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Iron in PDB 5zdq: Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B

Protein crystallography data

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B, PDB code: 5zdq 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) 42.89 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.017, 137.920, 63.058, 90.00, 106.08, 90.00
R / Rfree (%) 18.5 / 22

Other elements in 5zdq:

The structure of Crystal Structure of Cyanide-Insensitive Alternative Oxidase From Trypanosoma Brucei with Colletochlorin B 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 Colletochlorin B (pdb code 5zdq). 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 Colletochlorin B, PDB code: 5zdq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5zdq

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


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

b:27.3
occ:1.00
 O A:OH503 1.9 16.9 1.0
OE1 A:GLU162 1.9 27.6 1.0
OE1 A:GLU266 2.1 25.5 1.0
OE2 A:GLU123 2.2 26.1 1.0
OE1 A:GLU123 2.2 29.0 1.0
ND1 A:HIS165 2.4 25.9 1.0
CD A:GLU123 2.5 26.2 1.0
CD A:GLU162 3.0 27.5 1.0
CD A:GLU266 3.0 25.6 1.0
CE1 A:HIS165 3.1 26.7 1.0
FE A:FE502 3.3 28.8 1.0
OE2 A:GLU266 3.3 26.8 1.0
OE2 A:GLU162 3.5 26.8 1.0
CG A:HIS165 3.5 26.4 1.0
CB A:HIS165 4.0 26.8 1.0
CG A:GLU123 4.0 24.9 1.0
CB A:ALA126 4.1 28.9 1.0
CG A:GLU162 4.2 26.5 1.0
NE2 A:HIS165 4.3 27.2 1.0
CAD A:RNB504 4.3 32.1 1.0
CG A:GLU266 4.4 24.6 1.0
CB A:GLU162 4.4 25.8 1.0
CA A:GLU162 4.4 25.4 1.0
CD2 A:HIS165 4.5 26.4 1.0
OH A:TYR220 4.8 33.3 1.0
CB A:GLU123 4.9 25.2 1.0
CG2 A:ILE262 4.9 28.8 1.0
O A:HOH633 4.9 25.6 1.0

Iron binding site 2 out of 8 in 5zdq

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


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

b:28.8
occ:1.00
 OE2 A:GLU162 2.0 26.8 1.0
OE1 A:GLU213 2.1 25.3 1.0
OE2 A:GLU213 2.2 25.9 1.0
OE2 A:GLU266 2.2 26.8 1.0
O A:OH503 2.2 16.9 1.0
CD A:GLU213 2.5 26.4 1.0
O A:HOH633 2.5 25.6 1.0
CD A:GLU162 2.9 27.5 1.0
CD A:GLU266 3.1 25.6 1.0
OE1 A:GLU162 3.1 27.6 1.0
FE A:FE501 3.3 27.3 1.0
OE1 A:GLU266 3.4 25.5 1.0
CG A:GLU213 4.0 25.3 1.0
CAI A:RNB504 4.0 31.2 1.0
OAE A:RNB504 4.2 29.3 1.0
O A:HOH611 4.2 12.8 1.0
CD2 A:HIS269 4.2 28.2 1.0
CB A:ALA126 4.2 28.9 1.0
CG A:GLU162 4.3 26.5 1.0
CG A:GLU266 4.3 24.6 1.0
CB A:GLU266 4.6 24.2 1.0
CB A:ALA216 4.7 27.8 1.0
OE2 A:GLU123 4.8 26.1 1.0
CA A:GLU266 4.8 25.3 1.0
CB A:GLU213 4.9 26.4 1.0
CAD A:RNB504 4.9 32.1 1.0

Iron binding site 3 out of 8 in 5zdq

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


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

b:45.1
occ:1.00
 OE1 B:GLU266 1.8 36.6 1.0
O B:OH503 2.1 26.5 1.0
OE1 B:GLU162 2.1 49.1 1.0
OE1 B:GLU123 2.2 43.0 1.0
OE2 B:GLU123 2.2 41.9 1.0
ND1 B:HIS165 2.3 36.9 1.0
CD B:GLU123 2.5 43.7 1.0
CD B:GLU266 2.9 37.1 1.0
CD B:GLU162 3.0 42.3 1.0
CE1 B:HIS165 3.1 37.1 1.0
OE2 B:GLU266 3.3 36.5 1.0
OE2 B:GLU162 3.4 40.7 1.0
CG B:HIS165 3.4 35.5 1.0
FE B:FE502 3.5 41.6 1.0
CB B:HIS165 3.8 36.5 1.0
CG B:GLU123 4.0 42.8 1.0
CG B:GLU266 4.1 34.3 1.0
CG B:GLU162 4.3 40.5 1.0
NE2 B:HIS165 4.3 37.6 1.0
CB B:ALA126 4.3 37.4 1.0
CB B:GLU162 4.4 39.1 1.0
CAD B:RNB504 4.4 47.1 1.0
CA B:GLU162 4.4 38.0 1.0
CD2 B:HIS165 4.5 36.0 1.0
OH B:TYR220 4.5 40.6 1.0
CE2 B:TYR220 4.8 37.0 1.0
CG2 B:ILE262 4.8 31.9 1.0
CB B:GLU123 4.8 43.0 1.0
O B:HOH614 4.9 44.7 1.0

Iron binding site 4 out of 8 in 5zdq

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


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

b:41.6
occ:1.00
 OE2 B:GLU266 2.0 36.5 1.0
OE2 B:GLU162 2.0 40.7 1.0
O B:HOH614 2.1 44.7 1.0
OE2 B:GLU213 2.2 39.1 1.0
O B:OH503 2.2 26.5 1.0
OE1 B:GLU213 2.3 38.9 1.0
CD B:GLU213 2.5 38.6 1.0
CD B:GLU266 2.9 37.1 1.0
CD B:GLU162 3.0 42.3 1.0
OE1 B:GLU266 3.2 36.6 1.0
OE1 B:GLU162 3.4 49.1 1.0
O B:HOH601 3.4 41.5 1.0
FE B:FE501 3.5 45.1 1.0
CAI B:RNB504 3.9 52.7 1.0
CG B:GLU213 4.0 37.7 1.0
CB B:ALA126 4.1 37.4 1.0
OAE B:RNB504 4.2 52.0 1.0
CG B:GLU266 4.3 34.3 1.0
CD2 B:HIS269 4.4 33.4 1.0
CG B:GLU162 4.4 40.5 1.0
OE2 B:GLU123 4.5 41.9 1.0
CB B:ALA216 4.5 30.3 1.0
CB B:GLU266 4.7 33.9 1.0
CAD B:RNB504 4.9 47.1 1.0
CA B:GLU266 5.0 32.9 1.0
CB B:GLU213 5.0 36.6 1.0

Iron binding site 5 out of 8 in 5zdq

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


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

b:42.9
occ:1.00
 O C:OH503 1.7 17.7 1.0
OE1 C:GLU162 2.0 36.6 1.0
OE1 C:GLU266 2.1 40.2 1.0
OE2 C:GLU123 2.2 42.3 1.0
OE1 C:GLU123 2.3 40.4 1.0
ND1 C:HIS165 2.5 31.8 1.0
CD C:GLU123 2.6 42.3 1.0
CD C:GLU266 3.0 40.3 1.0
CD C:GLU162 3.0 33.0 1.0
OE2 C:GLU266 3.2 42.0 1.0
CE1 C:HIS165 3.2 32.3 1.0
OE2 C:GLU162 3.3 31.3 1.0
FE C:FE502 3.3 33.1 1.0
CG C:HIS165 3.7 31.3 1.0
CG C:GLU123 4.1 42.6 1.0
CAD C:RNB504 4.2 41.1 1.0
CB C:HIS165 4.2 33.4 1.0
CG C:GLU162 4.3 31.7 1.0
CB C:ALA126 4.3 40.1 1.0
CG C:GLU266 4.4 37.1 1.0
NE2 C:HIS165 4.4 32.1 1.0
O C:HOH612 4.5 37.2 1.0
CB C:GLU162 4.6 31.0 1.0
CA C:GLU162 4.6 30.8 1.0
CD2 C:HIS165 4.7 32.1 1.0
OH C:TYR220 4.7 45.5 1.0
CB C:GLU123 4.9 40.9 1.0
CE2 C:TYR220 4.9 45.7 1.0
CG2 C:ILE262 4.9 31.6 1.0

Iron binding site 6 out of 8 in 5zdq

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


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

b:33.1
occ:1.00
 O C:HOH612 2.0 37.2 1.0
OE1 C:GLU213 2.1 37.9 1.0
OE2 C:GLU162 2.1 31.3 1.0
OE2 C:GLU266 2.1 42.0 1.0
O C:OH503 2.3 17.7 1.0
OE2 C:GLU213 2.4 39.6 1.0
CD C:GLU213 2.6 38.3 1.0
CD C:GLU162 3.1 33.0 1.0
CD C:GLU266 3.1 40.3 1.0
FE C:FE501 3.3 42.9 1.0
OE1 C:GLU162 3.4 36.6 1.0
OE1 C:GLU266 3.6 40.2 1.0
CD2 C:HIS269 3.9 29.3 1.0
CAI C:RNB504 4.0 45.2 1.0
OAE C:RNB504 4.1 46.9 1.0
CG C:GLU213 4.1 37.7 1.0
O C:HOH637 4.1 26.7 1.0
CB C:ALA126 4.1 40.1 1.0
CG C:GLU266 4.3 37.1 1.0
CG C:GLU162 4.4 31.7 1.0
CB C:GLU266 4.6 36.3 1.0
CB C:ALA216 4.6 35.6 1.0
CA C:GLU266 4.7 34.6 1.0
CG C:HIS269 4.8 30.2 1.0
NE2 C:HIS269 4.8 30.4 1.0
CB C:GLU213 4.9 36.3 1.0
CB C:HIS269 5.0 31.1 1.0

Iron binding site 7 out of 8 in 5zdq

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


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

b:28.8
occ:1.00
 OE1 D:GLU266 1.9 28.2 1.0
O D:OH503 2.0 14.9 1.0
OE1 D:GLU162 2.0 32.0 1.0
OE2 D:GLU123 2.1 31.6 1.0
OE1 D:GLU123 2.1 32.0 1.0
ND1 D:HIS165 2.4 22.3 1.0
CD D:GLU123 2.4 29.5 1.0
CD D:GLU266 2.9 26.0 1.0
CD D:GLU162 2.9 30.4 1.0
CE1 D:HIS165 3.1 23.0 1.0
OE2 D:GLU266 3.2 26.9 1.0
OE2 D:GLU162 3.3 34.6 1.0
FE D:FE502 3.4 27.9 1.0
CG D:HIS165 3.5 22.4 1.0
CG D:GLU123 3.9 27.2 1.0
CB D:HIS165 4.0 23.5 1.0
CG D:GLU162 4.3 27.1 1.0
CG D:GLU266 4.3 25.4 1.0
CB D:ALA126 4.3 25.2 1.0
NE2 D:HIS165 4.3 23.7 1.0
CAD D:RNB504 4.5 28.6 1.0
CA D:GLU162 4.5 24.2 1.0
CB D:GLU162 4.5 25.8 1.0
CD2 D:HIS165 4.5 22.4 1.0
OH D:TYR220 4.6 30.1 1.0
CG2 D:ILE262 4.7 24.2 1.0
CB D:GLU123 4.7 27.5 1.0
CE2 D:TYR220 4.9 31.1 1.0
O D:GLU162 5.0 23.6 1.0

Iron binding site 8 out of 8 in 5zdq

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


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

b:27.9
occ:1.00
 OE2 D:GLU162 1.9 34.6 1.0
O D:OH503 2.0 14.9 1.0
OE2 D:GLU213 2.1 28.4 1.0
OE2 D:GLU266 2.2 26.9 1.0
OE1 D:GLU213 2.3 29.2 1.0
O D:HOH630 2.4 40.1 1.0
CD D:GLU213 2.5 29.1 1.0
CD D:GLU162 3.0 30.4 1.0
CD D:GLU266 3.1 26.0 1.0
OE1 D:GLU162 3.4 32.0 1.0
FE D:FE501 3.4 28.8 1.0
OE1 D:GLU266 3.5 28.2 1.0
CB D:ALA126 3.9 25.2 1.0
O D:HOH635 3.9 33.3 1.0
CAI D:RNB504 4.0 30.3 1.0
CG D:GLU213 4.0 28.7 1.0
OAE D:RNB504 4.1 33.0 1.0
ND1 D:HIS269 4.2 31.3 1.0
CG D:GLU162 4.2 27.1 1.0
CG D:GLU266 4.4 25.4 1.0
OE2 D:GLU123 4.6 31.6 1.0
CB D:ALA216 4.7 27.0 1.0
CB D:GLU266 4.7 24.5 1.0
CA D:GLU266 4.9 24.8 1.0
OE1 D:GLU123 5.0 32.0 1.0
CE1 D:HIS269 5.0 28.6 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 13:05:38 2024

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