Atomistry » Iron » PDB 6zkh-6zzu » 6zkj
Atomistry »
  Iron »
    PDB 6zkh-6zzu »
      6zkj »

Iron in PDB 6zkj: Complex I with Nadh, OPEN3

Enzymatic activity of Complex I with Nadh, OPEN3

All present enzymatic activity of Complex I with Nadh, OPEN3:
1.6.99.3; 7.1.1.2;

Other elements in 6zkj:

The structure of Complex I with Nadh, OPEN3 also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Complex I with Nadh, OPEN3 (pdb code 6zkj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Complex I with Nadh, OPEN3, PDB code: 6zkj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 1 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:21.4
occ:1.00
FE1 1:SF4501 0.0 21.4 1.0
S2 1:SF4501 2.3 19.3 1.0
S3 1:SF4501 2.3 31.8 1.0
S4 1:SF4501 2.3 62.6 1.0
SG 1:CYS365 2.3 19.0 1.0
FE2 1:SF4501 2.7 37.0 1.0
FE3 1:SF4501 2.7 26.8 1.0
FE4 1:SF4501 2.8 31.5 1.0
CB 1:CYS365 2.9 18.9 1.0
OG 1:SER358 3.3 17.9 1.0
S1 1:SF4501 4.2 57.3 1.0
CA 1:CYS365 4.3 20.5 1.0
CD2 1:LEU407 4.4 33.2 1.0
N 1:CYS359 4.4 22.4 1.0
CB 1:SER358 4.5 24.2 1.0
CB 1:LEU407 4.7 20.1 1.0
C 1:CYS365 4.7 23.1 1.0
N 1:ARG366 4.8 21.9 1.0
N 1:GLY360 4.8 20.3 1.0
CA 1:SER358 4.8 27.5 1.0
CG 1:LEU407 5.0 30.2 1.0
C 1:SER358 5.0 32.5 1.0

Iron binding site 2 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 2 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:37.0
occ:1.00
FE2 1:SF4501 0.0 37.0 1.0
S3 1:SF4501 2.3 31.8 1.0
S1 1:SF4501 2.3 57.3 1.0
S4 1:SF4501 2.4 62.6 1.0
FE3 1:SF4501 2.5 26.8 1.0
FE4 1:SF4501 2.5 31.5 1.0
FE1 1:SF4501 2.7 21.4 1.0
SG 1:CYS362 3.1 32.3 1.0
N 1:CYS362 3.4 24.3 1.0
S2 1:SF4501 3.8 19.3 1.0
CB 1:CYS362 3.9 18.4 1.0
CB 1:GLN361 4.0 19.0 1.0
CA 1:CYS362 4.1 19.8 1.0
N 1:GLN361 4.1 20.0 1.0
CB 1:CYS365 4.2 18.9 1.0
O 1:CYS362 4.3 20.2 1.0
C 1:GLN361 4.3 20.6 1.0
CA 1:GLN361 4.4 40.4 1.0
CB 1:ILE404 4.6 26.5 1.0
C 1:CYS362 4.6 15.0 1.0
CD1 1:ILE404 4.7 17.8 1.0
SG 1:CYS365 4.7 19.0 1.0
N 1:ILE404 4.7 26.2 1.0
CG1 1:ILE404 4.8 16.7 1.0
SG 1:CYS359 4.8 35.1 1.0
OE1 1:GLN361 4.9 19.1 1.0
CG 1:GLN361 4.9 21.2 1.0

Iron binding site 3 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 3 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:26.8
occ:1.00
FE3 1:SF4501 0.0 26.8 1.0
S4 1:SF4501 2.3 62.6 1.0
S1 1:SF4501 2.3 57.3 1.0
S2 1:SF4501 2.4 19.3 1.0
FE4 1:SF4501 2.4 31.5 1.0
FE2 1:SF4501 2.5 37.0 1.0
FE1 1:SF4501 2.7 21.4 1.0
SG 1:CYS359 3.0 35.1 1.0
S3 1:SF4501 3.7 31.8 1.0
CD 1:PRO203 3.8 19.3 1.0
CB 1:CYS359 3.9 20.5 1.0
N 1:CYS359 4.0 22.4 1.0
CB 1:GLN361 4.1 19.0 1.0
CG 1:PRO203 4.1 24.1 1.0
N 1:GLN361 4.2 20.0 1.0
CA 1:CYS359 4.4 25.4 1.0
N 1:GLY360 4.4 20.3 1.0
OE1 1:GLN361 4.5 19.1 1.0
CG1 1:ILE185 4.6 22.8 1.0
C 1:CYS359 4.7 19.5 1.0
SG 1:CYS405 4.7 29.5 1.0
CA 1:GLN361 4.8 40.4 1.0
CD1 1:ILE185 4.8 36.1 1.0
OG 1:SER358 5.0 17.9 1.0
SG 1:CYS365 5.0 19.0 1.0

Iron binding site 4 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 4 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:31.5
occ:1.00
FE4 1:SF4501 0.0 31.5 1.0
S2 1:SF4501 2.3 19.3 1.0
S1 1:SF4501 2.3 57.3 1.0
S3 1:SF4501 2.3 31.8 1.0
FE3 1:SF4501 2.4 26.8 1.0
FE2 1:SF4501 2.5 37.0 1.0
FE1 1:SF4501 2.8 21.4 1.0
SG 1:CYS405 3.0 29.5 1.0
N 1:CYS405 3.7 18.8 1.0
S4 1:SF4501 3.8 62.6 1.0
CB 1:CYS405 3.9 20.5 1.0
CG 1:PRO203 4.2 24.1 1.0
CA 1:CYS405 4.2 22.5 1.0
O 1:CYS405 4.4 25.9 1.0
C 1:CYS405 4.5 20.6 1.0
CB 1:ILE404 4.5 26.5 1.0
N 1:ILE404 4.6 26.2 1.0
CD 1:PRO203 4.6 19.3 1.0
C 1:ILE404 4.7 24.4 1.0
CB 1:LEU407 4.7 20.1 1.0
CB 1:PRO203 4.8 22.6 1.0
CD1 1:ILE185 4.8 36.1 1.0
CA 1:ILE404 4.8 24.5 1.0
SG 1:CYS365 4.9 19.0 1.0
SG 1:CYS362 4.9 32.3 1.0
CB 1:CYS365 4.9 18.9 1.0

Iron binding site 5 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 5 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:0.7
occ:1.00
FE1 2:FES300 0.0 0.7 1.0
S2 2:FES300 2.2 47.5 1.0
S1 2:FES300 2.2 50.7 1.0
SG 2:CYS108 2.3 51.1 1.0
SG 2:CYS103 2.3 43.9 1.0
FE2 2:FES300 3.0 45.6 1.0
CB 2:CYS103 3.3 33.9 1.0
CB 2:CYS108 3.3 42.8 1.0
OG1 2:THR105 3.5 53.4 1.0
N 2:CYS108 4.2 37.5 1.0
CA 2:CYS144 4.3 30.2 1.0
CA 2:CYS108 4.3 39.0 1.0
N 2:LEU145 4.4 28.7 1.0
SD 2:MET153 4.5 59.0 1.0
CA 2:CYS103 4.6 35.2 1.0
C 2:CYS103 4.6 29.0 1.0
O 2:CYS103 4.6 37.6 1.0
SG 2:CYS144 4.7 58.3 1.0
N 2:THR105 4.8 33.6 1.0
CB 2:CYS144 4.8 37.9 1.0
CB 2:THR105 4.8 34.1 1.0
CG 2:MET153 4.9 54.7 1.0
C 2:CYS144 4.9 30.9 1.0
SG 2:CYS148 4.9 40.6 1.0

Iron binding site 6 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 6 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe300

b:45.6
occ:1.00
FE2 2:FES300 0.0 45.6 1.0
S2 2:FES300 2.2 47.5 1.0
S1 2:FES300 2.2 50.7 1.0
SG 2:CYS148 2.3 40.6 1.0
SG 2:CYS144 2.3 58.3 1.0
FE1 2:FES300 3.0 0.7 1.0
CB 2:CYS144 3.4 37.9 1.0
N 2:GLY146 3.7 32.1 1.0
CB 2:CYS148 3.7 42.9 1.0
CA 2:CYS144 3.8 30.2 1.0
CA 2:CYS148 4.1 41.9 1.0
N 2:ALA147 4.1 40.0 1.0
N 2:LEU145 4.1 28.7 1.0
CA 2:GLY146 4.2 31.2 1.0
C 2:CYS144 4.2 30.9 1.0
N 2:CYS148 4.2 44.4 1.0
OG1 2:THR105 4.2 53.4 1.0
N 1:GLY103 4.3 31.2 1.0
CA 1:PRO102 4.4 35.1 1.0
SG 2:CYS103 4.6 43.9 1.0
C 2:GLY146 4.6 37.8 1.0
C 2:ALA147 4.7 45.3 1.0
C 2:LEU145 4.8 34.6 1.0
SG 2:CYS108 4.9 51.1 1.0
O 1:GLU101 4.9 52.6 1.0
CB 2:PRO107 4.9 31.8 1.0
C 1:PRO102 4.9 33.9 1.0
CG 2:PRO107 5.0 31.9 1.0
O 2:CYS144 5.0 34.8 1.0

Iron binding site 7 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 7 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE1 3:SF4801 0.0 74.9 1.0
S2 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
SG 3:CYS114 2.3 35.3 1.0
FE4 3:SF4801 2.7 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE3 3:SF4801 2.7 74.9 1.0
CB 3:CYS114 3.4 19.7 1.0
S1 3:SF4801 3.9 74.9 1.0
CG 3:GLN117 4.0 17.7 1.0
NE2 3:HIS101 4.2 46.2 1.0
NE2 3:GLN117 4.4 21.3 1.0
CD 3:GLN117 4.4 17.3 1.0
CB 3:LEU116 4.4 14.2 1.0
N 3:GLN117 4.6 55.5 1.0
N 3:GLY206 4.6 8.3 1.0
CD2 3:LEU116 4.7 9.6 1.0
CA 3:CYS114 4.8 22.1 1.0
SG 3:CYS108 4.8 22.0 1.0
CA 3:VAL205 4.8 13.8 1.0
SG 3:CYS105 4.8 28.4 1.0
CB 3:GLN110 4.8 13.6 1.0
CB 3:GLN117 4.9 28.1 1.0
CE1 3:HIS101 4.9 58.8 1.0
CG 3:GLN110 4.9 18.1 1.0
CB 3:VAL205 5.0 24.6 1.0

Iron binding site 8 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 8 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE2 3:SF4801 0.0 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
SG 3:CYS105 2.3 28.4 1.0
FE3 3:SF4801 2.7 74.9 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE4 3:SF4801 2.7 74.9 1.0
NE2 3:GLN117 3.4 21.3 1.0
CB 3:CYS105 3.4 8.8 1.0
CA 3:CYS105 3.5 5.2 1.0
N 3:CYS105 3.8 10.7 1.0
S2 3:SF4801 3.9 74.9 1.0
CG 3:GLN117 4.1 17.7 1.0
CE 4:MET342 4.1 53.3 1.0
CD 3:GLN117 4.1 17.3 1.0
NE2 3:HIS101 4.2 46.2 1.0
C 3:ASP104 4.7 12.1 1.0
CD2 3:HIS101 4.7 47.9 1.0
SG 3:CYS108 4.8 22.0 1.0
SG 3:CYS114 4.8 35.3 1.0
C 3:CYS105 4.8 14.8 1.0
CB 3:CYS108 4.9 19.0 1.0
CG1 4:ILE346 4.9 17.6 1.0

Iron binding site 9 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 9 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE3 3:SF4801 0.0 74.9 1.0
NE2 3:HIS101 1.9 46.2 1.0
S2 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
S4 3:SF4801 2.3 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE4 3:SF4801 2.7 74.9 1.0
CE1 3:HIS101 2.8 58.8 1.0
CD2 3:HIS101 2.9 47.9 1.0
S3 3:SF4801 3.9 74.9 1.0
ND1 3:HIS101 3.9 33.8 1.0
CG 3:HIS101 4.0 51.9 1.0
CD2 3:LEU116 4.3 9.6 1.0
O 3:PRO102 4.4 26.9 1.0
CE 4:MET342 4.5 53.3 1.0
CB 3:ARG152 4.7 33.1 1.0
SG 3:CYS105 4.7 28.4 1.0
CG 3:ARG152 4.7 42.8 1.0
SG 3:CYS114 4.8 35.3 1.0
SG 3:CYS108 4.9 22.0 1.0
CD 3:ARG152 4.9 60.9 1.0
N 3:GLY206 5.0 8.3 1.0

Iron binding site 10 out of 28 in 6zkj

Go back to Iron Binding Sites List in 6zkj
Iron binding site 10 out of 28 in the Complex I with Nadh, OPEN3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Complex I with Nadh, OPEN3 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:74.9
occ:1.00
FE4 3:SF4801 0.0 74.9 1.0
S2 3:SF4801 2.3 74.9 1.0
S3 3:SF4801 2.3 74.9 1.0
S1 3:SF4801 2.3 74.9 1.0
SG 3:CYS108 2.3 22.0 1.0
FE1 3:SF4801 2.7 74.9 1.0
FE2 3:SF4801 2.7 74.9 1.0
FE3 3:SF4801 2.7 74.9 1.0
CB 3:CYS108 3.1 19.0 1.0
S4 3:SF4801 3.9 74.9 1.0
N 3:GLY206 4.2 8.3 1.0
CD 3:ARG152 4.3 60.9 1.0
CA 3:GLY206 4.4 12.3 1.0
CB 3:GLN110 4.5 13.6 1.0
NE2 3:HIS101 4.5 46.2 1.0
CA 3:CYS105 4.5 5.2 1.0
CA 3:CYS108 4.6 13.1 1.0
SG 3:CYS114 4.7 35.3 1.0
N 3:CYS105 4.8 10.7 1.0
NE 3:ARG152 4.8 50.7 1.0
SG 3:CYS105 4.8 28.4 1.0
N 3:GLY111 4.9 10.6 1.0
C 3:ASP104 4.9 12.1 1.0
CG 3:ARG152 4.9 42.8 1.0
NH1 3:ARG152 4.9 35.5 1.0
O 3:ASP104 5.0 15.0 1.0

Reference:

D.Kampjut, L.A.Sazanov. The Coupling Mechanism of Mammalian Respiratory Complex I. Science V. 370 2020.
ISSN: ESSN 1095-9203
PubMed: 32972993
DOI: 10.1126/SCIENCE.ABC4209
Page generated: Wed Aug 7 19:36:00 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy