N C:PRO453 4.6 30.1 1.0
O C:PRO453 4.7 28.2 1.0
CA C:ALA388 4.7 20.6 1.0
CA C:TRP455 4.7 23.5 1.0
CA C:PRO453 4.7 29.4 1.0
ND1 C:HIS387 4.8 43.5 1.0
O C:HOH1242 4.8 48.3 1.0
CB C:ASP454 4.8 26.0 1.0
CB C:THR390 4.9 22.7 1.0
CG C:HIS387 4.9 33.5 1.0
O C:HOH237 5.0 25.8 1.0

Calcium binding site 6 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 6 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1502

b:21.9
occ:1.00
 OD1 D:ASN1028 2.4 21.2 1.0
O C:HOH113 2.4 18.4 1.0
OE2 C:GLU424 2.4 20.9 1.0
O C:HOH1107 2.4 20.0 1.0
O D:HOH1120 2.5 21.8 1.0
O D:HOH225 2.5 20.1 1.0
O C:HOH141 2.5 22.4 1.0
CD C:GLU424 3.3 23.3 1.0
CG D:ASN1028 3.4 21.4 1.0
ND2 D:ASN1028 3.9 23.0 1.0
OE1 C:GLU424 3.9 21.9 1.0
O D:HOH1144 4.2 26.5 1.0
O C:LYS412 4.2 26.7 1.0
CB C:GLU424 4.2 19.9 1.0
O C:HOH1561 4.2 27.6 1.0
O D:HOH1304 4.2 34.3 1.0
CG C:GLU424 4.2 21.9 1.0
CA C:GLU424 4.4 22.2 1.0
OE1 D:GLN1031 4.5 19.8 1.0
N C:GLN425 4.6 22.9 1.0
CA C:GLY413 4.7 24.4 1.0
O D:LEU1024 4.8 21.7 1.0
O C:SER414 4.8 20.8 1.0
CB D:ASN1028 4.8 21.4 1.0
O C:GLN425 4.8 20.8 1.0
OH C:TYR426 4.9 26.0 1.0

Calcium binding site 7 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 7 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1067

b:23.3
occ:1.00
 OE2 D:GLU424 2.3 24.3 1.0
OD1 C:ASN1028 2.3 20.2 1.0
O C:HOH180 2.4 19.3 1.0
O D:HOH254 2.4 21.0 1.0
O D:HOH1085 2.5 21.5 1.0
O C:HOH356 2.5 23.0 1.0
O D:HOH1122 2.6 21.0 1.0
CD D:GLU424 3.2 25.0 1.0
CG C:ASN1028 3.4 21.8 1.0
ND2 C:ASN1028 3.8 23.7 1.0
OE1 D:GLU424 3.9 23.4 1.0
O D:HOH1430 4.1 28.8 1.0
CG D:GLU424 4.2 21.6 1.0
CB D:GLU424 4.2 23.4 1.0
O D:HOH1161 4.2 28.3 1.0
O D:LYS412 4.3 26.7 1.0
O D:HOH1086 4.3 29.5 1.0
CA D:GLU424 4.5 23.3 1.0
OE1 C:GLN1031 4.5 19.1 1.0
CA D:GLY413 4.6 22.8 1.0
N D:GLN425 4.6 23.4 1.0
O C:LEU1024 4.7 20.8 1.0
CB C:ASN1028 4.7 21.9 1.0
O D:GLN425 4.8 22.3 1.0
O D:SER414 4.8 20.6 1.0
OH D:TYR426 4.9 28.1 1.0

Calcium binding site 8 out of 8 in 3fg3

Go back to Calcium Binding Sites List in 3fg3
Calcium binding site 8 out of 8 in the Crystal Structure of DELTA413-417:Gs I805W Lox


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 DELTA413-417:Gs I805W Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1501

b:23.4
occ:1.00
 O D:GLY389 2.3 21.5 1.0
OD2 D:ASP452 2.3 34.5 1.0
O D:HOH1080 2.3 28.1 1.0
O D:HIS387 2.3 19.3 1.0
O D:ASP452 2.4 28.2 1.0
O D:ASP454 2.4 22.8 1.0
CG D:ASP452 3.3 36.0 1.0
C D:HIS387 3.4 20.8 1.0
C D:GLY389 3.5 21.9 1.0
C D:ASP452 3.5 30.2 1.0
C D:ASP454 3.6 23.5 1.0
CB D:ASP452 3.7 33.1 1.0
N D:ASP454 4.0 24.6 1.0
N D:GLY389 4.1 21.8 1.0
CA D:HIS387 4.1 22.2 1.0
C D:ALA388 4.1 21.9 1.0
CB D:HIS387 4.2 24.6 1.0
C D:PRO453 4.2 27.6 1.0
CA D:ASP452 4.2 33.5 1.0
CA D:ASP454 4.3 25.5 1.0
O D:ALA388 4.3 21.2 1.0
CA D:GLY389 4.4 21.5 1.0
OD1 D:ASP452 4.4 35.0 1.0
N D:ALA388 4.4 19.9 1.0
N D:THR390 4.4 22.1 1.0
CA D:THR390 4.4 22.7 1.0
N D:PRO453 4.5 28.9 1.0
O D:PRO453 4.5 28.5 1.0
N D:TRP455 4.6 21.9 1.0
CZ3 D:TRP478 4.6 22.1 1.0
CA D:ALA388 4.6 20.4 1.0
CA D:PRO453 4.7 28.2 1.0
CB D:ASP454 4.7 24.8 1.0
CA D:TRP455 4.7 21.0 1.0
O D:HOH2361 4.8 45.4 1.0
CB D:THR390 4.9 24.2 1.0
ND1 D:HIS387 4.9 38.3 1.0

Reference:

D.B.Neau, N.C.Gilbert, S.G.Bartlett, W.Boeglin, A.R.Brash, M.E.Newcomer. The 1.85 A Structure of An 8R-Lipoxygenase Suggests A General Model For Lipoxygenase Product Specificity. Biochemistry V. 48 7906 2009.
ISSN: ISSN 0006-2960
PubMed: 19594169
DOI: 10.1021/BI900084M
Page generated: Sat Dec 12 04:11:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy