Iron in PDB 6j55: Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii

Enzymatic activity of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii

All present enzymatic activity of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii, PDB code: 6j55 was solved by K.H.Lee, T.O.Dao, K.Asaithambi, B.K.Na, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.57 / 2.33
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 127.486, 127.486, 327.064, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 24.8

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii (pdb code 6j55). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii, PDB code: 6j55:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 1 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:23.9
occ:1.00
 OD2 A:ASP161 2.1 22.5 1.0
O A:HOH348 2.4 24.1 1.0
NE2 A:HIS78 2.4 20.6 1.0
NE2 A:HIS27 2.4 22.0 1.0
NE2 A:HIS165 2.4 19.0 1.0
CD2 A:HIS78 3.1 19.3 1.0
CG A:ASP161 3.1 23.6 1.0
CD2 A:HIS165 3.2 23.4 1.0
CD2 A:HIS27 3.3 16.9 1.0
CE1 A:HIS27 3.3 20.5 1.0
OD1 A:ASP161 3.5 25.9 1.0
CE1 A:HIS165 3.5 24.2 1.0
CE1 A:HIS78 3.5 22.1 1.0
CH2 A:TRP128 4.3 21.9 1.0
CG A:HIS78 4.3 25.7 1.0
CZ2 A:TRP128 4.3 20.7 1.0
CB A:ASP161 4.4 21.8 1.0
CG A:HIS165 4.4 24.3 1.0
ND1 A:HIS27 4.4 23.3 1.0
CG A:HIS27 4.4 25.4 1.0
ND1 A:HIS78 4.5 22.1 1.0
CB A:TRP163 4.5 23.4 1.0
ND1 A:HIS165 4.5 22.6 1.0
NE2 A:GLN74 4.7 21.2 1.0
CG A:TRP163 4.7 18.2 1.0
CB A:ALA166 4.8 23.2 1.0

Iron binding site 2 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 2 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:27.5
occ:1.00
 OD2 B:ASP161 2.2 25.2 1.0
NE2 B:HIS78 2.3 28.7 1.0
O B:HOH350 2.3 18.2 1.0
NE2 B:HIS165 2.4 21.5 1.0
NE2 B:HIS27 2.4 25.0 1.0
CD2 B:HIS78 3.1 26.0 1.0
CD2 B:HIS165 3.1 21.7 1.0
CG B:ASP161 3.2 25.6 1.0
CD2 B:HIS27 3.3 25.2 1.0
CE1 B:HIS27 3.4 24.0 1.0
CE1 B:HIS78 3.4 21.7 1.0
CE1 B:HIS165 3.5 26.4 1.0
OD1 B:ASP161 3.6 26.8 1.0
CH2 B:TRP128 4.3 26.3 1.0
CG B:HIS78 4.3 31.3 1.0
CZ2 B:TRP128 4.3 25.2 1.0
CG B:HIS165 4.4 20.3 1.0
ND1 B:HIS78 4.4 30.7 1.0
CG B:HIS27 4.4 26.1 1.0
CB B:ASP161 4.4 23.2 1.0
ND1 B:HIS27 4.4 24.3 1.0
CB B:TRP163 4.5 23.1 1.0
ND1 B:HIS165 4.5 20.6 1.0
CG B:TRP163 4.7 22.1 1.0
NE2 B:GLN74 4.9 23.6 1.0
CB B:ALA166 4.9 22.9 1.0

Iron binding site 3 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 3 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:24.0
occ:1.00
 OD2 C:ASP161 2.1 26.4 1.0
NE2 C:HIS27 2.3 23.1 1.0
NE2 C:HIS165 2.4 21.7 1.0
NE2 C:HIS78 2.4 18.9 1.0
O C:HOH340 2.5 23.0 1.0
CD2 C:HIS78 3.0 17.0 1.0
CG C:ASP161 3.1 26.5 1.0
CD2 C:HIS165 3.2 18.6 1.0
CE1 C:HIS27 3.3 24.4 1.0
CD2 C:HIS27 3.3 18.6 1.0
CE1 C:HIS165 3.4 22.8 1.0
OD1 C:ASP161 3.4 22.9 1.0
CE1 C:HIS78 3.5 21.9 1.0
CZ2 C:TRP128 4.2 20.0 1.0
CH2 C:TRP128 4.2 19.7 1.0
CG C:HIS78 4.3 25.4 1.0
CB C:ASP161 4.4 20.6 1.0
ND1 C:HIS27 4.4 20.2 1.0
CG C:HIS165 4.4 24.0 1.0
CG C:HIS27 4.4 19.5 1.0
CB C:TRP163 4.4 20.8 1.0
ND1 C:HIS78 4.5 23.7 1.0
ND1 C:HIS165 4.5 24.9 1.0
CG C:TRP163 4.7 22.6 1.0
CB C:ALA166 4.8 20.9 1.0
NE2 C:GLN74 4.8 18.7 1.0
CD1 C:TRP163 4.9 19.4 1.0

Iron binding site 4 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 4 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:26.5
occ:1.00
 OD1 D:ASP161 2.1 24.2 1.0
NE2 D:HIS165 2.3 19.8 1.0
O D:HOH374 2.4 24.3 1.0
NE2 D:HIS78 2.4 26.5 1.0
NE2 D:HIS27 2.4 24.1 1.0
CD2 D:HIS78 3.1 23.9 1.0
CD2 D:HIS165 3.1 17.2 1.0
CG D:ASP161 3.2 27.2 1.0
CD2 D:HIS27 3.3 20.4 1.0
CE1 D:HIS165 3.4 21.8 1.0
CE1 D:HIS27 3.4 21.5 1.0
CE1 D:HIS78 3.4 23.7 1.0
OD2 D:ASP161 3.6 28.1 1.0
CZ2 D:TRP128 4.3 23.3 1.0
CG D:HIS78 4.3 23.8 1.0
CG D:HIS165 4.3 20.9 1.0
CH2 D:TRP128 4.4 22.2 1.0
CB D:TRP163 4.4 23.5 1.0
ND1 D:HIS165 4.4 22.2 1.0
ND1 D:HIS78 4.4 25.7 1.0
CB D:ASP161 4.4 21.4 1.0
ND1 D:HIS27 4.5 23.1 1.0
CG D:HIS27 4.5 22.2 1.0
CG D:TRP163 4.7 21.9 1.0
CB D:ALA166 4.8 25.4 1.0
NE2 D:GLN74 4.9 23.6 1.0

Iron binding site 5 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 5 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:30.7
occ:1.00
 O E:HOH317 2.1 29.7 1.0
NE2 E:HIS78 2.3 26.9 1.0
OD2 E:ASP161 2.3 38.4 1.0
NE2 E:HIS165 2.4 33.0 1.0
NE2 E:HIS27 2.4 37.1 1.0
CD2 E:HIS78 2.9 28.5 1.0
CE1 E:HIS165 3.3 31.1 1.0
CG E:ASP161 3.3 34.1 1.0
CE1 E:HIS27 3.3 35.5 1.0
CD2 E:HIS27 3.3 36.1 1.0
CD2 E:HIS165 3.3 33.6 1.0
CE1 E:HIS78 3.4 32.8 1.0
OD1 E:ASP161 3.8 37.1 1.0
CG E:HIS78 4.2 32.2 1.0
CZ2 E:TRP128 4.3 33.0 1.0
CH2 E:TRP128 4.4 32.3 1.0
ND1 E:HIS27 4.4 37.3 1.0
ND1 E:HIS165 4.4 36.5 1.0
ND1 E:HIS78 4.4 28.5 1.0
CB E:ASP161 4.4 33.4 1.0
CG E:HIS27 4.4 39.0 1.0
CG E:HIS165 4.5 34.9 1.0
CB E:TRP163 4.7 28.7 1.0
CG E:TRP163 4.8 33.1 1.0
CB E:ALA166 5.0 27.8 1.0
NE2 E:GLN74 5.0 30.6 1.0

