Atomistry » Iron » PDB 5ylw-5zm3 » 5zdr
Atomistry »
  Iron »
    PDB 5ylw-5zm3 »
      5zdr »

Iron in PDB 5zdr: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative

Protein crystallography data

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 5zdr was solved by T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.81 / 2.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 152.308, 219.682, 63.481, 90.00, 114.89, 90.00
R / Rfree (%) 20.7 / 25.7

Other elements in 5zdr:

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative (pdb code 5zdr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative, PDB code: 5zdr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 1 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.5
occ:1.00
O A:OH503 1.8 14.1 1.0
OE1 A:GLU266 1.9 24.3 1.0
OE1 A:GLU162 2.0 22.8 1.0
OE1 A:GLU123 2.0 23.5 1.0
ND1 A:HIS165 2.3 28.3 1.0
OE2 A:GLU123 2.4 24.6 1.0
CD A:GLU123 2.6 24.8 1.0
CD A:GLU162 2.8 25.7 1.0
CD A:GLU266 2.9 22.2 1.0
CE1 A:HIS165 3.1 29.1 1.0
OE2 A:GLU162 3.1 26.2 1.0
OE2 A:GLU266 3.2 18.8 1.0
CG A:HIS165 3.4 28.5 1.0
FE A:FE502 3.7 29.6 1.0
CB A:HIS165 3.8 28.0 1.0
CG A:GLU123 4.1 26.0 1.0
CG A:GLU162 4.1 25.4 1.0
NE2 A:HIS165 4.3 30.4 1.0
CG A:GLU266 4.3 21.1 1.0
CD2 A:HIS165 4.4 26.7 1.0
CB A:GLU162 4.5 26.5 1.0
CA A:GLU162 4.5 26.9 1.0
CB A:ALA126 4.6 35.4 1.0
CAX A:CHW504 4.8 31.5 1.0
OH A:TYR220 4.8 36.1 1.0
CG2 A:ILE262 4.8 32.9 1.0

Iron binding site 2 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 2 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:29.6
occ:1.00
OE2 A:GLU162 2.0 26.2 1.0
OE2 A:GLU266 2.1 18.8 1.0
OE1 A:GLU213 2.3 26.0 1.0
O A:OH503 2.4 14.1 1.0
OE2 A:GLU213 2.4 25.4 1.0
O A:HOH621 2.6 35.5 1.0
CD A:GLU213 2.6 26.2 1.0
CD A:GLU162 3.2 25.7 1.0
CD A:GLU266 3.3 22.2 1.0
OE1 A:GLU162 3.7 22.8 1.0
FE A:FE501 3.7 31.5 1.0
CB A:ALA126 3.8 35.4 1.0
OE1 A:GLU266 3.8 24.3 1.0
O A:HOH609 4.0 29.4 1.0
CG A:GLU213 4.1 27.6 1.0
CAN A:CHW504 4.1 32.1 1.0
OAM A:CHW504 4.3 34.6 1.0
ND1 A:HIS269 4.3 39.0 1.0
CG A:GLU162 4.4 25.4 1.0
CG A:GLU266 4.5 21.1 1.0
OE2 A:GLU123 4.6 24.6 1.0
CB A:ALA216 4.6 32.1 1.0
CB A:GLU266 4.8 22.8 1.0
CA A:ALA126 4.9 34.2 1.0
CB A:GLU213 5.0 27.5 1.0

Iron binding site 3 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 3 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.0
occ:1.00
OE1 B:GLU266 1.8 26.9 1.0
OE1 B:GLU162 2.0 22.9 1.0
O B:OH503 2.1 14.1 1.0
OE2 B:GLU123 2.2 30.6 1.0
OE1 B:GLU123 2.3 37.4 1.0
ND1 B:HIS165 2.4 19.9 1.0
CD B:GLU123 2.5 34.4 1.0
CD B:GLU266 2.7 30.3 1.0
OE2 B:GLU266 3.0 27.5 1.0
FE B:FE502 3.1 30.1 1.0
CE1 B:HIS165 3.1 20.1 1.0
CD B:GLU162 3.1 25.6 1.0
CG B:HIS165 3.6 21.0 1.0
OE2 B:GLU162 3.8 26.1 1.0
CG B:GLU123 4.1 32.9 1.0
CB B:HIS165 4.1 23.4 1.0
CG B:GLU266 4.1 30.1 1.0
CG B:GLU162 4.2 24.0 1.0
CB B:GLU162 4.3 22.3 1.0
NE2 B:HIS165 4.3 19.7 1.0
CA B:GLU162 4.3 22.6 1.0
CB B:ALA126 4.4 28.6 1.0
O B:HOH603 4.5 22.6 1.0
CD2 B:HIS165 4.5 20.3 1.0
CAX B:CHW504 4.7 39.0 1.0
OH B:TYR220 4.7 26.1 1.0
CB B:GLU123 4.8 31.8 1.0
O B:GLU162 4.9 25.0 1.0
CE2 B:TYR220 4.9 27.4 1.0
CG2 B:ILE262 4.9 23.3 1.0
OE1 B:GLU213 5.0 24.2 1.0

