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Iron in PDB 4ogq: Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex

Enzymatic activity of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex

All present enzymatic activity of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex:
1.10.9.1;

Protein crystallography data

The structure of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex, PDB code: 4ogq was solved by S.S.Hasan, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.57 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.228, 159.228, 365.879, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.2

Other elements in 4ogq:

The structure of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex 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 Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex (pdb code 4ogq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex, PDB code: 4ogq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 1 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:48.2
occ:1.00
FE A:HEM301 0.0 48.2 1.0
NB A:HEM301 2.1 55.3 1.0
NC A:HEM301 2.1 65.7 1.0
NA A:HEM301 2.1 63.8 1.0
ND A:HEM301 2.1 54.5 1.0
NE2 A:HIS187 2.3 39.4 1.0
NE2 A:HIS86 2.4 37.9 1.0
C4D A:HEM301 3.1 52.0 1.0
C4B A:HEM301 3.1 44.7 1.0
C1D A:HEM301 3.1 52.0 1.0
C4C A:HEM301 3.1 52.1 1.0
C1C A:HEM301 3.1 52.9 1.0
C1A A:HEM301 3.1 45.2 1.0
C1B A:HEM301 3.1 60.3 1.0
C4A A:HEM301 3.1 45.6 1.0
CD2 A:HIS86 3.2 37.4 1.0
CE1 A:HIS187 3.3 49.6 1.0
CD2 A:HIS187 3.3 42.2 1.0
CHA A:HEM301 3.4 46.9 1.0
CHD A:HEM301 3.4 52.6 1.0
CHC A:HEM301 3.4 48.5 1.0
CE1 A:HIS86 3.5 45.5 1.0
CHB A:HEM301 3.5 56.1 1.0
C3D A:HEM301 4.3 59.2 1.0
C2D A:HEM301 4.3 51.9 1.0
C3B A:HEM301 4.3 49.4 1.0
C2B A:HEM301 4.3 47.9 1.0
C3C A:HEM301 4.3 69.4 1.0
C2C A:HEM301 4.3 59.7 1.0
C3A A:HEM301 4.3 50.0 1.0
C2A A:HEM301 4.3 54.3 1.0
CG A:HIS86 4.4 55.7 1.0
ND1 A:HIS187 4.4 52.0 1.0
CG A:HIS187 4.4 46.6 1.0
ND1 A:HIS86 4.5 44.7 1.0
NE2 A:GLN47 4.6 44.4 1.0

Iron binding site 2 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 2 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:51.9
occ:1.00
FE A:HEM302 0.0 51.9 1.0
NA A:HEM302 2.0 43.7 1.0
NB A:HEM302 2.0 73.8 1.0
NC A:HEM302 2.1 60.4 1.0
ND A:HEM302 2.1 71.2 1.0
NE2 A:HIS202 2.4 40.7 1.0
NE2 A:HIS100 2.5 53.1 1.0
CD2 A:HIS100 3.0 52.3 1.0
C4A A:HEM302 3.0 59.3 1.0
C1C A:HEM302 3.0 64.8 1.0
C1A A:HEM302 3.0 53.6 1.0
C4B A:HEM302 3.0 54.2 1.0
C1B A:HEM302 3.1 54.7 1.0
C4C A:HEM302 3.1 61.7 1.0
C4D A:HEM302 3.1 51.7 1.0
C1D A:HEM302 3.1 61.6 1.0
CD2 A:HIS202 3.3 44.7 1.0
CHC A:HEM302 3.4 61.6 1.0
CHB A:HEM302 3.4 58.4 1.0
CHA A:HEM302 3.4 54.6 1.0
CE1 A:HIS202 3.4 65.5 1.0
CHD A:HEM302 3.5 55.0 1.0
CE1 A:HIS100 3.7 75.7 1.0
C2C A:HEM302 4.2 61.1 1.0
C3A A:HEM302 4.2 56.6 1.0
C3C A:HEM302 4.3 59.8 1.0
C2A A:HEM302 4.3 53.8 1.0
C3B A:HEM302 4.3 59.7 1.0
C2B A:HEM302 4.3 57.4 1.0
C3D A:HEM302 4.3 57.9 1.0
CG A:HIS100 4.3 54.3 1.0
C2D A:HEM302 4.3 56.5 1.0
CG A:HIS202 4.5 61.9 1.0
ND1 A:HIS202 4.5 73.8 1.0
ND1 A:HIS100 4.6 76.7 1.0

Iron binding site 3 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 3 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:59.3
occ:1.00
FE A:HEM303 0.0 59.3 1.0
NB A:HEM303 2.1 69.3 1.0
NC A:HEM303 2.1 82.1 1.0
NA A:HEM303 2.1 85.5 1.0
ND A:HEM303 2.1 57.6 1.0
O A:HOH401 2.5 59.7 1.0
C1C A:HEM303 3.1 71.0 1.0
C4B A:HEM303 3.1 71.1 1.0
C4A A:HEM303 3.1 71.1 1.0
C1B A:HEM303 3.1 63.8 1.0
C1A A:HEM303 3.1 68.5 1.0
C4C A:HEM303 3.1 54.9 1.0
C4D A:HEM303 3.1 52.1 1.0
C1D A:HEM303 3.1 49.2 1.0
CHC A:HEM303 3.4 75.1 1.0
CHB A:HEM303 3.5 60.1 1.0
CHD A:HEM303 3.5 49.5 1.0
CHA A:HEM303 3.5 52.9 1.0
CZ B:PHE40 3.8 52.1 1.0
C6 B:UMQ203 3.8 0.9 0.5
CE2 B:PHE40 4.0 62.1 1.0
C2C A:HEM303 4.3 64.7 1.0
C3A A:HEM303 4.3 83.6 1.0
C3B A:HEM303 4.3 68.8 1.0
C2B A:HEM303 4.3 66.2 1.0
C2A A:HEM303 4.3 81.2 1.0
C3C A:HEM303 4.3 65.4 1.0
C3D A:HEM303 4.3 52.0 1.0
C2D A:HEM303 4.3 56.0 1.0
CMA A:HEM302 4.4 49.0 1.0
O A:TYR34 4.4 61.3 1.0
CA A:GLY38 4.5 47.5 1.0
O6 B:UMQ203 4.5 1.0 0.5
O2A A:HEM302 4.5 65.7 1.0
O5 B:UMQ203 4.5 88.3 0.5
N A:GLY38 4.6 48.3 1.0
CAA A:HEM302 4.6 46.2 1.0
C5 B:UMQ203 4.7 94.5 0.5
CE1 B:PHE40 4.7 50.2 1.0
CBA A:HEM302 4.9 58.3 1.0

Iron binding site 4 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 4 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:62.9
occ:1.00
FE C:HEM301 0.0 62.9 1.0
NA C:HEM301 2.0 60.9 1.0
NC C:HEM301 2.0 46.4 1.0
NB C:HEM301 2.0 62.3 1.0
ND C:HEM301 2.1 71.6 1.0
NE2 C:HIS26 2.5 73.8 1.0
N C:TYR1 2.6 87.3 1.0
C4A C:HEM301 3.0 71.3 1.0
C1A C:HEM301 3.0 75.7 1.0
C1B C:HEM301 3.1 59.9 1.0
C1C C:HEM301 3.1 63.5 1.0
C4C C:HEM301 3.1 59.2 1.0
C4B C:HEM301 3.1 49.5 1.0
C4D C:HEM301 3.1 74.1 1.0
C1D C:HEM301 3.1 69.4 1.0
CA C:TYR1 3.2 77.6 1.0
CD2 C:HIS26 3.4 72.6 1.0
CHB C:HEM301 3.4 68.1 1.0
CHC C:HEM301 3.4 50.8 1.0
CHA C:HEM301 3.4 71.9 1.0
CHD C:HEM301 3.4 65.4 1.0
CE1 C:HIS26 3.6 88.8 1.0
C C:TYR1 3.8 81.6 1.0
O C:TYR1 4.1 79.1 1.0
C3A C:HEM301 4.2 67.9 1.0
C2A C:HEM301 4.2 73.6 1.0
C2C C:HEM301 4.3 60.1 1.0
C2B C:HEM301 4.3 60.4 1.0
C3B C:HEM301 4.3 58.0 1.0
C3C C:HEM301 4.3 55.9 1.0
C3D C:HEM301 4.3 80.8 1.0
C2D C:HEM301 4.3 71.7 1.0
CB C:TYR1 4.5 77.1 1.0
CG C:HIS26 4.6 82.8 1.0
ND1 C:HIS26 4.6 0.6 1.0
N C:PRO2 4.7 73.3 1.0
CG C:TYR1 4.7 81.0 1.0
CE3 C:TRP4 4.9 82.1 1.0
ND2 C:ASN154 5.0 0.1 1.0
CD C:PRO2 5.0 68.1 1.0

