Atomistry » Iron » PDB 6xz8-6yf4 » 6y11
Atomistry »
  Iron »
    PDB 6xz8-6yf4 »
      6y11 »

Iron in PDB 6y11: Respiratory Complex I From Thermus Thermophilus

Protein crystallography data

The structure of Respiratory Complex I From Thermus Thermophilus, PDB code: 6y11 was solved by J.Gutierrez-Fernandez, G.S.Minhas, L.A.Sazanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.67 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.280, 340.890, 263.300, 90.00, 100.57, 90.00
R / Rfree (%) 20.4 / 22.9

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 64;

Binding sites:

The binding sites of Iron atom in the Respiratory Complex I From Thermus Thermophilus (pdb code 6y11). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 64 binding sites of Iron where determined in the Respiratory Complex I From Thermus Thermophilus, PDB code: 6y11:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 1 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:75.0
occ:1.00
 FE1 1:SF4501 0.0 75.0 1.0
S4 1:SF4501 2.3 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
SG 1:CYS356 2.3 0.9 1.0
FE2 1:SF4501 2.6 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.8 75.0 1.0
CB 1:CYS356 3.1 47.8 1.0
N 1:CYS356 3.4 61.2 1.0
CA 1:CYS356 3.9 52.7 1.0
S1 1:SF4501 3.9 75.0 1.0
SG 1:CYS400 4.2 84.2 1.0
CB 1:PHE399 4.3 87.1 1.0
CB 1:CYS359 4.3 0.9 1.0
N 1:PHE399 4.4 85.3 1.0
N 1:CYS400 4.4 93.8 1.0
C 1:LYS355 4.5 63.7 1.0
SG 1:CYS359 4.5 100.0 1.0
CB 1:LYS355 4.5 77.4 1.0
N 1:LYS355 4.6 53.8 1.0
CA 1:LYS355 4.8 66.3 1.0
CA 1:PHE399 4.8 92.2 1.0
SG 1:CYS353 4.8 72.4 1.0
CB 1:SER398 4.9 73.1 1.0
O 1:CYS356 4.9 52.0 1.0
C 1:CYS356 4.9 59.5 1.0

Iron binding site 2 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 2 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:75.0
occ:1.00
 FE2 1:SF4501 0.0 75.0 1.0
S4 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
SG 1:CYS359 2.3 100.0 1.0
FE1 1:SF4501 2.6 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.7 75.0 1.0
CB 1:CYS359 3.1 0.9 1.0
OG 1:SER352 3.2 59.4 1.0
S2 1:SF4501 3.8 75.0 1.0
CB 1:SER352 4.3 58.2 1.0
SG 1:CYS400 4.4 84.2 1.0
N 1:CYS353 4.4 64.5 1.0
CD2 1:LEU402 4.6 0.1 1.0
CA 1:CYS359 4.6 0.0 1.0
CB 1:LEU402 4.6 0.8 1.0
N 1:GLY354 4.6 84.0 1.0
SG 1:CYS356 4.7 0.9 1.0
CB 1:CYS356 4.7 47.8 1.0
N 1:ARG360 4.7 0.6 1.0
CA 1:SER352 4.8 72.6 1.0
SG 1:CYS353 4.9 72.4 1.0
C 1:CYS359 4.9 0.9 1.0
N 1:CYS356 4.9 61.2 1.0
CG 1:LEU402 5.0 97.1 1.0

Iron binding site 3 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 3 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:75.0
occ:1.00
 FE3 1:SF4501 0.0 75.0 1.0
SG 1:CYS400 1.8 84.2 1.0
S4 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
FE2 1:SF4501 2.7 75.0 1.0
FE1 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.7 75.0 1.0
CB 1:CYS400 3.4 84.5 1.0
S3 1:SF4501 3.9 75.0 1.0
O 1:CYS400 3.9 79.0 1.0
CB 1:LEU402 4.0 0.8 1.0
N 1:CYS400 4.0 93.8 1.0
CA 1:CYS400 4.1 90.1 1.0
CD1 1:ILE181 4.2 96.2 1.0
C 1:CYS400 4.3 86.7 1.0
CG 1:PRO199 4.6 84.2 1.0
N 1:LEU402 4.7 0.9 1.0
SG 1:CYS359 4.8 100.0 1.0
SG 1:CYS356 4.8 0.9 1.0
SG 1:CYS353 4.8 72.4 1.0
CD1 1:LEU402 4.9 86.1 1.0
CG 1:LEU402 4.9 97.1 1.0
CA 1:LEU402 4.9 1.0 1.0

Iron binding site 4 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 4 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:75.0
occ:1.00
 FE4 1:SF4501 0.0 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
SG 1:CYS353 2.3 72.4 1.0
FE2 1:SF4501 2.7 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE1 1:SF4501 2.8 75.0 1.0
CB 1:CYS353 3.3 61.1 1.0
N 1:GLY354 3.5 84.0 1.0
N 1:LYS355 3.6 53.8 1.0
N 1:CYS353 3.7 64.5 1.0
CA 1:CYS353 3.9 57.0 1.0
S4 1:SF4501 4.0 75.0 1.0
C 1:CYS353 4.1 86.1 1.0
CB 1:LYS355 4.1 77.4 1.0
SG 1:CYS400 4.3 84.2 1.0
OG 1:SER352 4.3 59.4 1.0
N 1:CYS356 4.4 61.2 1.0
CA 1:LYS355 4.4 66.3 1.0
C 1:GLY354 4.5 55.0 1.0
CA 1:GLY354 4.5 71.8 1.0
CD 1:PRO199 4.8 85.1 1.0
CD1 1:ILE181 4.8 96.2 1.0
SG 1:CYS356 4.9 0.9 1.0
SG 1:CYS359 4.9 100.0 1.0
C 1:SER352 4.9 67.1 1.0
C 1:LYS355 5.0 63.7 1.0

Iron binding site 5 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 5 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:75.5
occ:1.00
 FE1 2:FES201 0.0 75.5 1.0
S1 2:FES201 2.2 75.5 1.0
S2 2:FES201 2.2 75.5 1.0
SG 2:CYS88 2.3 83.5 1.0
SG 2:CYS83 2.3 0.8 1.0
FE2 2:FES201 3.0 75.5 1.0
CB 2:CYS88 3.4 77.1 1.0
CB 2:CYS83 3.5 0.5 1.0
CG2 2:VAL133 4.2 0.1 1.0
N 2:CYS88 4.2 76.3 1.0
CA 2:CYS124 4.2 0.1 1.0
N 2:LEU125 4.3 97.5 1.0
OG1 2:THR85 4.3 85.8 1.0
CB 2:THR85 4.4 90.7 1.0
CA 2:CYS88 4.4 75.0 1.0
SG 2:CYS124 4.5 0.4 1.0
N 2:THR85 4.7 84.9 1.0
CB 2:VAL133 4.7 0.4 1.0
CB 2:CYS124 4.8 0.8 1.0
CA 2:CYS83 4.8 95.0 1.0
O 2:SER127 4.8 0.2 1.0
C 2:CYS83 4.8 94.1 1.0
C 2:CYS124 4.8 1.0 1.0
O 2:THR85 4.9 0.1 1.0
O 2:CYS83 4.9 92.4 1.0
CA 2:THR85 5.0 91.8 1.0
SG 2:CYS128 5.0 0.8 1.0

Iron binding site 6 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 6 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:75.5
occ:1.00
 FE2 2:FES201 0.0 75.5 1.0
S1 2:FES201 2.2 75.5 1.0
S2 2:FES201 2.2 75.5 1.0
SG 2:CYS124 2.3 0.4 1.0
SG 2:CYS128 2.3 0.8 1.0
FE1 2:FES201 3.0 75.5 1.0
CB 2:CYS124 3.6 0.8 1.0
CB 2:CYS128 3.6 0.1 1.0
CA 2:CYS128 3.9 0.3 1.0
N 2:CYS128 4.0 1.0 1.0
N 2:GLY126 4.0 0.0 1.0
CA 2:CYS124 4.1 0.1 1.0
N 2:SER127 4.2 0.6 1.0
C 2:SER127 4.3 0.4 1.0
N 1:GLY99 4.3 0.1 1.0
N 2:LEU125 4.4 97.5 1.0
CA 1:PRO98 4.4 0.9 1.0
CA 2:GLY126 4.4 0.9 1.0
C 2:CYS124 4.6 1.0 1.0
O 2:SER127 4.6 0.2 1.0
CB 1:PRO98 4.6 0.1 1.0
SG 2:CYS83 4.7 0.8 1.0
C 2:GLY126 4.7 1.0 1.0
CB 2:SER87 4.8 1.0 1.0
C 1:PRO98 4.9 0.0 1.0
CA 2:SER127 4.9 0.7 1.0
SG 2:CYS88 5.0 83.5 1.0

Iron binding site 7 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 7 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:52.3
occ:1.00
 FE1 3:SF4801 0.0 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
S3 3:SF4801 2.3 52.3 1.0
SG 3:CYS128 2.3 73.9 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE3 3:SF4801 2.7 52.3 1.0
FE2 3:SF4801 2.8 52.3 1.0
CB 3:CYS128 3.2 69.8 1.0
S1 3:SF4801 3.9 52.3 1.0
CG 3:GLN131 4.1 41.4 1.0
NE2 3:HIS115 4.2 80.3 1.0
CD 3:GLN131 4.5 32.7 1.0
N 3:GLN131 4.5 32.3 1.0
CB 3:LEU130 4.6 61.0 1.0
CB 3:GLN131 4.6 42.3 1.0
CA 3:CYS128 4.7 72.4 1.0
CB 3:LYS124 4.7 80.0 1.0
SG 3:CYS122 4.7 55.8 1.0
NE2 3:GLN131 4.8 43.1 1.0
SG 3:CYS119 4.8 57.7 1.0
CD2 3:HIS115 4.8 79.8 1.0
CG1 3:VAL232 4.9 74.3 1.0
OE1 3:GLN131 4.9 32.6 1.0
CD2 3:LEU130 5.0 73.7 1.0

Iron binding site 8 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 8 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:52.3
occ:1.00
 FE2 3:SF4801 0.0 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
S1 3:SF4801 2.3 52.3 1.0
S3 3:SF4801 2.3 52.3 1.0
SG 3:CYS119 2.3 57.7 1.0
FE3 3:SF4801 2.7 52.3 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE1 3:SF4801 2.8 52.3 1.0
CA 3:CYS119 3.1 48.3 1.0
CB 3:CYS119 3.2 49.2 1.0
N 3:CYS119 3.5 57.7 1.0
NE2 3:GLN131 3.7 43.1 1.0
S2 3:SF4801 3.9 52.3 1.0
CG 3:GLN131 4.2 41.4 1.0
CD 3:GLN131 4.2 32.7 1.0
C 3:ASP118 4.4 66.1 1.0
CG1 4:ILE325 4.5 56.0 1.0
C 3:CYS119 4.5 59.2 1.0
CB 3:CYS122 4.6 60.3 1.0
SD 4:MET321 4.6 79.9 1.0
CD2 3:HIS115 4.7 79.8 1.0
SG 3:CYS122 4.8 55.8 1.0
NE2 3:HIS115 4.8 80.3 1.0
SG 3:CYS128 4.9 73.9 1.0
O 3:CYS119 4.9 57.8 1.0

Iron binding site 9 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 9 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:52.3
occ:1.00
 FE3 3:SF4801 0.0 52.3 1.0
NE2 3:HIS115 2.1 80.3 1.0
S1 3:SF4801 2.3 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
CD2 3:HIS115 2.4 79.8 1.0
FE2 3:SF4801 2.7 52.3 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE1 3:SF4801 2.7 52.3 1.0
CE1 3:HIS115 3.4 80.2 1.0
CG 3:HIS115 3.7 87.5 1.0
S3 3:SF4801 3.9 52.3 1.0
ND1 3:HIS115 4.1 79.3 1.0
CE 4:MET321 4.4 48.7 1.0
SD 4:MET321 4.6 79.9 1.0
CD2 3:LEU130 4.6 73.7 1.0
SG 3:CYS119 4.7 57.7 1.0
CG 3:ARG180 4.7 77.2 1.0
SG 3:CYS122 4.7 55.8 1.0
SG 3:CYS128 4.8 73.9 1.0
CB 3:HIS115 4.9 91.1 1.0
CD 3:ARG180 5.0 76.5 1.0
N 3:CYS119 5.0 57.7 1.0

Iron binding site 10 out of 64 in 6y11

Go back to Iron Binding Sites List in 6y11
Iron binding site 10 out of 64 in the Respiratory Complex I From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Respiratory Complex I From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:52.3
occ:1.00
 FE4 3:SF4801 0.0 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S1 3:SF4801 2.3 52.3 1.0
SG 3:CYS122 2.3 55.8 1.0
S3 3:SF4801 2.3 52.3 1.0
FE1 3:SF4801 2.7 52.3 1.0
FE2 3:SF4801 2.7 52.3 1.0
FE3 3:SF4801 2.7 52.3 1.0
CB 3:CYS122 3.0 60.3 1.0
S4 3:SF4801 3.8 52.3 1.0
CB 3:LYS124 4.1 80.0 1.0
CA 3:CYS119 4.3 48.3 1.0
N 3:CYS119 4.4 57.7 1.0
NE2 3:HIS115 4.4 80.3 1.0
CD 3:ARG180 4.5 76.5 1.0
CA 3:CYS122 4.5 56.1 1.0
NE 3:ARG180 4.6 69.8 1.0
C 3:ASP118 4.6 66.1 1.0
SG 3:CYS128 4.7 73.9 1.0
N 3:GLY233 4.7 56.8 1.0
SG 3:CYS119 4.9 57.7 1.0
O 3:ASP118 4.9 76.8 1.0
CD2 3:HIS115 4.9 79.8 1.0
CB 3:ASP118 5.0 75.5 1.0

Reference:

J.Gutierrez-Fernandez, K.Kaszuba, G.S.Minhas, R.Baradaran, M.Tambalo, D.T.Gallagher, L.A.Sazanov. Key Role of Quinone in the Mechanism of Respiratory Complex I. Nat Commun V. 11 4135 2020.
ISSN: ESSN 2041-1723
PubMed: 32811817
DOI: 10.1038/S41467-020-17957-0
Page generated: Wed Aug 7 15:48:53 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