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Iron in PDB 5zdp: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol

Protein crystallography data

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol, PDB code: 5zdp 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) 39.32 / 2.71
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 259.501, 63.109, 138.273, 90.00, 122.21, 90.00
R / Rfree (%) 19.2 / 24.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol (pdb code 5zdp). 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 Ferulenol, PDB code: 5zdp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5zdp

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Iron binding site 1 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:44.9
occ:1.00
 OE1 A:GLU123 1.8 34.1 1.0
OE1 A:GLU266 1.8 50.2 1.0
OE1 A:GLU162 2.0 34.8 1.0
O A:OH503 2.2 16.1 1.0
OE2 A:GLU123 2.3 34.5 1.0
CD A:GLU123 2.3 35.4 1.0
ND1 A:HIS165 2.7 39.7 1.0
CD A:GLU266 2.9 43.0 1.0
CD A:GLU162 3.0 37.5 1.0
OE2 A:GLU266 3.2 40.9 1.0
OE2 A:GLU162 3.4 36.0 1.0
CE1 A:HIS165 3.4 40.8 1.0
FE A:FE502 3.5 38.9 1.0
CG A:HIS165 3.8 37.3 1.0
CG A:GLU123 3.8 37.6 1.0
CAK A:9AU505 3.9 65.8 1.0
CG A:GLU266 4.2 39.1 1.0
CB A:HIS165 4.2 36.7 1.0
CAJ A:9AU505 4.3 61.5 1.0
OH A:TYR220 4.3 31.2 1.0
CB A:ALA126 4.4 38.9 1.0
CG A:GLU162 4.4 35.5 1.0
CE2 A:TYR220 4.6 30.8 1.0
NE2 A:HIS165 4.7 38.2 1.0
CB A:GLU162 4.7 36.4 1.0
CA A:GLU162 4.8 36.2 1.0
CG2 A:ILE262 4.8 32.8 1.0
CB A:GLU123 4.8 38.1 1.0
CD2 A:HIS165 4.9 36.9 1.0
O A:GLU162 4.9 42.6 1.0
CAM A:9AU505 5.0 62.2 1.0
CZ A:TYR220 5.0 31.4 1.0

Iron binding site 2 out of 8 in 5zdp

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Iron binding site 2 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:38.9
occ:1.00
 OE2 A:GLU162 1.8 36.0 1.0
OE2 A:GLU266 2.2 40.9 1.0
OE2 A:GLU213 2.3 37.6 1.0
O A:OH503 2.5 16.1 1.0
OE1 A:GLU213 2.5 36.1 1.0
CD A:GLU213 2.7 37.0 1.0
CD A:GLU162 2.9 37.5 1.0
O2 A:OXY504 2.9 29.9 1.0
O1 A:OXY504 2.9 30.8 1.0
CD A:GLU266 3.1 43.0 1.0
OE1 A:GLU162 3.4 34.8 1.0
OE1 A:GLU266 3.5 50.2 1.0
FE A:FE501 3.5 44.9 1.0
ND1 A:HIS269 3.9 43.2 1.0
CB A:ALA126 4.0 38.9 1.0
CG A:GLU162 4.1 35.5 1.0
CG A:GLU213 4.2 35.1 1.0
CG A:GLU266 4.4 39.1 1.0
CB A:GLU266 4.6 40.1 1.0
CE1 A:HIS269 4.7 42.1 1.0
CAK A:9AU505 4.8 65.8 1.0
OE2 A:GLU123 4.8 34.5 1.0
CA A:GLU266 4.8 39.6 1.0
CG A:HIS269 4.9 40.3 1.0
CB A:ALA216 4.9 36.9 1.0
CAM A:9AU505 5.0 62.2 1.0

