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Potassium 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:

Iron (Fe) 16 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Human Ferredoxin-1 (FDX1) in Complex with Iron- Sulfur Cluster, PDB code: 3p1m:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 1 out of 8 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 Potassium with other atoms in the K 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:K192

b:54.4
occ:1.00
 OHB A:FLC6 2.3 53.4 1.0
O A:SER177 2.4 37.9 1.0
OD1 A:ASP179 2.9 43.0 1.0
CB A:FLC6 3.4 53.5 1.0
CG A:ASP179 3.4 35.8 1.0
C A:SER177 3.5 39.0 1.0
OD2 A:ASP179 3.6 34.1 1.0
CG A:FLC6 3.9 54.8 1.0
CA A:FLC6 4.0 51.3 1.0
OG2 A:FLC6 4.2 58.7 1.0
N A:ASP179 4.2 35.0 1.0
OG A:SER177 4.2 43.1 1.0
CGC A:FLC6 4.3 58.9 1.0
N A:SER177 4.4 40.1 1.0
C A:ILE178 4.4 37.0 1.0
CA A:SER177 4.4 41.2 1.0
N A:ILE178 4.5 39.3 1.0
CA A:ILE178 4.6 37.6 1.0
OA2 A:FLC6 4.6 48.5 1.0
CB A:ASP179 4.6 34.0 1.0
CBC A:FLC6 4.6 54.2 1.0
CAC A:FLC6 4.7 48.7 1.0
CA A:ASP179 4.7 34.6 1.0
OB2 A:FLC6 4.7 57.2 1.0
CG A:ARG175 4.8 34.5 1.0
O A:ILE178 4.9 37.9 1.0
CB A:SER177 4.9 42.6 1.0

Potassium binding site 2 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 2 out of 8 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 Potassium with other atoms in the K 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
B:K193

b:66.7
occ:1.00
 O B:HOH201 2.3 26.4 1.0
OHB B:FLC192 2.6 67.2 1.0
O H:SER177 2.7 46.3 1.0
OD1 H:ASP179 2.8 48.8 1.0
CG H:ASP179 3.6 44.4 1.0
OG H:SER177 3.8 53.3 1.0
C H:SER177 3.8 48.7 1.0
OD2 H:ASP179 3.9 47.6 1.0
CB B:FLC192 4.0 67.3 1.0
OA1 B:FLC192 4.0 69.2 1.0
OB2 B:FLC192 4.3 68.5 1.0
CG B:FLC192 4.4 65.3 1.0
N H:SER177 4.4 51.9 1.0
N H:ASP179 4.4 43.1 1.0
CA H:SER177 4.5 51.9 1.0
CBC B:FLC192 4.6 69.0 1.0
C H:ILE178 4.6 45.6 1.0
CB H:SER177 4.7 53.5 1.0
N H:ILE178 4.7 48.7 1.0
CB H:ASP179 4.7 41.7 1.0
CGC B:FLC192 4.8 61.8 1.0
CAC B:FLC192 4.8 68.8 1.0
CA H:ASP179 4.8 42.6 1.0
CA H:ILE178 4.8 46.0 1.0
CG H:ARG175 4.9 44.9 1.0

Potassium binding site 3 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 3 out of 8 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 Potassium with other atoms in the K 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
C:K192

b:53.1
occ:1.00
 O C:SER177 2.4 36.9 1.0
OB2 C:FLC5 2.8 59.6 1.0
OHB C:FLC5 2.8 57.8 1.0
OD1 C:ASP179 2.9 41.1 1.0
O C:HOH203 3.4 31.3 1.0
CG C:ASP179 3.6 35.1 1.0
C C:SER177 3.6 38.3 1.0
CBC C:FLC5 3.6 59.3 1.0
OD2 C:ASP179 3.8 36.2 1.0
CB C:FLC5 3.8 58.1 1.0
OA2 C:FLC5 3.8 55.0 1.0
OG1 C:FLC5 4.2 64.1 1.0
N C:ASP179 4.2 34.6 1.0
OG C:SER177 4.3 41.1 1.0
CAC C:FLC5 4.4 53.9 1.0
CG C:ARG175 4.4 34.8 1.0
N C:SER177 4.4 39.5 1.0
C C:ILE178 4.4 36.5 1.0
N C:ILE178 4.5 38.9 1.0
CA C:SER177 4.5 40.6 1.0
CA C:ILE178 4.5 37.1 1.0
OB1 C:FLC5 4.6 62.6 1.0
CA C:FLC5 4.7 56.0 1.0
CB C:ASP179 4.7 33.1 1.0
CD C:ARG175 4.8 32.0 1.0
CA C:ASP179 4.8 34.2 1.0
CGC C:FLC5 4.9 62.9 1.0
CG C:FLC5 4.9 59.7 1.0

Potassium binding site 4 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 4 out of 8 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 Potassium with other atoms in the K 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
D:K192

b:58.5
occ:1.00
 O D:SER177 2.6 45.8 1.0
O D:HOH205 2.7 27.5 1.0
OHB D:FLC2 2.7 64.1 1.0
OD1 D:ASP179 2.9 50.1 1.0
OG D:SER177 3.2 51.0 1.0
OG1 D:FLC2 3.3 63.7 1.0
CB D:FLC2 3.5 63.6 1.0
C D:SER177 3.6 48.1 1.0
CA D:FLC2 3.6 63.1 1.0
CG D:ASP179 3.7 45.5 1.0
CG D:FLC2 3.8 64.1 1.0
CGC D:FLC2 3.9 65.0 1.0
N D:ASP179 4.2 42.9 1.0
OD2 D:ASP179 4.3 49.0 1.0
N D:SER177 4.3 50.8 1.0
CA D:SER177 4.3 51.0 1.0
CB D:SER177 4.3 51.7 1.0
C D:ILE178 4.4 45.0 1.0
N D:ILE178 4.5 48.1 1.0
CA D:ILE178 4.5 45.5 1.0
CG D:ARG175 4.6 44.1 1.0
CB D:ASP179 4.6 42.0 1.0
CAC D:FLC2 4.6 62.3 1.0
CA D:ASP179 4.7 42.6 1.0
OA1 D:FLC2 4.8 61.1 1.0
CBC D:FLC2 4.9 65.0 1.0

Potassium binding site 5 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 5 out of 8 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 Potassium with other atoms in the K 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
E:K192

b:72.3
occ:1.00
 OD1 E:ASP179 2.6 47.9 1.0
O E:SER177 2.7 45.1 1.0
OHB E:FLC4 2.8 71.8 1.0
CG E:ASP179 3.2 44.5 1.0
OD2 E:ASP179 3.6 45.0 1.0
OG2 E:FLC4 3.8 65.9 1.0
C E:SER177 3.8 46.8 1.0
N E:ASP179 3.9 40.0 1.0
CB E:ASP179 4.1 39.8 1.0
OA2 E:FLC4 4.1 72.8 1.0
CB E:FLC4 4.1 71.8 1.0
C E:ILE178 4.1 41.8 1.0
CA E:ASP179 4.3 40.1 1.0
CA E:ILE178 4.3 42.1 1.0
OB1 E:FLC4 4.4 72.8 1.0
N E:ILE178 4.5 45.5 1.0
CGC E:FLC4 4.5 66.4 1.0
CBC E:FLC4 4.6 72.5 1.0
OG E:SER177 4.6 54.7 1.0
CG E:ARG175 4.6 43.0 1.0
CG E:FLC4 4.7 69.3 1.0
O D:LEU144 4.7 37.5 1.0
O E:ILE178 4.7 43.6 1.0
CA E:SER177 4.9 50.8 1.0
CAC E:FLC4 5.0 73.7 1.0

Potassium binding site 6 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 6 out of 8 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 Potassium with other atoms in the K 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
F:K8

b:42.6
occ:1.00
 O F:SER177 2.6 45.1 1.0
O C:HOH222 2.6 25.9 1.0
OHB C:FLC8 2.7 69.6 1.0
OD1 F:ASP179 2.9 42.5 1.0
OG2 C:FLC8 3.3 70.3 1.0
CG F:ASP179 3.7 40.3 1.0
C F:SER177 3.8 43.5 1.0
OA2 C:FLC8 3.9 67.0 1.0
CGC C:FLC8 3.9 70.8 1.0
CAC C:FLC8 4.0 66.6 1.0
N F:ASP179 4.1 36.9 1.0
CB C:FLC8 4.1 69.4 1.0
OD2 F:ASP179 4.2 45.5 1.0
CG F:ARG175 4.2 33.5 1.0
OA1 C:FLC8 4.3 63.8 1.0
OG1 C:FLC8 4.3 71.6 1.0
C F:ILE178 4.4 39.2 1.0
CA F:ILE178 4.5 39.5 1.0
N F:ILE178 4.5 42.7 1.0
CA C:FLC8 4.5 67.9 1.0
CG C:FLC8 4.6 69.4 1.0
OG F:SER177 4.6 49.3 1.0
CD F:ARG175 4.6 31.0 1.0
CB F:ASP179 4.7 36.6 1.0
NE F:ARG175 4.7 29.0 1.0
N F:SER177 4.7 44.8 1.0
CA F:ASP179 4.8 36.8 1.0
CA F:SER177 4.8 45.5 1.0
O C:LEU144 5.0 26.6 1.0

Potassium binding site 7 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 7 out of 8 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 Potassium with other atoms in the K 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
G:K193

b:50.0
occ:1.00
 O G:SER177 2.4 37.4 1.0
O A:HOH197 2.8 30.8 1.0
OD1 G:ASP179 3.0 39.6 1.0
OHB G:FLC192 3.0 71.9 1.0
O G:HOH47 3.1 52.9 1.0
C G:SER177 3.5 39.9 1.0
OG1 G:FLC192 3.7 74.5 1.0
CG G:ASP179 3.8 38.9 1.0
OG G:SER177 3.9 45.7 1.0
CGC G:FLC192 4.0 74.1 1.0
N G:ASP179 4.0 35.3 1.0
OA2 G:FLC192 4.2 68.5 1.0
CAC G:FLC192 4.2 68.6 1.0
OG2 G:FLC192 4.3 73.8 1.0
CB G:FLC192 4.3 72.0 1.0
CG G:ARG175 4.3 31.4 1.0
OD2 G:ASP179 4.3 45.9 1.0
N G:SER177 4.4 42.6 1.0
N G:ILE178 4.4 39.8 1.0
OA1 G:FLC192 4.4 65.3 1.0
CA G:SER177 4.4 42.7 1.0
CA G:ILE178 4.5 37.9 1.0
C G:ILE178 4.5 37.7 1.0
CA G:FLC192 4.7 70.1 1.0
CA G:ASP179 4.7 35.6 1.0
CG G:FLC192 4.8 72.2 1.0
CB G:ASP179 4.8 35.3 1.0
CB G:SER177 4.8 44.4 1.0
CD G:ARG175 4.9 30.3 1.0

Potassium binding site 8 out of 8 in 3p1m

Go back to Potassium Binding Sites List in 3p1m
Potassium binding site 8 out of 8 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 Potassium with other atoms in the K 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
H:K192

b:71.0
occ:1.00
 O B:SER177 2.6 50.2 1.0
OD1 B:ASP179 2.6 51.6 1.0
OHB H:FLC7 3.1 65.2 1.0
OA1 H:FLC7 3.4 63.2 1.0
OB2 H:FLC7 3.4 65.4 1.0
CG B:ASP179 3.6 48.3 1.0
C B:SER177 3.7 52.4 1.0
OD2 B:ASP179 4.2 51.5 1.0
CB H:FLC7 4.2 65.2 1.0
CAC H:FLC7 4.2 63.0 1.0
CBC H:FLC7 4.3 65.5 1.0
C B:ILE178 4.3 47.1 1.0
N B:ASP179 4.3 44.9 1.0
CG B:ARG175 4.4 48.4 1.0
CA B:ILE178 4.5 47.9 1.0
OG B:SER177 4.5 60.8 1.0
N B:ILE178 4.5 51.2 1.0
CB B:ASP179 4.6 44.3 1.0
O B:ILE178 4.6 49.4 1.0
N B:SER177 4.7 58.4 1.0
CA B:SER177 4.8 57.3 1.0
CA B:ASP179 4.8 44.5 1.0
CD B:ARG175 4.8 45.9 1.0
CA H:FLC7 4.8 64.0 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: Mon Aug 12 08:59:52 2024

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