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Iron in PDB 2e75: Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus

Enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus

All present enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus:
1.10.99.1;

Protein crystallography data

The structure of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus, PDB code: 2e75 was solved by W.A.Cramer, E.Yamashita, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.94 / 3.55
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.164, 159.164, 362.269, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 26.7

Other elements in 2e75:

The structure of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms
Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus (pdb code 2e75). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus, PDB code: 2e75:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2e75

Go back to Iron Binding Sites List in 2e75
Iron binding site 1 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:13.4
occ:1.00
 FE A:HEM301 0.0 13.4 1.0
NB A:HEM301 1.8 5.8 1.0
NA A:HEM301 1.8 11.8 1.0
NE2 A:HIS86 1.9 8.5 1.0
NE2 A:HIS187 1.9 13.2 1.0
ND A:HEM301 2.0 15.4 1.0
NC A:HEM301 2.1 5.6 1.0
C4A A:HEM301 2.7 2.8 1.0
CE1 A:HIS187 2.7 23.8 1.0
CE1 A:HIS86 2.7 18.1 1.0
C1B A:HEM301 2.8 10.9 1.0
C4B A:HEM301 2.9 28.6 1.0
C1D A:HEM301 2.9 13.6 1.0
C4C A:HEM301 3.0 6.9 1.0
CD2 A:HIS86 3.0 7.8 1.0
C1A A:HEM301 3.0 23.9 1.0
CD2 A:HIS187 3.1 15.9 1.0
CHB A:HEM301 3.1 17.0 1.0
C4D A:HEM301 3.1 17.9 1.0
C1C A:HEM301 3.2 28.2 1.0
CHD A:HEM301 3.2 25.5 1.0
CHC A:HEM301 3.4 33.9 1.0
CHA A:HEM301 3.6 24.8 1.0
ND1 A:HIS187 3.9 22.0 1.0
ND1 A:HIS86 3.9 28.5 1.0
C3A A:HEM301 4.0 2.1 1.0
C3B A:HEM301 4.1 28.8 1.0
CG A:HIS86 4.1 12.9 1.0
C2B A:HEM301 4.1 28.2 1.0
CG A:HIS187 4.1 11.2 1.0
C2A A:HEM301 4.2 3.7 1.0
C2D A:HEM301 4.2 12.4 1.0
C3C A:HEM301 4.2 30.3 1.0
C3D A:HEM301 4.3 10.3 1.0
C2C A:HEM301 4.4 42.4 1.0

Iron binding site 2 out of 6 in 2e75

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Iron binding site 2 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:9.7
occ:1.00
 FE A:HEM302 0.0 9.7 1.0
NE2 A:HIS202 1.9 15.1 1.0
NB A:HEM302 1.9 2.6 1.0
NC A:HEM302 1.9 2.0 1.0
ND A:HEM302 1.9 11.7 1.0
NA A:HEM302 2.0 8.1 1.0
NE2 A:HIS100 2.1 7.3 1.0
CE1 A:HIS100 2.5 21.7 1.0
CE1 A:HIS202 2.7 22.8 1.0
C1D A:HEM302 2.8 7.5 1.0
C4C A:HEM302 2.8 2.0 1.0
C4B A:HEM302 2.9 2.0 1.0
CD2 A:HIS202 3.0 27.0 1.0
C1A A:HEM302 3.0 10.4 1.0
C1B A:HEM302 3.0 13.4 1.0
C1C A:HEM302 3.0 2.0 1.0
C4A A:HEM302 3.1 7.2 1.0
C4D A:HEM302 3.1 14.4 1.0
CHD A:HEM302 3.1 2.0 1.0
CHC A:HEM302 3.3 3.5 1.0
CD2 A:HIS100 3.3 27.0 1.0
CHA A:HEM302 3.4 2.0 1.0
CHB A:HEM302 3.5 3.1 1.0
ND1 A:HIS100 3.8 54.7 1.0
ND1 A:HIS202 3.9 32.4 1.0
CG A:HIS202 4.0 36.1 1.0
C3C A:HEM302 4.1 3.4 1.0
C2D A:HEM302 4.1 10.5 1.0
C3B A:HEM302 4.1 11.9 1.0
C2B A:HEM302 4.2 15.4 1.0
C2A A:HEM302 4.2 43.9 1.0
CG A:HIS100 4.2 37.1 1.0
C3A A:HEM302 4.2 36.7 1.0
C3D A:HEM302 4.3 2.0 1.0
C2C A:HEM302 4.3 2.0 1.0

Iron binding site 3 out of 6 in 2e75

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Iron binding site 3 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:36.1
occ:1.00
 FE A:HEM303 0.0 36.1 1.0
NA A:HEM303 2.0 41.4 1.0
NC A:HEM303 2.1 37.2 1.0
NB A:HEM303 2.1 32.8 1.0
OH A:QNO501 2.2 56.5 1.0
ND A:HEM303 2.2 18.0 1.0
O A:HOH1107 2.3 3.7 1.0
C4A A:HEM303 2.9 29.4 1.0
C4C A:HEM303 3.0 29.0 1.0
C1C A:HEM303 3.0 47.9 1.0
C1D A:HEM303 3.0 30.3 1.0
C1B A:HEM303 3.1 47.8 1.0
C1A A:HEM303 3.1 52.7 1.0
C4B A:HEM303 3.1 34.5 1.0
CE2 B:PHE40 3.2 69.7 1.0
CZ B:PHE40 3.2 59.7 1.0
C4D A:HEM303 3.3 30.2 1.0
CHD A:HEM303 3.3 37.6 1.0
CHB A:HEM303 3.4 49.5 1.0
CHC A:HEM303 3.5 54.3 1.0
N1 A:QNO501 3.5 63.8 1.0
C61 A:QNO501 3.5 45.8 1.0
CHA A:HEM303 3.6 50.9 1.0
C6 A:QNO501 4.0 53.9 1.0
C3A A:HEM303 4.1 39.0 1.0
C3C A:HEM303 4.1 23.1 1.0
C2C A:HEM303 4.2 21.3 1.0
C2A A:HEM303 4.3 48.9 1.0
C2D A:HEM303 4.3 29.3 1.0
C2B A:HEM303 4.3 37.9 1.0
C3B A:HEM303 4.3 23.8 1.0
C3D A:HEM303 4.4 28.2 1.0
CD2 B:PHE40 4.6 76.0 1.0
CE1 B:PHE40 4.6 63.9 1.0
C2 A:QNO501 4.6 63.4 1.0
C62 A:QNO501 4.6 61.7 1.0
O A:TYR34 4.8 39.0 1.0
O2A A:HEM302 5.0 47.9 1.0

Iron binding site 4 out of 6 in 2e75

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Iron binding site 4 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:35.0
occ:1.00
 FE C:HEM301 0.0 35.0 1.0
NA C:HEM301 1.8 20.6 1.0
NC C:HEM301 1.9 24.0 1.0
ND C:HEM301 2.0 33.7 1.0
N C:TYR1 2.0 27.9 1.0
NE2 C:HIS26 2.1 38.4 1.0
NB C:HEM301 2.1 29.7 1.0
CD2 C:HIS26 2.8 36.5 1.0
C1A C:HEM301 2.8 28.8 1.0
CA C:TYR1 2.9 38.7 1.0
C4A C:HEM301 2.9 24.4 1.0
C4D C:HEM301 2.9 44.0 1.0
C4C C:HEM301 2.9 7.1 1.0
C1C C:HEM301 3.0 37.0 1.0
C1B C:HEM301 3.0 33.0 1.0
C1D C:HEM301 3.1 50.8 1.0
CHA C:HEM301 3.1 33.6 1.0
C4B C:HEM301 3.2 24.4 1.0
CE1 C:HIS26 3.3 52.0 1.0
CHB C:HEM301 3.3 32.4 1.0
CHD C:HEM301 3.5 27.9 1.0
CHC C:HEM301 3.5 8.2 1.0
C C:TYR1 3.6 38.3 1.0
O C:TYR1 4.0 43.3 1.0
CG C:HIS26 4.0 51.8 1.0
C2A C:HEM301 4.1 33.7 1.0
C3A C:HEM301 4.1 40.5 1.0
C3C C:HEM301 4.1 23.4 1.0
C2C C:HEM301 4.2 28.1 1.0
ND1 C:HIS26 4.2 53.8 1.0
C3D C:HEM301 4.2 36.6 1.0
CB C:TYR1 4.2 48.7 1.0
C2D C:HEM301 4.3 49.4 1.0
C2B C:HEM301 4.3 46.8 1.0
C3B C:HEM301 4.4 39.1 1.0
N C:PRO2 4.4 37.5 1.0
CE3 C:TRP4 4.7 61.1 1.0
CG C:TYR1 4.7 51.3 1.0
CD C:PRO2 4.7 39.5 1.0
OD1 C:ASN154 4.9 34.2 1.0
CZ3 C:TRP4 4.9 57.4 1.0

