Atomistry » Iron » PDB 1fca-1fnp » 1fdd
Atomistry »
  Iron »
    PDB 1fca-1fnp »
      1fdd »

Iron in PDB 1fdd: Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster

Protein crystallography data

The structure of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster, PDB code: 1fdd was solved by C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.600, 55.600, 95.900, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster (pdb code 1fdd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster, PDB code: 1fdd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 1 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:14.3
occ:1.00
FE1 A:SF4107 0.0 14.3 1.0
S4 A:SF4107 2.3 14.9 1.0
S2 A:SF4107 2.3 15.4 1.0
S3 A:SF4107 2.3 14.8 1.0
SG A:CYS39 2.3 12.6 1.0
FE3 A:SF4107 2.7 14.1 1.0
FE2 A:SF4107 2.7 16.4 1.0
FE4 A:SF4107 2.7 16.7 1.0
CB A:CYS39 3.3 11.2 1.0
CA A:CYS39 3.8 11.9 1.0
S1 A:SF4107 3.8 13.6 1.0
SG A:CYS24 4.0 14.2 1.0
N A:ASP41 4.1 12.1 1.0
N A:ILE40 4.1 13.5 1.0
C A:CYS39 4.4 13.4 1.0
CB A:PHE2 4.4 11.8 1.0
CA A:ASP41 4.6 14.2 1.0
CG2 A:ILE34 4.7 6.3 1.0
CD1 A:PHE2 4.7 15.4 1.0
N A:CYS42 4.7 14.9 1.0
SG A:CYS45 4.8 14.0 1.0
CG A:PHE2 4.8 13.4 1.0
SG A:CYS20 4.9 14.3 1.0
SG A:CYS42 4.9 15.0 1.0
N A:PHE2 5.0 11.7 1.0
C A:ILE40 5.0 14.2 1.0

Iron binding site 2 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 2 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:16.4
occ:1.00
FE2 A:SF4107 0.0 16.4 1.0
S3 A:SF4107 2.3 14.8 1.0
S1 A:SF4107 2.3 13.6 1.0
S4 A:SF4107 2.3 14.9 1.0
SG A:CYS42 2.3 15.0 1.0
FE3 A:SF4107 2.7 14.1 1.0
FE1 A:SF4107 2.7 14.3 1.0
FE4 A:SF4107 2.7 16.7 1.0
CB A:CYS42 3.6 15.0 1.0
N A:CYS42 3.6 14.9 1.0
S2 A:SF4107 3.9 15.4 1.0
N A:ALA43 3.9 12.7 1.0
CA A:CYS42 4.0 15.2 1.0
CD A:PRO21 4.1 14.0 1.0
N A:LEU44 4.2 13.4 1.0
C A:CYS42 4.2 13.3 1.0
CB A:LEU44 4.6 14.7 1.0
SG A:CYS45 4.6 14.0 1.0
C A:ASP41 4.6 14.9 1.0
SG A:CYS39 4.7 12.6 1.0
CG A:PRO21 4.7 12.8 1.0
N A:ASP41 4.7 12.1 1.0
CA A:ALA43 4.8 12.6 1.0
SG A:CYS20 4.8 14.3 1.0
CG1 A:ILE40 4.8 14.0 1.0
N A:CYS45 4.9 14.7 1.0
C A:ALA43 4.9 13.4 1.0
CA A:ASP41 4.9 14.2 1.0
CA A:LEU44 5.0 15.7 1.0

Iron binding site 3 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 3 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:14.1
occ:1.00
FE3 A:SF4107 0.0 14.1 1.0
S4 A:SF4107 2.3 14.9 1.0
S1 A:SF4107 2.3 13.6 1.0
SG A:CYS45 2.3 14.0 1.0
S2 A:SF4107 2.3 15.4 1.0
FE1 A:SF4107 2.7 14.3 1.0
FE2 A:SF4107 2.7 16.4 1.0
FE4 A:SF4107 2.8 16.7 1.0
CB A:CYS45 3.3 13.2 1.0
S3 A:SF4107 3.9 14.8 1.0
N A:CYS45 4.0 14.7 1.0
CA A:CYS45 4.3 13.5 1.0
CE1 A:PHE25 4.4 10.3 1.0
CB A:PHE2 4.4 11.8 1.0
CZ A:PHE25 4.4 9.7 1.0
CG A:PHE2 4.6 13.4 1.0
SG A:CYS42 4.7 15.0 1.0
SG A:CYS39 4.7 12.6 1.0
CD1 A:ILE34 4.7 8.4 1.0
N A:LEU44 4.7 13.4 1.0
SG A:CYS20 4.9 14.3 1.0
N A:ALA43 5.0 12.7 1.0

Iron binding site 4 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 4 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:16.7
occ:1.00
FE4 A:SF4107 0.0 16.7 1.0
S1 A:SF4107 2.3 13.6 1.0
S2 A:SF4107 2.3 15.4 1.0
S3 A:SF4107 2.3 14.8 1.0
SG A:CYS20 2.3 14.3 1.0
FE1 A:SF4107 2.7 14.3 1.0
FE2 A:SF4107 2.7 16.4 1.0
FE3 A:SF4107 2.8 14.1 1.0
CB A:CYS20 3.4 15.0 1.0
SG A:CYS24 3.5 14.2 1.0
CA A:CYS20 3.7 15.5 1.0
S4 A:SF4107 3.9 14.9 1.0
CE1 A:PHE25 4.1 10.3 1.0
CD A:PRO21 4.3 14.0 1.0
C A:CYS20 4.5 17.0 1.0
CG2 A:VAL22 4.5 11.1 1.0
N A:PRO21 4.6 14.4 1.0
SG A:CYS42 4.7 15.0 1.0
CD1 A:PHE25 4.8 10.9 1.0
SG A:CYS45 4.8 14.0 1.0
N A:CYS20 4.9 16.6 1.0
SG A:CYS39 4.9 12.6 1.0
CZ A:PHE25 4.9 9.7 1.0

Iron binding site 5 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 5 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:15.4
occ:1.00
FE1 A:F3S108 0.0 15.4 1.0
S2 A:F3S108 2.2 14.9 1.0
SG A:CYS16 2.3 15.0 1.0
S3 A:F3S108 2.3 13.2 1.0
S1 A:F3S108 2.3 13.7 1.0
FE4 A:F3S108 2.6 14.4 1.0
FE3 A:F3S108 2.7 14.4 1.0
CB A:CYS16 3.3 13.6 1.0
S4 A:F3S108 3.9 13.6 1.0
N A:CYS16 4.0 14.2 1.0
CA A:THR14 4.1 14.3 1.0
N A:THR14 4.1 13.8 1.0
CA A:CYS16 4.3 13.2 1.0
C A:THR14 4.5 13.6 1.0
CD1 A:LEU32 4.5 14.2 1.0
N A:ASN15 4.6 14.8 1.0
SG A:CYS49 4.7 13.8 1.0
CG A:LEU32 4.7 14.4 1.0
CD1 A:ILE54 4.7 9.9 1.0
SG A:CYS8 4.8 10.2 1.0
CB A:LEU32 5.0 10.8 1.0
CE2 A:PHE25 5.0 9.7 1.0

Iron binding site 6 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 6 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:14.4
occ:1.00
FE3 A:F3S108 0.0 14.4 1.0
S1 A:F3S108 2.3 13.7 1.0
S4 A:F3S108 2.3 13.6 1.0
SG A:CYS8 2.3 10.2 1.0
S3 A:F3S108 2.3 13.2 1.0
FE4 A:F3S108 2.6 14.4 1.0
FE1 A:F3S108 2.7 15.4 1.0
CB A:CYS8 3.2 7.5 1.0
S2 A:F3S108 3.9 14.9 1.0
CA A:CYS8 3.9 9.5 1.0
CA A:LYS12 4.1 13.0 1.0
N A:TYR13 4.4 14.1 1.0
N A:LYS12 4.4 13.1 1.0
CG1 A:VAL4 4.5 6.8 1.0
O A:CYS8 4.6 12.4 1.0
SG A:CYS49 4.6 13.8 1.0
C A:LYS12 4.7 12.6 1.0
C A:CYS8 4.7 12.3 1.0
CB A:LEU32 4.7 10.8 1.0
CG A:LEU32 4.8 14.4 1.0
SG A:CYS16 4.8 15.0 1.0
N A:LEU32 5.0 7.4 1.0
N A:THR14 5.0 13.8 1.0

Iron binding site 7 out of 7 in 1fdd

Go back to Iron Binding Sites List in 1fdd
Iron binding site 7 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Azotobacter Vinelandii Ferredoxin I: Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:14.4
occ:1.00
FE4 A:F3S108 0.0 14.4 1.0
S4 A:F3S108 2.3 13.6 1.0
SG A:CYS49 2.3 13.8 1.0
S2 A:F3S108 2.3 14.9 1.0
S3 A:F3S108 2.3 13.2 1.0
FE1 A:F3S108 2.6 15.4 1.0
FE3 A:F3S108 2.6 14.4 1.0
CB A:CYS49 3.3 12.9 1.0
S1 A:F3S108 3.9 13.7 1.0
CA A:CYS49 3.9 14.4 1.0
CD A:PRO50 4.4 13.8 1.0
C A:CYS49 4.6 14.3 1.0
CB A:ALA51 4.6 15.0 1.0
SG A:CYS16 4.7 15.0 1.0
SG A:CYS8 4.7 10.2 1.0
N A:ALA51 4.7 15.1 1.0
CB A:ALA53 4.7 9.2 1.0
N A:PRO50 4.7 15.0 1.0
CD2 A:TYR13 4.8 11.1 1.0
CB A:CYS8 4.9 7.5 1.0
CB A:TYR13 4.9 12.0 1.0
CB A:CYS16 4.9 13.6 1.0
N A:TYR13 5.0 14.1 1.0

Reference:

B.Shen, L.L.Martin, J.N.Butt, F.A.Armstrong, C.D.Stout, G.M.Jensen, P.J.Stephens, G.N.La Mar, C.M.Gorst, B.K.Burgess. Azotobacter Vinelandii Ferredoxin I. Aspartate 15 Facilitates Proton Transfer to the Reduced [3FE-4S] Cluster. J.Biol.Chem. V. 268 25928 1993.
ISSN: ISSN 0021-9258
PubMed: 8245026
Page generated: Sun Dec 13 14:13:33 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