Atomistry » Iron » PDB 5ym3-5zm4 » 5zdq
Atomistry »
  Iron »
    PDB 5ym3-5zm4 »
      5zdq »

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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Go back to Iron Binding Sites List in 5zdq
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy