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Iron in PDB 3p1m: Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster

Protein crystallography data

The structure of Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster, PDB code: 3p1m was solved by A.Chaikuad, C.Johansson, T.Krojer, W.W.Yue, C.Phillips, J.E.Bray, A.C.W.Pike, J.R.C.Muniz, M.Vollmar, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C.Bountra, K.Kavanagh, U.Oppermann, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.91 / 2.54
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 76.576, 76.576, 234.410, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 24.1

Other elements in 3p1m:

The structure of Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster also contains other interesting chemical elements:

Potassium (K) 8 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster (pdb code 3p1m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster, PDB code: 3p1m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 3p1m

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Iron binding site 1 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:36.4
occ:1.00
FE1 A:FES2 0.0 36.4 1.0
SG A:CYS106 2.1 44.0 1.0
SG A:CYS112 2.1 43.7 1.0
S1 A:FES2 2.2 34.3 1.0
S2 A:FES2 2.2 31.4 1.0
FE2 A:FES2 2.9 33.2 1.0
CB A:CYS106 3.2 42.4 1.0
CB A:CYS112 3.5 43.3 1.0
N A:CYS112 3.6 41.6 1.0
N A:CYS106 3.8 42.8 1.0
CA A:CYS112 3.9 42.1 1.0
CA A:CYS106 3.9 43.8 1.0
O A:CYS112 4.0 40.1 1.0
C A:CYS112 4.1 41.0 1.0
N A:GLY108 4.2 44.7 1.0
N A:ALA111 4.3 42.4 1.0
C A:CYS106 4.4 44.8 1.0
OG1 A:THR114 4.4 37.5 1.0
C A:ALA111 4.4 42.9 1.0
SG A:CYS115 4.5 37.0 1.0
N A:GLU107 4.5 45.9 1.0
CA A:GLY108 4.6 43.8 1.0
SG A:CYS152 4.6 41.2 1.0
N A:THR109 4.6 43.9 1.0
N A:LEU110 4.7 42.1 1.0
CA A:GLY104 4.8 42.1 1.0
C A:GLY104 4.8 43.1 1.0
N A:ALA105 4.9 42.9 1.0
CA A:ALA111 4.9 42.8 1.0
N A:SER113 4.9 41.2 1.0
C A:ALA105 5.0 44.0 1.0
O A:CYS106 5.0 44.7 1.0

Iron binding site 2 out of 16 in 3p1m

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Iron binding site 2 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe2

b:33.2
occ:1.00
FE2 A:FES2 0.0 33.2 1.0
SG A:CYS115 2.1 37.0 1.0
SG A:CYS152 2.1 41.2 1.0
S2 A:FES2 2.2 31.4 1.0
S1 A:FES2 2.2 34.3 1.0
FE1 A:FES2 2.9 36.4 1.0
CB A:CYS152 3.1 39.4 1.0
CB A:CYS115 3.3 36.5 1.0
N A:CYS152 4.1 35.0 1.0
CA A:CYS152 4.2 38.6 1.0
CA A:GLY108 4.3 43.8 1.0
SG A:CYS106 4.4 44.0 1.0
CA A:CYS115 4.5 34.1 1.0
SG A:CYS112 4.5 43.7 1.0
N A:CYS115 4.5 33.8 1.0
CB A:LEU150 4.6 28.1 1.0
N A:GLY108 4.7 44.7 1.0
O A:CYS112 4.8 40.1 1.0

Iron binding site 3 out of 16 in 3p1m

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Iron binding site 3 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3

b:40.5
occ:1.00
FE1 B:FES3 0.0 40.5 1.0
SG B:CYS106 2.1 57.8 1.0
SG B:CYS112 2.1 57.2 1.0
S1 B:FES3 2.2 38.9 1.0
S2 B:FES3 2.2 39.1 1.0
FE2 B:FES3 2.9 43.0 1.0
CB B:CYS106 3.2 57.9 1.0
N B:CYS112 3.4 56.8 1.0
CB B:CYS112 3.4 56.8 1.0
N B:CYS106 3.8 57.5 1.0
CA B:CYS112 3.8 56.7 1.0
O B:CYS112 3.9 55.0 1.0
CA B:CYS106 4.0 58.5 1.0
C B:CYS112 4.0 55.4 1.0
N B:ALA111 4.1 57.6 1.0
N B:GLY108 4.2 56.6 1.0
SG B:CYS115 4.3 44.0 1.0
C B:CYS106 4.4 58.7 1.0
N B:LEU110 4.5 57.8 1.0
C B:ALA111 4.5 58.1 1.0
N B:GLU107 4.6 58.0 1.0
CA B:GLY108 4.6 56.6 1.0
SG B:CYS152 4.6 51.8 1.0
OG1 B:THR114 4.6 46.1 1.0
N B:THR109 4.7 58.6 1.0
CA B:LEU110 4.8 57.3 1.0
N B:SER113 4.8 55.2 1.0
N B:ALA105 4.9 55.8 1.0
CA B:ALA111 4.9 58.7 1.0
N B:THR114 4.9 42.1 1.0
C B:LEU110 5.0 57.8 1.0
C B:GLY104 5.0 55.0 1.0
O B:CYS106 5.0 59.6 1.0
CA B:GLY104 5.0 53.7 1.0

Iron binding site 4 out of 16 in 3p1m

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Iron binding site 4 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3

b:43.0
occ:1.00
FE2 B:FES3 0.0 43.0 1.0
SG B:CYS152 2.1 51.8 1.0
SG B:CYS115 2.1 44.0 1.0
S2 B:FES3 2.2 39.1 1.0
S1 B:FES3 2.2 38.9 1.0
FE1 B:FES3 2.9 40.5 1.0
CB B:CYS152 3.2 49.1 1.0
CB B:CYS115 3.2 43.1 1.0
CA B:GLY108 4.2 56.6 1.0
CA B:CYS152 4.4 48.1 1.0
SG B:CYS106 4.4 57.8 1.0
N B:CYS152 4.4 45.1 1.0
SG B:CYS112 4.4 57.2 1.0
CA B:CYS115 4.5 41.6 1.0
N B:CYS115 4.5 41.6 1.0
CB B:LEU150 4.6 40.8 1.0
N B:GLY108 4.6 56.6 1.0
CD1 B:LEU150 4.9 41.3 1.0
N B:LEU110 4.9 57.8 1.0
O B:CYS112 5.0 55.0 1.0
C B:GLY108 5.0 58.1 1.0

Iron binding site 5 out of 16 in 3p1m

Go back to Iron Binding Sites List in 3p1m
Iron binding site 5 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe4

b:36.0
occ:1.00
FE1 C:FES4 0.0 36.0 1.0
SG C:CYS106 2.0 40.9 1.0
SG C:CYS112 2.1 39.5 1.0
S2 C:FES4 2.2 30.3 1.0
S1 C:FES4 2.2 35.1 1.0
FE2 C:FES4 2.9 31.6 1.0
CB C:CYS112 3.4 39.0 1.0
CB C:CYS106 3.4 40.1 1.0
N C:CYS112 3.6 37.7 1.0
N C:CYS106 3.8 40.4 1.0
CA C:CYS112 3.9 38.0 1.0
CA C:CYS106 4.0 41.8 1.0
O C:CYS112 4.1 36.5 1.0
N C:GLY108 4.1 42.8 1.0
C C:CYS112 4.2 36.8 1.0
N C:ALA111 4.2 39.8 1.0
C C:CYS106 4.4 42.9 1.0
C C:ALA111 4.4 39.7 1.0
SG C:CYS152 4.5 42.1 1.0
CA C:GLY108 4.5 42.1 1.0
SG C:CYS115 4.5 37.5 1.0
N C:GLU107 4.5 43.8 1.0
N C:LEU110 4.5 40.3 1.0
N C:THR109 4.6 42.9 1.0
OG1 C:THR114 4.7 36.5 1.0
CA C:LEU110 4.8 38.9 1.0
C C:GLY104 4.9 39.6 1.0
CA C:GLY104 4.9 38.5 1.0
CA C:ALA111 4.9 40.2 1.0
N C:ALA105 4.9 39.5 1.0
N C:SER113 4.9 36.3 1.0
O C:CYS106 5.0 43.1 1.0
C C:ALA105 5.0 41.6 1.0

