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Iron in PDB 2e76: Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus

Enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus

All present enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus:
1.10.99.1;

Protein crystallography data

The structure of Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus, PDB code: 2e76 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) 41.27 / 3.41
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.227, 157.227, 363.295, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 25.6

Other elements in 2e76:

The structure of Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) From M.Laminosus (pdb code 2e76). 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus, PDB code: 2e76:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 2e76

Go back to Iron Binding Sites List in 2e76
Iron binding site 1 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:21.3
occ:1.00
 FE A:HEM301 0.0 21.3 1.0
NB A:HEM301 1.7 14.7 1.0
NE2 A:HIS86 1.7 11.5 1.0
NA A:HEM301 1.9 16.5 1.0
NE2 A:HIS187 1.9 7.6 1.0
ND A:HEM301 2.0 14.7 1.0
NC A:HEM301 2.1 18.5 1.0
CE1 A:HIS187 2.6 10.9 1.0
CE1 A:HIS86 2.7 35.4 1.0
C4B A:HEM301 2.8 26.1 1.0
CD2 A:HIS86 2.8 27.1 1.0
C1B A:HEM301 2.9 39.4 1.0
C4A A:HEM301 2.9 27.8 1.0
C1A A:HEM301 2.9 14.7 1.0
C1D A:HEM301 3.0 21.8 1.0
C4D A:HEM301 3.0 17.8 1.0
C4C A:HEM301 3.1 5.5 1.0
C1C A:HEM301 3.1 14.3 1.0
CD2 A:HIS187 3.1 17.5 1.0
CHC A:HEM301 3.3 31.1 1.0
CHA A:HEM301 3.3 25.0 1.0
CHB A:HEM301 3.3 30.6 1.0
CHD A:HEM301 3.4 15.8 1.0
ND1 A:HIS187 3.8 25.5 1.0
ND1 A:HIS86 3.8 16.9 1.0
CG A:HIS86 3.9 35.0 1.0
C3B A:HEM301 4.0 41.5 1.0
CG A:HIS187 4.1 16.2 1.0
C2B A:HEM301 4.1 42.2 1.0
C3A A:HEM301 4.1 16.9 1.0
C2A A:HEM301 4.2 18.6 1.0
C2D A:HEM301 4.2 9.8 1.0
C3C A:HEM301 4.3 20.7 1.0
C3D A:HEM301 4.3 30.6 1.0
C2C A:HEM301 4.4 36.9 1.0
CA A:GLY135 4.9 37.6 1.0

Iron binding site 2 out of 6 in 2e76

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Iron binding site 2 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:23.6
occ:1.00
 FE A:HEM302 0.0 23.6 1.0
NC A:HEM302 1.9 10.2 1.0
NA A:HEM302 1.9 18.1 1.0
ND A:HEM302 1.9 32.1 1.0
NE2 A:HIS202 1.9 32.4 1.0
NB A:HEM302 1.9 25.1 1.0
NE2 A:HIS100 2.1 22.5 1.0
CE1 A:HIS202 2.7 54.2 1.0
CE1 A:HIS100 2.7 38.4 1.0
C1A A:HEM302 2.8 18.3 1.0
C1C A:HEM302 2.9 12.2 1.0
C4D A:HEM302 2.9 45.1 1.0
C4B A:HEM302 2.9 28.7 1.0
C4C A:HEM302 2.9 14.2 1.0
C1D A:HEM302 3.0 31.3 1.0
C4A A:HEM302 3.0 27.7 1.0
CD2 A:HIS202 3.1 30.4 1.0
C1B A:HEM302 3.1 35.8 1.0
CHA A:HEM302 3.2 27.5 1.0
CHC A:HEM302 3.2 24.0 1.0
CD2 A:HIS100 3.3 21.1 1.0
CHD A:HEM302 3.4 30.3 1.0
CHB A:HEM302 3.5 27.8 1.0
ND1 A:HIS202 3.9 31.1 1.0
ND1 A:HIS100 4.0 36.4 1.0
CG A:HIS202 4.1 35.2 1.0
C2C A:HEM302 4.1 18.4 1.0
C2A A:HEM302 4.1 41.0 1.0
C3C A:HEM302 4.1 23.6 1.0
C3D A:HEM302 4.2 14.8 1.0
C3B A:HEM302 4.2 25.0 1.0
C3A A:HEM302 4.2 42.1 1.0
C2D A:HEM302 4.2 19.8 1.0
CG A:HIS100 4.3 39.4 1.0
C2B A:HEM302 4.3 26.2 1.0

Iron binding site 3 out of 6 in 2e76

Go back to Iron Binding Sites List in 2e76
Iron binding site 3 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:49.1
occ:1.00
 FE A:HEM303 0.0 49.1 1.0
OBD B:TDS1202 1.5 64.4 1.0
NA A:HEM303 1.9 64.7 1.0
NB A:HEM303 2.0 48.1 1.0
ND A:HEM303 2.1 48.5 1.0
NC A:HEM303 2.1 44.0 1.0
O A:HOH1106 2.5 14.4 1.0
CAM B:TDS1202 2.8 78.8 1.0
C4A A:HEM303 2.9 50.5 1.0
C1B A:HEM303 3.0 41.1 1.0
C1D A:HEM303 3.0 45.7 1.0
C4C A:HEM303 3.0 36.3 1.0
C1A A:HEM303 3.0 87.7 1.0
C4B A:HEM303 3.1 48.4 1.0
C1C A:HEM303 3.2 55.0 1.0
C4D A:HEM303 3.2 55.0 1.0
CHB A:HEM303 3.2 47.6 1.0
CHD A:HEM303 3.3 53.4 1.0
CAL B:TDS1202 3.3 85.5 1.0
CHA A:HEM303 3.5 67.7 1.0
OAK B:TDS1202 3.6 77.7 1.0
CHC A:HEM303 3.6 54.5 1.0
CZ B:PHE40 3.6 93.7 1.0
CAN B:TDS1202 3.8 81.7 1.0
C3A A:HEM303 4.1 55.0 1.0
CE1 B:PHE40 4.2 66.7 1.0
C2A A:HEM303 4.2 73.2 1.0
OAO B:TDS1202 4.2 90.2 1.0
C2B A:HEM303 4.2 36.2 1.0
C3C A:HEM303 4.2 42.7 1.0
C3B A:HEM303 4.3 30.2 1.0
CAD B:TDS1202 4.3 80.9 1.0
C2D A:HEM303 4.3 38.3 1.0
C2C A:HEM303 4.3 39.0 1.0
C3D A:HEM303 4.4 59.6 1.0
CMA A:HEM302 4.8 16.6 1.0
O2A A:HEM302 4.8 50.2 1.0
O A:TYR34 4.8 38.0 1.0
CE2 B:PHE40 4.9 0.2 1.0
CAF B:TDS1202 4.9 84.1 1.0
CA A:GLY38 5.0 37.2 1.0
CAJ B:TDS1202 5.0 63.2 1.0

Iron binding site 4 out of 6 in 2e76

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Iron binding site 4 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:31.9
occ:1.00
 FE C:HEM301 0.0 31.9 1.0
NA C:HEM301 1.9 22.9 1.0
N C:TYR1 2.0 52.8 1.0
NC C:HEM301 2.0 25.8 1.0
ND C:HEM301 2.1 40.7 1.0
NB C:HEM301 2.1 33.2 1.0
NE2 C:HIS26 2.1 46.8 1.0
C4A C:HEM301 2.9 15.5 1.0
C4C C:HEM301 2.9 17.6 1.0
C1A C:HEM301 2.9 40.9 1.0
CA C:TYR1 2.9 59.4 1.0
CE1 C:HIS26 3.0 57.8 1.0
C1B C:HEM301 3.0 27.8 1.0
C1D C:HEM301 3.0 49.3 1.0
C4D C:HEM301 3.1 48.4 1.0
C4B C:HEM301 3.1 39.8 1.0
CD2 C:HIS26 3.1 61.6 1.0
C1C C:HEM301 3.2 20.6 1.0
CHD C:HEM301 3.3 35.2 1.0
CHB C:HEM301 3.3 37.6 1.0
CHA C:HEM301 3.4 27.5 1.0
CHC C:HEM301 3.6 18.3 1.0
C C:TYR1 3.8 55.5 1.0
C2A C:HEM301 4.1 36.9 1.0
ND1 C:HIS26 4.1 80.2 1.0
C3A C:HEM301 4.1 44.6 1.0
C3C C:HEM301 4.2 29.2 1.0
O C:TYR1 4.2 49.0 1.0
CG C:HIS26 4.2 70.4 1.0
CB C:TYR1 4.3 69.9 1.0
C2B C:HEM301 4.3 49.5 1.0
C2C C:HEM301 4.3 11.6 1.0
C3B C:HEM301 4.3 34.8 1.0
C2D C:HEM301 4.3 60.8 1.0
C3D C:HEM301 4.3 41.2 1.0
CE3 C:TRP4 4.5 78.3 1.0
N C:PRO2 4.6 50.9 1.0
CG C:TYR1 4.7 75.0 1.0
CZ3 C:TRP4 4.8 73.9 1.0
CD C:PRO2 5.0 52.3 1.0

Iron binding site 5 out of 6 in 2e76

Go back to Iron Binding Sites List in 2e76
Iron binding site 5 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:72.3
occ:1.00
 FE1 D:FES200 0.0 72.3 1.0
SG D:CYS126 2.0 77.8 1.0
SG D:CYS108 2.0 56.1 1.0
S2 D:FES200 2.2 59.3 1.0
S1 D:FES200 2.2 70.4 1.0
FE2 D:FES200 2.9 69.8 1.0
CB D:CYS126 3.0 45.4 1.0
OG D:SER131 3.4 0.1 1.0
CB D:HIS110 3.6 55.5 1.0
CB D:CYS108 3.7 36.8 1.0
ND1 D:HIS110 4.0 52.7 1.0
CB D:CYS128 4.0 70.4 1.0
CG D:HIS110 4.2 53.7 1.0
CA D:CYS126 4.3 62.2 1.0
N D:HIS129 4.4 72.5 1.0
ND1 D:HIS129 4.5 51.3 1.0
CB D:SER131 4.6 82.1 1.0
N D:SER131 4.7 68.5 1.0
CA D:HIS110 4.7 62.2 1.0
N D:GLY130 4.7 67.8 1.0
C D:CYS126 4.8 73.8 1.0
CA D:CYS128 4.8 70.9 1.0
N D:HIS110 4.8 66.0 1.0
N D:CYS128 4.8 65.6 1.0
N D:LEU111 4.9 64.4 1.0
N D:CYS113 4.9 46.5 1.0
CA D:CYS108 5.0 58.6 1.0
N D:GLY112 5.0 52.0 1.0

Iron binding site 6 out of 6 in 2e76

Go back to Iron Binding Sites List in 2e76
Iron binding site 6 out of 6 in the Crystal Structure of the Cytochrome B6F Complex with Tridecyl- Stigmatellin (Tds) 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 Tridecyl- Stigmatellin (Tds) From M.Laminosus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:69.8
occ:1.00
 FE2 D:FES200 0.0 69.8 1.0
ND1 D:HIS129 1.7 51.3 1.0
ND1 D:HIS110 2.1 52.7 1.0
S1 D:FES200 2.2 70.4 1.0
S2 D:FES200 2.2 59.3 1.0
CE1 D:HIS129 2.5 71.7 1.0
CE1 D:HIS110 2.9 64.8 1.0
FE1 D:FES200 2.9 72.3 1.0
CG D:HIS129 3.0 62.8 1.0
CG D:HIS110 3.2 53.7 1.0
CB D:HIS129 3.5 70.6 1.0
N D:HIS129 3.6 72.5 1.0
CB D:HIS110 3.7 55.5 1.0
CB D:CYS128 3.7 70.4 1.0
NE2 D:HIS129 3.7 61.9 1.0
CD2 D:HIS129 3.9 52.9 1.0
NE2 D:HIS110 4.1 60.0 1.0
CA D:HIS129 4.1 67.3 1.0
C D:CYS128 4.2 74.2 1.0
N D:LEU111 4.2 64.4 1.0
CD2 D:HIS110 4.3 46.8 1.0
CA D:CYS128 4.5 70.9 1.0
SG D:CYS108 4.6 56.1 1.0
CD2 D:LEU111 4.6 28.6 1.0
SG D:CYS126 4.7 77.8 1.0
CD1 D:LEU111 4.8 32.7 1.0
C D:HIS129 4.8 66.5 1.0
CA D:HIS110 4.9 62.2 1.0
CB D:LEU111 4.9 53.2 1.0
N D:GLY130 5.0 67.8 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 00:49:46 2025

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