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Calcium in PDB 3fg4: Crystal Structure of DELTA413-417:Gs I805A Lox

Enzymatic activity of Crystal Structure of DELTA413-417:Gs I805A Lox

All present enzymatic activity of Crystal Structure of DELTA413-417:Gs I805A Lox:
1.13.11.40;

Protein crystallography data

The structure of Crystal Structure of DELTA413-417:Gs I805A Lox, PDB code: 3fg4 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) 30.03 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.361, 170.382, 104.900, 90.00, 95.51, 90.00
R / Rfree (%) 16.8 / 23.9

Other elements in 3fg4:

The structure of Crystal Structure of DELTA413-417:Gs I805A Lox also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of DELTA413-417:Gs I805A Lox (pdb code 3fg4). 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 I805A Lox, PDB code: 3fg4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 1 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1501

b:22.2
occ:1.00
 O A:ASP454 2.3 18.2 1.0
OD2 A:ASP452 2.3 21.2 1.0
O A:HOH241 2.3 23.0 1.0
O A:HIS387 2.3 22.7 1.0
O A:ASP452 2.3 23.4 1.0
O A:GLY389 2.3 19.0 1.0
CG A:ASP452 3.2 27.8 1.0
C A:HIS387 3.4 23.2 1.0
C A:ASP452 3.4 24.4 1.0
C A:ASP454 3.5 19.2 1.0
C A:GLY389 3.6 19.1 1.0
CB A:ASP452 3.6 25.4 1.0
CA A:HIS387 4.1 24.9 1.0
N A:GLY389 4.1 19.0 1.0
N A:ASP454 4.1 20.3 1.0
CA A:ASP452 4.1 26.2 1.0
C A:ALA388 4.2 20.1 1.0
C A:PRO453 4.2 21.2 1.0
CB A:HIS387 4.2 25.8 1.0
OD1 A:ASP452 4.3 31.4 1.0
CA A:ASP454 4.3 19.7 1.0
N A:ALA388 4.4 20.7 1.0
N A:PRO453 4.4 23.1 1.0
CA A:GLY389 4.4 17.7 1.0
O A:PRO453 4.5 21.6 1.0
N A:TRP455 4.5 18.9 1.0
O A:ALA388 4.5 19.3 1.0
N A:THR390 4.5 20.3 1.0
CA A:THR390 4.5 19.9 1.0
CZ3 A:TRP478 4.6 20.6 1.0
CA A:PRO453 4.6 21.9 1.0
CA A:ALA388 4.7 20.1 1.0
CA A:TRP455 4.7 19.0 1.0
CB A:ASP454 4.8 19.8 1.0
ND1 A:HIS387 4.8 38.6 1.0
CB A:THR390 4.9 18.8 1.0
O A:HOH253 5.0 23.0 1.0
O A:HOH262 5.0 23.6 1.0
CG A:HIS387 5.0 32.5 1.0

Calcium binding site 2 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 2 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1502

b:21.8
occ:1.00
 OE2 A:GLU424 2.3 20.8 1.0
O A:HOH247 2.3 19.0 1.0
O A:HOH344 2.3 16.9 1.0
O A:HOH343 2.3 25.0 1.0
OD1 B:ASN1028 2.4 21.5 1.0
O A:HOH226 2.4 18.1 1.0
O B:HOH345 2.4 15.4 1.0
CD A:GLU424 3.2 18.8 1.0
CG B:ASN1028 3.4 18.4 1.0
OE1 A:GLU424 3.8 23.3 1.0
ND2 B:ASN1028 3.8 11.8 1.0
O A:HOH4 4.0 19.5 1.0
O A:HOH248 4.1 23.8 1.0
CB A:GLU424 4.1 20.0 1.0
CG A:GLU424 4.2 19.4 1.0
O A:HOH155 4.2 20.2 1.0
O A:LYS412 4.2 27.7 1.0
OE1 B:GLN1031 4.5 18.7 1.0
CA A:GLU424 4.6 20.5 1.0
N A:GLN425 4.7 21.1 1.0
CA A:GLY413 4.7 24.8 1.0
O A:SER414 4.7 21.0 1.0
O B:LEU1024 4.8 23.3 1.0
CB B:ASN1028 4.8 18.0 1.0
OH A:TYR426 4.8 21.9 1.0
O A:GLN425 4.9 19.8 1.0
O A:HOH1093 4.9 25.5 1.0