Iron binding site 6 out of 16 in 3p1m

Go back to Iron Binding Sites List in 3p1m
Iron binding site 6 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe4

b:31.6
occ:1.00
FE2 C:FES4 0.0 31.6 1.0
SG C:CYS115 2.0 37.5 1.0
SG C:CYS152 2.1 42.1 1.0
S2 C:FES4 2.2 30.3 1.0
S1 C:FES4 2.2 35.1 1.0
FE1 C:FES4 2.9 36.0 1.0
CB C:CYS152 3.2 39.1 1.0
CB C:CYS115 3.2 36.5 1.0
SG C:CYS112 4.2 39.5 1.0
CA C:CYS152 4.4 38.2 1.0
N C:CYS152 4.4 34.6 1.0
CA C:GLY108 4.4 42.1 1.0
CA C:CYS115 4.5 34.0 1.0
N C:CYS115 4.5 33.6 1.0
SG C:CYS106 4.6 40.9 1.0
CB C:LEU150 4.6 27.9 1.0
N C:GLY108 4.8 42.8 1.0
O C:CYS112 5.0 36.5 1.0

Iron binding site 7 out of 16 in 3p1m

Go back to Iron Binding Sites List in 3p1m
Iron binding site 7 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe5

b:45.0
occ:1.00
FE1 D:FES5 0.0 45.0 1.0
SG D:CYS106 2.0 55.7 1.0
SG D:CYS112 2.1 53.8 1.0
S1 D:FES5 2.2 45.9 1.0
S2 D:FES5 2.2 42.3 1.0
FE2 D:FES5 3.0 44.1 1.0
CB D:CYS106 3.1 55.8 1.0
CB D:CYS112 3.5 53.3 1.0
N D:CYS112 3.5 54.1 1.0
N D:CYS106 3.6 55.4 1.0
CA D:CYS106 3.8 56.8 1.0
CA D:CYS112 3.9 53.5 1.0
N D:GLY108 4.1 55.1 1.0
C D:CYS112 4.2 51.9 1.0
N D:ALA111 4.2 56.0 1.0
O D:CYS112 4.2 51.9 1.0
C D:CYS106 4.2 57.6 1.0
SG D:CYS115 4.4 45.6 1.0
N D:GLU107 4.4 56.9 1.0
N D:LEU110 4.5 55.9 1.0
C D:ALA111 4.5 55.9 1.0
CA D:GLY108 4.5 54.8 1.0
OG1 D:THR114 4.6 44.9 1.0
N D:THR109 4.6 57.0 1.0
SG D:CYS152 4.6 54.4 1.0
CA D:LEU110 4.8 55.5 1.0
O D:CYS106 4.8 58.8 1.0
N D:ALA105 4.8 53.1 1.0
C D:ALA105 4.9 56.4 1.0
C D:GLY104 4.9 52.8 1.0
CA D:ALA111 4.9 57.0 1.0
N D:SER113 4.9 51.2 1.0
CA D:GLY104 5.0 50.9 1.0

Iron binding site 8 out of 16 in 3p1m

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Iron binding site 8 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