Iron binding site 5 out of 6 in 2e75

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Iron binding site 5 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:0.1
occ:1.00
 FE1 D:FES200 0.0 0.1 1.0
SG D:CYS108 1.3 86.5 1.0
S1 D:FES200 2.2 95.9 1.0
S2 D:FES200 2.2 89.5 1.0
SG D:CYS126 2.4 85.1 1.0
OG D:SER131 3.0 76.7 1.0
CB D:CYS108 3.1 82.8 1.0
FE2 D:FES200 3.2 90.2 1.0
CB D:CYS126 3.3 75.0 1.0
CB D:HIS110 3.7 60.8 1.0
OH D:TYR133 4.2 70.2 1.0
N D:THR109 4.3 84.3 1.0
N D:HIS110 4.3 72.2 1.0
CB D:ALA144 4.3 98.9 1.0
CA D:CYS108 4.3 85.2 1.0
CB D:SER131 4.3 84.9 1.0
N D:LEU111 4.4 78.2 1.0
ND1 D:HIS110 4.5 76.2 1.0
C D:CYS108 4.5 85.8 1.0
CG D:HIS110 4.6 71.4 1.0
CA D:HIS110 4.6 67.3 1.0
CA D:CYS126 4.8 82.3 1.0
C D:HIS110 4.9 78.4 1.0
N D:SER131 5.0 93.2 1.0
CB D:HIS129 5.0 96.2 1.0

Iron binding site 6 out of 6 in 2e75

Go back to Iron Binding Sites List in 2e75
Iron binding site 6 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus


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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:90.2
occ:1.00
 FE2 D:FES200 0.0 90.2 1.0
S2 D:FES200 2.2 89.5 1.0
ND1 D:HIS129 2.2 62.8 1.0
S1 D:FES200 2.2 95.9 1.0
CB D:HIS129 2.7 96.2 1.0
ND1 D:HIS110 2.8 76.2 1.0
CG D:HIS129 2.8 85.5 1.0
FE1 D:FES200 3.2 0.1 1.0
CE1 D:HIS129 3.4 95.6 1.0
CE1 D:HIS110 3.6 0.2 1.0
CG D:HIS110 3.8 71.4 1.0
CA D:HIS129 3.9 99.2 1.0
N D:HIS129 4.0 0.0 1.0
CB D:HIS110 4.0 60.8 1.0
CD2 D:HIS129 4.0 94.7 1.0
N D:LEU111 4.1 78.2 1.0
SG D:CYS126 4.1 85.1 1.0
SG D:CYS108 4.1 86.5 1.0
CB D:CYS128 4.2 98.4 1.0
NE2 D:HIS129 4.3 75.2 1.0
CB D:LEU111 4.3 63.4 1.0
C D:CYS128 4.6 0.3 1.0
CG D:PRO143 4.6 0.5 1.0
C D:HIS129 4.7 99.1 1.0
NE2 D:HIS110 4.7 0.9 1.0
CA D:LEU111 4.7 71.2 1.0
CD2 D:HIS110 4.9 1.0 1.0
CG D:LEU111 4.9 78.5 1.0
SG D:CYS113 4.9 0.6 1.0
CA D:CYS128 5.0 99.2 1.0

Reference:

E.Yamashita, H.Zhang, W.A.Cramer. Structure of the Cytochrome B(6)F Complex: Quinone Analogue Inhibitors As Ligands of Heme C(N) J.Mol.Biol. V. 370 39 2007.
ISSN: ISSN 0022-2836
PubMed: 17498743
DOI: 10.1016/J.JMB.2007.04.011
Page generated: Thu Jul 17 00:49:43 2025

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