Calcium binding site 3 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 3 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1067

b:18.5
occ:1.00
 OD1 A:ASN1028 2.3 18.7 1.0
OE2 B:GLU424 2.3 20.5 1.0
O A:HOH20 2.3 15.0 1.0
O B:HOH332 2.4 20.2 1.0
O B:HOH331 2.4 20.3 1.0
O A:HOH330 2.4 22.6 1.0
O B:HOH333 2.4 17.5 1.0
CD B:GLU424 3.3 25.4 1.0
CG A:ASN1028 3.4 19.6 1.0
ND2 A:ASN1028 3.9 20.7 1.0
OE1 B:GLU424 4.0 20.6 1.0
O B:HOH1379 4.2 36.5 1.0
O A:HOH334 4.2 21.8 1.0
CB B:GLU424 4.2 15.0 1.0
CG B:GLU424 4.3 20.4 1.0
O B:LYS412 4.3 24.6 1.0
CA B:GLU424 4.5 17.1 1.0
OE1 A:GLN1031 4.5 16.6 1.0
O A:HOH321 4.5 21.3 1.0
O A:LEU1024 4.6 18.7 1.0
N B:GLN425 4.7 21.1 1.0
CA B:GLY413 4.7 18.7 1.0
CB A:ASN1028 4.7 16.5 1.0
O B:GLN425 4.8 22.8 1.0
OH B:TYR426 4.9 28.8 1.0
CA A:ASN1028 5.0 18.1 1.0

Calcium binding site 4 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 4 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1501

b:23.4
occ:1.00
 OD2 B:ASP452 2.3 27.7 1.0
O B:GLY389 2.3 20.4 1.0
O B:ASP452 2.3 22.1 1.0
O B:HIS387 2.3 19.7 1.0
O B:HOH346 2.3 23.0 1.0
O B:ASP454 2.3 25.0 1.0
CG B:ASP452 3.2 32.1 1.0
C B:HIS387 3.4 21.9 1.0
C B:ASP452 3.5 23.5 1.0
C B:GLY389 3.5 22.5 1.0
C B:ASP454 3.5 28.5 1.0
CB B:ASP452 3.6 26.3 1.0
N B:GLY389 4.0 20.3 1.0
CA B:HIS387 4.0 19.4 1.0
C B:ALA388 4.1 18.7 1.0
N B:ASP454 4.1 22.0 1.0
CB B:HIS387 4.1 22.4 1.0
CA B:ASP452 4.2 27.4 1.0
OD1 B:ASP452 4.3 36.1 1.0
O B:ALA388 4.3 22.3 1.0
C B:PRO453 4.3 24.6 1.0
CA B:ASP454 4.3 22.1 1.0
CA B:GLY389 4.3 15.8 1.0
N B:ALA388 4.4 21.2 1.0
ND1 B:HIS387 4.4 37.0 1.0
N B:THR390 4.5 19.6 1.0
CZ3 B:TRP478 4.5 23.9 1.0
N B:PRO453 4.5 24.0 1.0
CA B:THR390 4.6 18.4 1.0
N B:TRP455 4.6 21.7 1.0
CA B:ALA388 4.6 18.0 1.0
O B:PRO453 4.7 23.1 1.0
CA B:PRO453 4.7 22.0 1.0
CG B:HIS387 4.7 39.0 1.0
CB B:ASP454 4.8 23.5 1.0
CA B:TRP455 4.8 23.2 1.0
CB B:THR390 4.9 22.5 1.0
O B:HOH1082 5.0 24.1 1.0

Calcium binding site 5 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 5 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1501

b:25.8
occ:1.00
 O C:ASP454 2.3 23.6 1.0
O C:GLY389 2.3 21.0 1.0
O C:HOH1206 2.3 29.5 1.0
O C:HIS387 2.3 20.0 1.0
O C:ASP452 2.3 26.3 1.0
OD2 C:ASP452 2.4 25.0 1.0
C C:HIS387 3.4 20.7 1.0
CG C:ASP452 3.4 32.8 1.0
C C:ASP452 3.5 31.5 1.0
C C:GLY389 3.5 27.8 1.0
C C:ASP454 3.5 27.2 1.0
CB C:ASP452 3.8 30.2 1.0
CA C:HIS387 4.0 22.1 1.0
CB C:HIS387 4.0 20.6 1.0
N C:ASP454 4.1 26.3 1.0
N C:GLY389 4.1 27.2 1.0
C C:ALA388 4.2 22.4 1.0
CA C:ASP452 4.3 34.5 1.0
C C:PRO453 4.3 26.9 1.0
CA C:ASP454 4.3 24.9 1.0
CA C:GLY389 4.4 22.3 1.0
N C:ALA388 4.4 15.0 1.0
O C:ALA388 4.4 27.0 1.0
CZ3 C:TRP478 4.4 24.4 1.0
N C:THR390 4.5 22.3 1.0
CA C:THR390 4.5 20.5 1.0
OD1 C:ASP452 4.5 39.6 1.0
N C:PRO453 4.5 28.7 1.0
N C:TRP455 4.5 20.3 1.0
ND1 C:HIS387 4.6 50.5 1.0
O C:PRO453 4.7 28.7 1.0
CA C:ALA388 4.7 20.5 1.0
CG C:HIS387 4.7 36.2 1.0
CA C:TRP455 4.7 21.6 1.0
CB C:ASP454 4.7 27.3 1.0
CA C:PRO453 4.7 25.4 1.0
CB C:THR390 4.9 21.0 1.0

Calcium binding site 6 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 6 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1502

b:19.8
occ:1.00
 O C:HOH1074 2.3 20.1 1.0
O C:HOH97 2.3 13.8 1.0
OD1 D:ASN1028 2.4 17.9 1.0
OE2 C:GLU424 2.4 21.7 1.0
O D:HOH1068 2.4 26.1 1.0
O D:HOH1079 2.4 21.6 1.0
O C:HOH1075 2.4 20.5 1.0
CD C:GLU424 3.3 24.6 1.0
CG D:ASN1028 3.4 21.1 1.0
ND2 D:ASN1028 3.8 11.7 1.0
OE1 C:GLU424 4.0 19.6 1.0
O C:LYS412 4.0 32.6 1.0
CB C:GLU424 4.1 17.2 1.0
O C:HOH1177 4.3 23.4 1.0
CG C:GLU424 4.3 26.1 1.0
O D:HOH1229 4.4 29.8 1.0
CA C:GLU424 4.4 22.4 1.0
OE1 D:GLN1031 4.5 19.3 1.0
N C:GLN425 4.5 24.5 1.0
CA C:GLY413 4.6 17.8 1.0
CB D:ASN1028 4.8 14.4 1.0
O C:SER414 4.8 19.4 1.0
O C:GLN425 4.8 21.3 1.0
O D:LEU1024 4.8 18.9 1.0
OH C:TYR426 4.9 30.6 1.0
C C:GLU424 5.0 23.9 1.0

Calcium binding site 7 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 7 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1067

b:20.8
occ:1.00
 OE2 D:GLU424 2.3 24.9 1.0
O D:HOH416 2.3 16.4 1.0
OD1 C:ASN1028 2.3 22.5 1.0
O D:HOH415 2.3 22.6 1.0
O C:HOH1109 2.3 22.0 1.0
O D:HOH1070 2.4 21.6 1.0
O D:HOH1069 2.4 20.6 1.0
CD D:GLU424 3.3 29.2 1.0
CG C:ASN1028 3.4 28.1 1.0
ND2 C:ASN1028 3.8 21.4 1.0
OE1 D:GLU424 4.0 25.6 1.0
O D:HOH1437 4.1 35.5 1.0
CG D:GLU424 4.2 25.2 1.0
CB D:GLU424 4.2 22.5 1.0
O D:HOH1108 4.3 17.8 1.0
O D:LYS412 4.3 30.3 1.0
O D:HOH1386 4.4 35.1 1.0
CA D:GLU424 4.5 24.8 1.0
OE1 C:GLN1031 4.5 17.4 1.0
CA D:GLY413 4.6 21.8 1.0
N D:GLN425 4.6 22.4 1.0
O C:LEU1024 4.6 27.4 1.0
O D:GLN425 4.7 27.7 1.0
CB C:ASN1028 4.8 26.0 1.0
O D:SER414 5.0 23.2 1.0
OH D:TYR426 5.0 31.1 1.0

Calcium binding site 8 out of 8 in 3fg4

Go back to Calcium Binding Sites List in 3fg4
Calcium binding site 8 out of 8 in the Crystal Structure of DELTA413-417:Gs I805A 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 I805A Lox within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1501

b:25.4
occ:1.00
 O D:GLY389 2.3 20.1 1.0
OD2 D:ASP452 2.3 36.4 1.0
O D:ASP454 2.3 27.2 1.0
O D:HIS387 2.3 21.3 1.0
O D:ASP452 2.3 25.1 1.0
O D:HOH1085 2.4 29.1 1.0
CG D:ASP452 3.3 32.3 1.0
C D:HIS387 3.4 21.3 1.0
C D:ASP452 3.4 27.5 1.0
C D:ASP454 3.5 26.1 1.0
C D:GLY389 3.5 20.6 1.0
CB D:ASP452 3.6 26.4 1.0
N D:ASP454 4.0 28.8 1.0
CA D:HIS387 4.0 21.8 1.0
N D:GLY389 4.1 15.8 1.0
CB D:HIS387 4.1 21.4 1.0
CA D:ASP452 4.2 34.2 1.0
C D:ALA388 4.2 19.3 1.0
C D:PRO453 4.2 29.1 1.0
CA D:ASP454 4.2 26.3 1.0
CA D:GLY389 4.4 17.4 1.0
OD1 D:ASP452 4.4 34.0 1.0
O D:ALA388 4.4 25.5 1.0
N D:ALA388 4.5 20.0 1.0
N D:THR390 4.5 21.8 1.0
N D:PRO453 4.5 28.4 1.0
CA D:THR390 4.5 19.6 1.0
CZ3 D:TRP478 4.5 20.9 1.0
N D:TRP455 4.6 26.0 1.0
CB D:ASP454 4.6 32.2 1.0
O D:PRO453 4.6 30.0 1.0
CA D:PRO453 4.7 26.8 1.0
CA D:ALA388 4.7 21.2 1.0
CA D:TRP455 4.8 22.4 1.0
ND1 D:HIS387 4.8 33.1 1.0
CG D:HIS387 4.9 34.3 1.0
CB D:THR390 5.0 26.1 1.0
O D:HOH1071 5.0 20.4 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 Jul 13 09:53:59 2024

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