Iron binding site 6 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 6 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:33.0
occ:1.00
 OD2 F:ASP161 2.2 38.1 1.0
NE2 F:HIS78 2.2 26.6 1.0
NE2 F:HIS165 2.4 39.1 1.0
NE2 F:HIS27 2.4 39.1 1.0
O F:HOH329 2.4 32.3 1.0
CD2 F:HIS78 3.0 31.7 1.0
CG F:ASP161 3.2 34.9 1.0
CE1 F:HIS78 3.3 31.1 1.0
CE1 F:HIS165 3.3 35.9 1.0
CD2 F:HIS27 3.3 35.0 1.0
CE1 F:HIS27 3.4 34.7 1.0
CD2 F:HIS165 3.4 39.3 1.0
OD1 F:ASP161 3.8 35.3 1.0
CG F:HIS78 4.2 33.9 1.0
CB F:ASP161 4.3 37.3 1.0
CH2 F:TRP128 4.3 34.1 1.0
ND1 F:HIS78 4.3 31.7 1.0
CZ2 F:TRP128 4.4 29.6 1.0
CB F:TRP163 4.4 30.8 1.0
ND1 F:HIS165 4.5 38.9 1.0
ND1 F:HIS27 4.5 43.1 1.0
CG F:HIS27 4.5 41.9 1.0
CG F:HIS165 4.5 37.5 1.0
CG F:TRP163 4.7 33.1 1.0
CB F:ALA166 4.9 37.6 1.0
NE2 F:GLN74 4.9 34.3 1.0
CD1 F:TRP163 4.9 32.6 1.0

Iron binding site 7 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 7 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:37.8
occ:1.00
 OD2 G:ASP161 2.1 38.2 1.0
NE2 G:HIS78 2.3 26.4 1.0
NE2 G:HIS165 2.3 41.2 1.0
O G:HOH329 2.3 36.0 1.0
NE2 G:HIS27 2.5 40.4 1.0
CD2 G:HIS78 3.1 31.1 1.0
CD2 G:HIS165 3.1 40.3 1.0
CG G:ASP161 3.2 42.9 1.0
CE1 G:HIS78 3.3 37.0 1.0
CE1 G:HIS27 3.3 39.9 1.0
CE1 G:HIS165 3.4 38.6 1.0
CD2 G:HIS27 3.4 39.3 1.0
OD1 G:ASP161 3.8 37.0 1.0
CG G:HIS78 4.3 30.7 1.0
CG G:HIS165 4.3 41.5 1.0
CZ2 G:TRP128 4.3 42.1 1.0
ND1 G:HIS78 4.3 32.3 1.0
CB G:ASP161 4.4 39.4 1.0
ND1 G:HIS165 4.4 43.8 1.0
ND1 G:HIS27 4.4 43.9 1.0
CB G:TRP163 4.5 37.8 1.0
CH2 G:TRP128 4.5 38.3 1.0
CG G:HIS27 4.5 41.2 1.0
CG G:TRP163 4.7 39.6 1.0
CB G:ALA166 4.7 35.4 1.0
NE2 G:GLN74 4.9 36.5 1.0
CD1 G:TRP163 5.0 34.6 1.0

Iron binding site 8 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 8 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:38.9
occ:1.00
 OD2 H:ASP161 2.1 30.1 1.0
NE2 H:HIS78 2.4 30.4 1.0
NE2 H:HIS27 2.4 35.9 1.0
NE2 H:HIS165 2.4 34.6 1.0
O H:HOH335 2.5 33.8 1.0
CD2 H:HIS78 3.0 36.8 1.0
CE1 H:HIS27 3.2 36.4 1.0
CD2 H:HIS165 3.2 38.3 1.0
CG H:ASP161 3.2 39.5 1.0
CD2 H:HIS27 3.3 33.4 1.0
CE1 H:HIS78 3.5 35.9 1.0
CE1 H:HIS165 3.5 36.1 1.0
OD1 H:ASP161 3.7 38.7 1.0
ND1 H:HIS27 4.3 39.4 1.0
CG H:HIS78 4.3 40.1 1.0
CH2 H:TRP128 4.3 43.0 1.0
CB H:TRP163 4.3 30.1 1.0
CZ2 H:TRP128 4.3 39.5 1.0
CG H:HIS27 4.4 41.5 1.0
CB H:ASP161 4.4 30.8 1.0
CG H:HIS165 4.4 34.0 1.0
ND1 H:HIS78 4.4 37.0 1.0
ND1 H:HIS165 4.5 37.8 1.0
CG H:TRP163 4.5 37.1 1.0
CB H:ALA166 4.7 33.0 1.0
CD1 H:TRP163 4.9 40.5 1.0
NE2 H:GLN74 4.9 37.3 1.0