Iron binding site 5 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 5 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe205

b:0.2
occ:1.00
FE1 D:FES205 0.0 0.2 1.0
S2 D:FES205 2.2 97.6 1.0
S1 D:FES205 2.2 96.5 1.0
SG D:CYS108 2.3 0.4 1.0
SG D:CYS126 2.3 0.7 1.0
CB D:CYS108 3.0 98.5 1.0
FE2 D:FES205 3.1 0.2 1.0
CB D:CYS126 3.3 0.6 1.0
OG D:SER131 4.1 0.4 1.0
CB D:SER131 4.2 0.6 1.0
CB D:HIS110 4.2 0.9 1.0
CB D:CYS128 4.4 98.8 1.0
CB D:CYS113 4.5 93.4 1.0
CA D:CYS108 4.5 99.3 1.0
ND1 D:HIS110 4.5 0.9 1.0
N D:CYS113 4.7 99.2 1.0
CA D:CYS126 4.7 0.9 1.0
O D:CYS113 4.8 0.5 1.0
N D:HIS129 4.8 0.9 1.0
ND1 D:HIS129 4.9 0.1 1.0
CG D:HIS110 4.9 0.8 1.0
N D:LEU111 4.9 0.3 1.0

Iron binding site 6 out of 6 in 4ogq

Go back to Iron Binding Sites List in 4ogq
Iron binding site 6 out of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe205

b:0.2
occ:1.00
FE2 D:FES205 0.0 0.2 1.0
ND1 D:HIS129 2.1 0.1 1.0
ND1 D:HIS110 2.1 0.9 1.0
S2 D:FES205 2.2 97.6 1.0
S1 D:FES205 2.2 96.5 1.0
CE1 D:HIS110 2.9 0.7 1.0
CG D:HIS129 3.0 0.1 1.0
CE1 D:HIS129 3.1 0.4 1.0
FE1 D:FES205 3.1 0.2 1.0
CG D:HIS110 3.2 0.8 1.0
CB D:HIS129 3.3 0.7 1.0
CB D:HIS110 3.6 0.9 1.0
N D:HIS129 3.8 0.9 1.0
CB D:CYS128 3.9 98.8 1.0
NE2 D:HIS110 4.1 0.1 1.0
CD2 D:HIS129 4.1 0.2 1.0
CA D:HIS129 4.1 0.3 1.0
NE2 D:HIS129 4.1 0.9 1.0
CD2 D:HIS110 4.2 0.9 1.0
CB D:LEU111 4.3 0.6 1.0
CG D:PRO143 4.5 0.9 1.0
C D:CYS128 4.5 0.3 1.0
N D:LEU111 4.5 0.3 1.0
SG D:CYS126 4.6 0.7 1.0
SG D:CYS108 4.6 0.4 1.0
OG D:SER131 4.7 0.4 1.0
CA D:CYS128 4.8 0.0 1.0
CA D:HIS110 4.9 0.1 1.0
C D:HIS110 4.9 0.8 1.0
C D:HIS129 4.9 0.2 1.0

Reference:

S.S.Hasan, W.A.Cramer. Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex. Structure V. 22 1008 2014.
ISSN: ISSN 0969-2126
PubMed: 24931468
DOI: 10.1016/J.STR.2014.05.004
Page generated: Mon Aug 5 08:09:45 2024

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