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 Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe5

b:44.1
occ:1.00
FE2 D:FES5 0.0 44.1 1.0
SG D:CYS152 2.1 54.4 1.0
SG D:CYS115 2.1 45.6 1.0
S2 D:FES5 2.2 42.3 1.0
S1 D:FES5 2.2 45.9 1.0
FE1 D:FES5 3.0 45.0 1.0
CB D:CYS152 3.2 51.5 1.0
CB D:CYS115 3.3 45.3 1.0
CA D:GLY108 4.3 54.8 1.0
CA D:CYS152 4.4 51.1 1.0
SG D:CYS106 4.4 55.7 1.0
N D:CYS152 4.4 48.3 1.0
SG D:CYS112 4.5 53.8 1.0
CA D:CYS115 4.5 43.6 1.0
CB D:LEU150 4.5 42.8 1.0
N D:CYS115 4.5 43.0 1.0
N D:GLY108 4.7 55.1 1.0
CD1 D:LEU150 4.9 41.7 1.0
N D:LEU110 4.9 55.9 1.0

Iron binding site 9 out of 16 in 3p1m

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Iron binding site 9 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe6

b:42.9
occ:1.00
FE1 E:FES6 0.0 42.9 1.0
SG E:CYS106 2.0 58.7 1.0
SG E:CYS112 2.1 58.4 1.0
S1 E:FES6 2.2 40.0 1.0
S2 E:FES6 2.2 41.7 1.0
FE2 E:FES6 2.9 41.6 1.0
CB E:CYS106 3.1 58.9 1.0
N E:CYS112 3.4 58.0 1.0
CB E:CYS112 3.4 58.3 1.0
N E:CYS106 3.7 58.9 1.0
CA E:CYS112 3.8 58.2 1.0
CA E:CYS106 3.9 59.7 1.0
O E:CYS112 4.0 56.5 1.0
C E:CYS112 4.0 56.9 1.0
N E:ALA111 4.1 58.4 1.0
N E:GLY108 4.2 57.2 1.0
C E:CYS106 4.3 59.7 1.0
SG E:CYS115 4.3 44.3 1.0
C E:ALA111 4.5 59.4 1.0
N E:LEU110 4.5 58.3 1.0
N E:GLU107 4.5 59.0 1.0
CA E:GLY108 4.6 57.1 1.0
N E:THR109 4.6 59.0 1.0
SG E:CYS152 4.6 52.4 1.0
OG1 E:THR114 4.7 44.1 1.0
CA E:LEU110 4.8 58.0 1.0
CA E:ALA111 4.8 59.7 1.0
N E:SER113 4.9 57.1 1.0
N E:ALA105 4.9 57.3 1.0
O E:CYS106 4.9 60.5 1.0
C E:LEU110 4.9 58.6 1.0
C E:ALA105 5.0 59.8 1.0
C E:GLY104 5.0 56.4 1.0
N E:THR114 5.0 41.2 1.0

Iron binding site 10 out of 16 in 3p1m

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Iron binding site 10 out of 16 in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe6

b:41.6
occ:1.00
FE2 E:FES6 0.0 41.6 1.0
SG E:CYS115 2.1 44.3 1.0
SG E:CYS152 2.1 52.4 1.0
S2 E:FES6 2.2 41.7 1.0
S1 E:FES6 2.3 40.0 1.0
FE1 E:FES6 2.9 42.9 1.0
CB E:CYS152 3.1 49.1 1.0
CB E:CYS115 3.2 43.0 1.0
CA E:GLY108 4.2 57.1 1.0
CA E:CYS152 4.4 48.3 1.0
SG E:CYS106 4.4 58.7 1.0
SG E:CYS112 4.4 58.4 1.0
N E:CYS152 4.4 45.6 1.0
CA E:CYS115 4.5 41.3 1.0
N E:CYS115 4.5 41.1 1.0
N E:GLY108 4.6 57.2 1.0
CB E:LEU150 4.7 42.0 1.0
N E:LEU110 5.0 58.3 1.0
CD1 E:LEU150 5.0 42.5 1.0
C E:GLY108 5.0 58.4 1.0

Reference:

A.Chaikuad, C.Johansson, T.Krojer, W.W.Yue, C.Phillips, J.E.Bray, A.C.W.Pike, J.R.C.Muniz, M.Vollmar, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C.Bountra, K.Kavanagh, U.Oppermann. Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron-Sulfur Cluster To Be Published.
Page generated: Sun Dec 13 15:16:22 2020

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