Iron binding site 3 out of 8 in 5zdp

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Iron binding site 3 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:28.6
occ:1.00
 OE1 B:GLU162 1.8 23.9 1.0
OE1 B:GLU266 1.8 30.9 1.0
O B:OH503 2.2 40.4 1.0
ND1 B:HIS165 2.4 23.5 1.0
OE2 B:GLU123 2.4 28.0 1.0
OE1 B:GLU123 2.6 26.4 1.0
CD B:GLU266 2.8 28.9 1.0
CD B:GLU123 2.9 27.8 1.0
CE1 B:HIS165 2.9 23.7 1.0
CD B:GLU162 3.0 22.9 1.0
OE2 B:GLU266 3.0 27.7 1.0
FE B:FE502 3.1 27.1 1.0
CG B:HIS165 3.5 24.8 1.0
CAK B:9AU505 3.6 44.1 1.0
OE2 B:GLU162 3.6 22.0 1.0
CB B:ALA126 4.1 38.4 1.0
CAJ B:9AU505 4.1 42.4 1.0
CB B:HIS165 4.1 25.2 1.0
NE2 B:HIS165 4.1 23.8 1.0
CG B:GLU266 4.1 29.7 1.0
CG B:GLU162 4.2 21.5 1.0
CG B:GLU123 4.3 26.2 1.0
CB B:GLU162 4.3 20.8 1.0
CD2 B:HIS165 4.4 24.0 1.0
CA B:GLU162 4.4 21.0 1.0
CAM B:9AU505 4.7 43.5 1.0
OH B:TYR220 4.8 38.1 1.0
CE2 B:TYR220 5.0 39.2 1.0

Iron binding site 4 out of 8 in 5zdp

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Iron binding site 4 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:27.1
occ:1.00
 O B:OH503 1.7 40.4 1.0
OE2 B:GLU266 2.0 27.7 1.0
OE1 B:GLU213 2.2 20.1 1.0
OE2 B:GLU162 2.3 22.0 1.0
OE2 B:GLU213 2.4 22.0 1.0
CD B:GLU213 2.6 22.8 1.0
CD B:GLU266 2.8 28.9 1.0
OE1 B:GLU162 2.9 23.9 1.0
CD B:GLU162 2.9 22.9 1.0
OE1 B:GLU266 3.0 30.9 1.0
FE B:FE501 3.1 28.6 1.0
O2 B:OXY504 3.2 48.4 1.0
O1 B:OXY504 3.3 43.2 1.0
CAK B:9AU505 4.0 44.1 1.0
CG B:GLU266 4.1 29.7 1.0
CG B:GLU213 4.1 25.2 1.0
CB B:ALA126 4.1 38.4 1.0
CAM B:9AU505 4.2 43.5 1.0
ND1 B:HIS269 4.3 27.2 1.0
CG B:GLU162 4.4 21.5 1.0
CB B:GLU266 4.5 30.8 1.0
CB B:ALA216 4.5 29.3 1.0
CA B:GLU266 4.9 30.1 1.0

Iron binding site 5 out of 8 in 5zdp

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Iron binding site 5 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:49.6
occ:1.00
 O C:OH503 1.7 24.2 1.0
OE1 C:GLU123 2.1 39.6 1.0
OE2 C:GLU123 2.1 39.9 1.0
OE1 C:GLU162 2.2 37.1 1.0
OE1 C:GLU266 2.3 28.9 1.0
CD C:GLU123 2.4 41.1 1.0
CAK C:9AU505 3.0 58.4 1.0
CD C:GLU266 3.0 29.5 1.0
OE2 C:GLU266 3.2 27.6 1.0
ND1 C:HIS165 3.2 32.3 1.0
CD C:GLU162 3.2 36.5 1.0
CAJ C:9AU505 3.3 56.2 1.0
FE C:FE502 3.3 35.2 1.0
OE2 C:GLU162 3.6 36.5 1.0
CG C:GLU123 3.9 41.8 1.0
CE1 C:HIS165 4.0 33.0 1.0
CB C:ALA126 4.1 46.1 1.0
CAM C:9AU505 4.2 58.8 1.0
CG C:HIS165 4.3 34.2 1.0
OH C:TYR220 4.3 40.0 1.0
CG C:GLU266 4.3 27.4 1.0
CE2 C:TYR220 4.5 39.0 1.0
CG C:GLU162 4.6 33.5 1.0
CB C:HIS165 4.6 35.8 1.0
CAL C:9AU505 4.6 56.4 1.0
O1 C:OXY504 4.7 50.6 1.0
CB C:GLU123 4.8 42.6 1.0
CB C:GLU162 4.8 32.9 1.0
CA C:GLU123 4.9 43.4 1.0
OE1 C:GLU213 4.9 29.7 1.0
CZ C:TYR220 4.9 38.0 1.0

Iron binding site 6 out of 8 in 5zdp

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Iron binding site 6 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:35.2
occ:1.00
 O C:OH503 1.9 24.2 1.0
OE1 C:GLU213 2.0 29.7 1.0
OE2 C:GLU213 2.0 29.5 1.0
OE2 C:GLU162 2.1 36.5 1.0
OE2 C:GLU266 2.2 27.6 1.0
CD C:GLU213 2.3 32.2 1.0
O2 C:OXY504 2.3 48.0 1.0
O1 C:OXY504 2.5 50.6 1.0
CD C:GLU162 3.0 36.5 1.0
OE1 C:GLU162 3.2 37.1 1.0
CD C:GLU266 3.3 29.5 1.0
FE C:FE501 3.3 49.6 1.0
CG C:GLU213 3.8 32.9 1.0
OE1 C:GLU266 3.8 28.9 1.0
CAK C:9AU505 3.9 58.4 1.0
CB C:ALA126 4.1 46.1 1.0
ND1 C:HIS269 4.2 29.7 1.0
CAM C:9AU505 4.3 58.8 1.0
CG C:GLU162 4.4 33.5 1.0
CG C:GLU266 4.5 27.4 1.0
OE2 C:GLU123 4.7 39.9 1.0
CB C:ALA216 4.7 41.3 1.0
CB C:GLU213 4.7 33.5 1.0
CB C:GLU266 4.7 27.9 1.0
CAJ C:9AU505 4.9 56.2 1.0
CA C:GLU266 5.0 28.0 1.0
CA C:GLU213 5.0 32.5 1.0

Iron binding site 7 out of 8 in 5zdp

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Iron binding site 7 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:51.2
occ:1.00
 OE1 D:GLU266 1.8 42.2 1.0
O D:OH503 2.1 14.3 1.0
OE2 D:GLU123 2.1 48.5 1.0
OE1 D:GLU162 2.2 56.6 1.0
OE1 D:GLU123 2.6 47.7 1.0
CD D:GLU123 2.7 50.2 1.0
ND1 D:HIS165 2.8 42.8 1.0
CD D:GLU266 2.8 45.7 1.0
CD D:GLU162 3.0 53.3 1.0
OE2 D:GLU266 3.3 41.9 1.0
OE2 D:GLU162 3.4 60.2 1.0
FE D:FE502 3.5 56.1 1.0
CE1 D:HIS165 3.6 42.7 1.0
CG D:HIS165 3.7 43.4 1.0
CAK D:9AU505 4.0 79.2 1.0
CB D:HIS165 4.1 41.5 1.0
CG D:GLU266 4.1 47.5 1.0
CG D:GLU123 4.2 52.6 1.0
CG D:GLU162 4.2 48.4 1.0
CB D:ALA126 4.3 44.2 1.0
CB D:GLU162 4.3 46.5 1.0
CA D:GLU162 4.3 43.3 1.0
CAJ D:9AU505 4.6 77.1 1.0
NE2 D:HIS165 4.6 43.1 1.0
OH D:TYR220 4.7 64.1 1.0
CD2 D:HIS165 4.8 42.5 1.0
CB D:GLU123 4.9 52.5 1.0
O D:GLU162 4.9 48.8 1.0
CA D:GLU123 5.0 49.5 1.0

Iron binding site 8 out of 8 in 5zdp

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Iron binding site 8 out of 8 in the Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Ferulenol


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 Ferulenol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe502

b:56.1
occ:1.00
 OE2 D:GLU162 1.9 60.2 1.0
OE2 D:GLU266 2.1 41.9 1.0
O D:OH503 2.3 14.3 1.0
OE2 D:GLU213 2.3 60.6 1.0
OE1 D:GLU213 2.9 67.3 1.0
O1 D:OXY504 2.9 48.7 1.0
CD D:GLU213 2.9 63.5 1.0
CD D:GLU162 3.0 53.3 1.0
O2 D:OXY504 3.0 45.6 1.0
CD D:GLU266 3.0 45.7 1.0
OE1 D:GLU266 3.4 42.2 1.0
OE1 D:GLU162 3.5 56.6 1.0
FE D:FE501 3.5 51.2 1.0
CB D:ALA126 3.9 44.2 1.0
CG D:GLU162 4.2 48.4 1.0
CG D:GLU266 4.3 47.5 1.0
CG D:GLU213 4.3 62.2 1.0
ND1 D:HIS269 4.5 47.8 1.0
CB D:GLU266 4.7 47.5 1.0
CB D:ALA216 4.8 52.2 1.0
CA D:GLU266 4.9 49.0 1.0
CA D:ALA126 5.0 45.9 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: Tue Aug 6 13:03:46 2024

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