Iron binding site 4 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 4 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:30.1
occ:1.00
OE2 B:GLU266 1.9 27.5 1.0
O B:HOH603 2.0 22.6 1.0
OE2 B:GLU162 2.2 26.1 1.0
O B:OH503 2.2 14.1 1.0
OE1 B:GLU213 2.2 24.2 1.0
OE2 B:GLU213 2.3 24.2 1.0
OE1 B:GLU162 2.4 22.9 1.0
CD B:GLU213 2.6 25.4 1.0
CD B:GLU162 2.6 25.6 1.0
CD B:GLU266 2.9 30.3 1.0
FE B:FE501 3.1 30.0 1.0
OE1 B:GLU266 3.3 26.9 1.0
CB B:ALA126 4.1 28.6 1.0
CG B:GLU266 4.1 30.1 1.0
CAN B:CHW504 4.1 34.0 1.0
CG B:GLU213 4.1 26.4 1.0
CG B:GLU162 4.2 24.0 1.0
OAM B:CHW504 4.2 31.7 1.0
ND1 B:HIS269 4.3 25.4 1.0
CB B:GLU266 4.5 30.2 1.0
OE1 B:GLU123 4.6 37.4 1.0
OE2 B:GLU123 4.6 30.6 1.0
CA B:GLU266 4.6 32.3 1.0
CB B:ALA216 4.8 31.0 1.0
CB B:GLU213 4.9 27.4 1.0
CE1 B:HIS269 5.0 25.1 1.0
CD B:GLU123 5.0 34.4 1.0

Iron binding site 5 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 5 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:43.2
occ:1.00
O C:OH503 1.8 11.5 1.0
OE1 C:GLU162 2.0 30.2 1.0
OE1 C:GLU266 2.1 38.0 1.0
OE2 C:GLU123 2.2 39.0 1.0
OE1 C:GLU123 2.3 37.2 1.0
ND1 C:HIS165 2.4 24.6 1.0
CD C:GLU123 2.6 38.8 1.0
CD C:GLU162 2.9 31.9 1.0
CD C:GLU266 3.1 42.7 1.0
CE1 C:HIS165 3.2 24.8 1.0
CG C:HIS165 3.4 25.3 1.0
OE2 C:GLU162 3.4 30.5 1.0
OE2 C:GLU266 3.4 43.0 1.0
FE C:FE502 3.4 35.6 1.0
CB C:HIS165 3.7 28.6 1.0
CG C:GLU123 4.1 39.1 1.0
CG C:GLU162 4.1 31.1 1.0
CB C:GLU162 4.2 30.4 1.0
CB C:ALA126 4.3 34.8 1.0
NE2 C:HIS165 4.3 25.4 1.0
CG C:GLU266 4.4 39.9 1.0
CA C:GLU162 4.4 31.3 1.0
CD2 C:HIS165 4.4 24.9 1.0
OH C:TYR220 4.7 44.7 1.0
O C:HOH601 4.7 33.6 1.0
CAX C:CHW504 4.8 57.0 1.0
O C:GLU162 4.9 35.1 1.0
CB C:GLU123 4.9 38.4 1.0
CG2 C:ILE262 5.0 28.8 1.0
CE2 C:TYR220 5.0 41.0 1.0

Iron binding site 6 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 6 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:35.6
occ:1.00
OE2 C:GLU162 2.0 30.5 1.0
O C:HOH601 2.0 33.6 1.0
OE1 C:GLU213 2.1 27.0 1.0
OE2 C:GLU213 2.2 25.9 1.0
OE2 C:GLU266 2.3 43.0 1.0
CD C:GLU213 2.4 29.7 1.0
O C:OH503 2.5 11.5 1.0
CD C:GLU162 3.0 31.9 1.0
CD C:GLU266 3.0 42.7 1.0
OE1 C:GLU162 3.4 30.2 1.0
OE1 C:GLU266 3.4 38.0 1.0
FE C:FE501 3.4 43.2 1.0
CAN C:CHW504 3.9 55.9 1.0
CB C:ALA126 3.9 34.8 1.0
CG C:GLU213 4.0 29.6 1.0
ND1 C:HIS269 4.0 36.9 1.0
OAM C:CHW504 4.1 62.9 1.0
CG C:GLU162 4.2 31.1 1.0
CG C:GLU266 4.2 39.9 1.0
CB C:GLU266 4.7 37.8 1.0
OE2 C:GLU123 4.7 39.0 1.0
CA C:GLU266 4.8 36.3 1.0
CB C:ALA216 4.8 39.0 1.0
CE1 C:HIS269 4.8 34.1 1.0
CB C:GLU213 4.8 30.1 1.0
CG C:HIS269 5.0 32.6 1.0

Iron binding site 7 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 7 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:44.3
occ:1.00
OE1 D:GLU266 1.8 29.7 1.0
O D:OH503 2.1 9.9 1.0
OE1 D:GLU123 2.1 27.3 1.0
OE2 D:GLU123 2.3 26.4 1.0
ND1 D:HIS165 2.3 41.4 1.0
OE1 D:GLU162 2.3 21.6 1.0
CD D:GLU123 2.5 29.9 1.0
CD D:GLU266 2.9 28.8 1.0
CE1 D:HIS165 3.1 42.4 1.0
OE2 D:GLU266 3.3 23.8 1.0
CG D:HIS165 3.3 40.9 1.0
CD D:GLU162 3.5 25.1 1.0
FE D:FE502 3.6 33.5 1.0
CB D:HIS165 3.7 37.4 1.0
CG D:GLU123 4.0 31.4 1.0
CG D:GLU266 4.2 28.4 1.0
NE2 D:HIS165 4.2 44.5 1.0
OE2 D:GLU162 4.3 23.2 1.0
CA D:GLU162 4.3 30.2 1.0
CG D:GLU162 4.3 26.4 1.0
CD2 D:HIS165 4.3 43.6 1.0
CB D:GLU162 4.4 28.9 1.0
OH D:TYR220 4.6 36.8 1.0
CG2 D:ILE262 4.7 31.7 1.0
CAX D:CHW504 4.8 51.8 1.0
CB D:GLU123 4.9 32.4 1.0
O D:HOH606 4.9 25.1 1.0
O D:GLU162 4.9 36.9 1.0
CB D:ALA126 4.9 47.5 1.0
CE2 D:TYR220 4.9 41.6 1.0

Iron binding site 8 out of 8 in 5zdr

Go back to Iron Binding Sites List in 5zdr
Iron binding site 8 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative


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 Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ascofuranone Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:33.5
occ:1.00
OE2 D:GLU266 2.0 23.8 1.0
O D:HOH606 2.1 25.1 1.0
OE2 D:GLU213 2.2 32.1 1.0
O D:OH503 2.2 9.9 1.0
OE2 D:GLU162 2.3 23.2 1.0
OE1 D:GLU162 2.6 21.6 1.0
OE1 D:GLU213 2.7 34.0 1.0
CD D:GLU162 2.8 25.1 1.0
CD D:GLU213 2.8 34.8 1.0
CD D:GLU266 3.1 28.8 1.0
OE1 D:GLU266 3.5 29.7 1.0
FE D:FE501 3.6 44.3 1.0
OAM D:CHW504 3.9 55.0 1.0
CAN D:CHW504 4.0 50.2 1.0
CG D:GLU162 4.3 26.4 1.0
CG D:GLU213 4.3 33.8 1.0
CB D:ALA126 4.3 47.5 1.0
CG D:GLU266 4.4 28.4 1.0
ND1 D:HIS269 4.6 29.3 1.0
OE2 D:GLU123 4.7 26.4 1.0
CB D:GLU266 4.7 29.7 1.0
CB D:ALA216 4.7 34.6 1.0
CA D:GLU266 4.9 29.1 1.0

Reference:

T.Shiba, D.K.Inaoka, G.Takahashi, C.Tsuge, Y.Kido, L.Young, S.Ueda, E.O.Balogun, T.Nara, T.Honma, A.Tanaka, M.Inoue, H.Saimoto, S.Harada, A.L.Moore, K.Kita. Insights Into the Ubiquinol/Dioxygen Binding and Proton Relay Pathways of the Alternative Oxidase. Biochim Biophys Acta V.1860 375 2019BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 30910528
DOI: 10.1016/J.BBABIO.2019.03.008
Page generated: Sun Dec 13 16:19:15 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