Iron binding site 9 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 9 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe201

b:40.2
occ:1.00
 OD2 I:ASP161 2.2 36.8 1.0
NE2 I:HIS165 2.4 42.5 1.0
NE2 I:HIS78 2.4 40.0 1.0
O I:HOH333 2.5 38.6 1.0
NE2 I:HIS27 2.6 39.4 1.0
CD2 I:HIS78 3.0 37.0 1.0
CD2 I:HIS165 3.2 44.8 1.0
CD2 I:HIS27 3.2 46.3 1.0
CG I:ASP161 3.3 43.7 1.0
CE1 I:HIS165 3.4 43.1 1.0
CE1 I:HIS78 3.6 44.2 1.0
CE1 I:HIS27 3.7 46.6 1.0
OD1 I:ASP161 3.8 39.3 1.0
CG I:HIS78 4.3 46.5 1.0
CH2 I:TRP128 4.3 40.0 1.0
CG I:HIS165 4.4 43.5 1.0
CZ2 I:TRP128 4.5 37.8 1.0
ND1 I:HIS165 4.5 44.8 1.0
CB I:ASP161 4.5 38.6 1.0
ND1 I:HIS78 4.5 46.5 1.0
CG I:HIS27 4.5 46.6 1.0
CB I:TRP163 4.6 44.1 1.0
ND1 I:HIS27 4.7 49.0 1.0
CB I:ALA166 4.8 43.1 1.0
CG I:TRP163 4.9 43.3 1.0

Iron binding site 10 out of 12 in 6j55

Go back to Iron Binding Sites List in 6j55
Iron binding site 10 out of 12 in the Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of An Iron Superoxide Dismutate (Fesod) From A Pathogenic Acanthamoeba Castellanii within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:51.3
occ:1.00
 OD2 J:ASP161 2.2 48.6 1.0
NE2 J:HIS165 2.4 45.5 1.0
NE2 J:HIS78 2.6 57.2 1.0
CE1 J:HIS27 2.6 54.5 1.0
CD2 J:HIS78 2.9 52.5 1.0
CD2 J:HIS165 3.2 49.0 1.0
CG J:ASP161 3.2 48.2 1.0
ND1 J:HIS27 3.5 53.0 1.0
NE2 J:HIS27 3.6 58.5 1.0
CE1 J:HIS165 3.6 48.1 1.0
OD1 J:ASP161 3.7 47.0 1.0
CE1 J:HIS78 3.9 55.2 1.0
CH2 J:TRP128 4.2 48.7 1.0
CG J:HIS78 4.3 59.6 1.0
CZ2 J:TRP128 4.3 51.4 1.0
CB J:TRP163 4.4 41.5 1.0
CG J:HIS165 4.4 51.0 1.0
CB J:ASP161 4.5 47.4 1.0
ND1 J:HIS165 4.6 45.1 1.0
CG J:TRP163 4.6 44.5 1.0
CB J:ALA166 4.7 46.8 1.0
ND1 J:HIS78 4.7 59.0 1.0
CG J:HIS27 4.7 61.0 1.0
CD2 J:HIS27 4.7 58.4 1.0
CD1 J:TRP163 5.0 42.8 1.0

Reference:

O.Dao, K.Asaithambi, B.K.Na, K.H.Lee. Crystal Structure of An Iron Superoxide Dismutase From the Pathogenic Amoeba Acanthamoeba Castellanii. Acta Crystallogr.,Sect.F V. 75 480 2019.
ISSN: ESSN 2053-230X
PubMed: 31282867
DOI: 10.1107/S2053230X19008112
Page generated: Tue Aug 6 23:17:25 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy