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Iron in PDB 4h44: 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120

Enzymatic activity of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120

All present enzymatic activity of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120:
1.10.9.1;

Protein crystallography data

The structure of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120, PDB code: 4h44 was solved by S.S.Hasan, E.Yamashita, D.Baniulis, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.55 / 2.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.127, 159.127, 364.373, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.6

Other elements in 4h44:

The structure of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 (pdb code 4h44). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120, PDB code: 4h44:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4h44

Go back to Iron Binding Sites List in 4h44
Iron binding site 1 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:31.9
occ:1.00
FE A:HEM301 0.0 31.9 1.0
HE1 A:HIS86 1.6 47.1 1.0
HE2 A:HIS86 1.9 38.1 1.0
NE2 A:HIS187 1.9 28.6 1.0
NB A:HEM301 2.0 34.0 1.0
CE1 A:HIS86 2.1 39.2 1.0
NA A:HEM301 2.1 39.5 1.0
NC A:HEM301 2.1 36.5 1.0
ND A:HEM301 2.2 30.5 1.0
NE2 A:HIS86 2.2 31.7 1.0
CE1 A:HIS187 2.8 37.0 1.0
HE1 A:HIS187 2.9 44.4 1.0
C4B A:HEM301 3.0 31.2 1.0
CD2 A:HIS187 3.1 33.5 1.0
C1B A:HEM301 3.1 36.9 1.0
C1C A:HEM301 3.1 33.1 1.0
C1A A:HEM301 3.1 32.7 1.0
C4A A:HEM301 3.1 31.3 1.0
C4D A:HEM301 3.1 38.4 1.0
C4C A:HEM301 3.1 35.5 1.0
C1D A:HEM301 3.2 45.2 1.0
HD2 A:HIS187 3.3 40.2 1.0
ND1 A:HIS86 3.4 46.2 1.0
CHC A:HEM301 3.4 34.5 1.0
CHB A:HEM301 3.4 36.0 1.0
CHA A:HEM301 3.4 36.3 1.0
CHD A:HEM301 3.5 34.6 1.0
CD2 A:HIS86 3.5 23.0 1.0
O A:HOH422 3.6 63.2 1.0
HD1 A:HIS86 3.9 55.4 1.0
ND1 A:HIS187 4.0 33.2 1.0
CG A:HIS86 4.1 31.9 1.0
CG A:HIS187 4.1 28.6 1.0
HD2 A:HIS86 4.2 27.6 1.0
HE21 A:GLN47 4.2 37.1 1.0
C3B A:HEM301 4.3 30.8 1.0
C2B A:HEM301 4.3 30.0 1.0
C3A A:HEM301 4.3 34.2 1.0
C2A A:HEM301 4.3 35.6 1.0
C2C A:HEM301 4.3 41.6 1.0
C3C A:HEM301 4.3 43.4 1.0
C3D A:HEM301 4.3 38.6 1.0
HA3 A:GLY135 4.4 44.8 1.0
C2D A:HEM301 4.4 41.6 1.0
HHC A:HEM301 4.4 41.4 1.0
HHB A:HEM301 4.4 43.2 1.0
HHA A:HEM301 4.4 43.5 1.0
HE22 A:GLN47 4.5 37.1 1.0
HHD A:HEM301 4.5 41.5 1.0
HA3 A:GLY51 4.6 38.3 1.0
HA2 A:GLY51 4.6 38.3 1.0
NE2 A:GLN47 4.6 31.0 1.0
HD2 A:PHE131 4.6 39.5 1.0
HD1 A:HIS187 4.7 39.8 1.0
HE3 A:MET54 4.8 42.0 1.0
HD12 A:LEU138 4.9 42.0 1.0
HE1 A:MET54 4.9 42.0 1.0

Iron binding site 2 out of 6 in 4h44

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Iron binding site 2 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:34.7
occ:1.00
FE A:HEM302 0.0 34.7 1.0
NA A:HEM302 2.0 23.3 1.0
NB A:HEM302 2.0 42.1 1.0
NC A:HEM302 2.1 34.4 1.0
NE2 A:HIS100 2.1 38.3 1.0
ND A:HEM302 2.1 43.0 1.0
NE2 A:HIS202 2.1 36.4 1.0
CE1 A:HIS202 3.0 32.4 1.0
CD2 A:HIS100 3.0 35.0 1.0
C4A A:HEM302 3.0 39.8 1.0
C1A A:HEM302 3.1 39.8 1.0
C1B A:HEM302 3.1 35.4 1.0
C4C A:HEM302 3.1 42.0 1.0
C1C A:HEM302 3.1 48.6 1.0
C4B A:HEM302 3.1 37.1 1.0
HE1 A:HIS202 3.1 38.9 1.0
CE1 A:HIS100 3.1 42.3 1.0
C4D A:HEM302 3.1 33.2 1.0
C1D A:HEM302 3.1 35.5 1.0
HD2 A:HIS100 3.1 42.0 1.0
CD2 A:HIS202 3.2 35.4 1.0
HE1 A:HIS100 3.3 50.7 1.0
CHB A:HEM302 3.4 39.3 1.0
CHA A:HEM302 3.4 39.2 1.0
CHD A:HEM302 3.4 35.9 1.0
CHC A:HEM302 3.4 41.7 1.0
HD2 A:HIS202 3.4 42.5 1.0
ND1 A:HIS202 4.1 35.5 1.0
CG A:HIS100 4.2 41.2 1.0
ND1 A:HIS100 4.2 44.5 1.0
HD11 A:ILE206 4.2 55.1 1.0
C3A A:HEM302 4.2 34.0 1.0
C2A A:HEM302 4.3 35.2 1.0
HG21 A:VAL104 4.3 56.8 1.0
C3C A:HEM302 4.3 42.4 1.0
C2C A:HEM302 4.3 45.0 1.0
CG A:HIS202 4.3 38.5 1.0
C2B A:HEM302 4.3 32.0 1.0
C3B A:HEM302 4.3 34.2 1.0
C3D A:HEM302 4.3 37.3 1.0
C2D A:HEM302 4.3 38.2 1.0
HHB A:HEM302 4.4 47.2 1.0
HHA A:HEM302 4.4 47.0 1.0
HHD A:HEM302 4.4 43.1 1.0
HHC A:HEM302 4.4 50.1 1.0
HG22 A:THR117 4.7 42.2 1.0
HA3 A:GLY121 4.7 46.7 1.0
HA3 A:GLY37 4.8 47.3 1.0
HA2 A:GLY121 4.9 46.7 1.0
HD1 A:HIS202 4.9 42.5 1.0
HA2 A:GLY37 4.9 47.3 1.0
HD1 A:HIS100 5.0 53.4 1.0
HD12 A:LEU124 5.0 36.1 1.0

Iron binding site 3 out of 6 in 4h44

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Iron binding site 3 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:47.8
occ:1.00
FE A:HEM303 0.0 47.8 1.0
O A:HOH401 1.7 27.3 1.0
NA A:HEM303 2.1 63.2 1.0
NC A:HEM303 2.1 60.1 1.0
NB A:HEM303 2.1 53.4 1.0
ND A:HEM303 2.1 54.9 1.0
H61 A:UMQ307 2.7 0.7 1.0
HZ B:PHE40 3.0 66.1 1.0
C1A A:HEM303 3.1 60.8 1.0
C4A A:HEM303 3.1 58.8 1.0
C4B A:HEM303 3.1 58.3 1.0
C1C A:HEM303 3.1 51.5 1.0
C1B A:HEM303 3.1 55.6 1.0
C1D A:HEM303 3.1 51.8 1.0
C4D A:HEM303 3.1 52.2 1.0
C4C A:HEM303 3.1 43.9 1.0
CHC A:HEM303 3.4 56.8 1.0
CHB A:HEM303 3.4 52.8 1.0
CHA A:HEM303 3.4 56.3 1.0
CHD A:HEM303 3.5 47.8 1.0
CZ B:PHE40 3.6 55.0 1.0
C6 A:UMQ307 3.7 0.6 1.0
HMA A:HEM302 3.8 39.0 1.0
HAAA A:HEM302 3.8 43.2 1.0
HE2 B:PHE40 3.9 69.8 1.0
HA3 A:GLY38 3.9 45.3 1.0
H62 A:UMQ307 4.0 0.7 1.0
CE2 B:PHE40 4.1 58.1 1.0
HMAA A:HEM302 4.2 39.0 1.0
O5 A:UMQ307 4.2 94.8 1.0
C2A A:HEM303 4.3 61.2 1.0
C3A A:HEM303 4.3 66.6 1.0
C3B A:HEM303 4.3 67.5 1.0
C2B A:HEM303 4.3 64.2 1.0
C2C A:HEM303 4.3 48.4 1.0
C2D A:HEM303 4.3 50.2 1.0
H A:GLY38 4.3 45.1 1.0
HHB A:HEM303 4.3 63.4 1.0
C3C A:HEM303 4.3 55.3 1.0
C3D A:HEM303 4.3 48.5 1.0
O2A A:HEM302 4.4 54.0 1.0
O A:TYR34 4.4 41.2 1.0
HA A:CYS35 4.4 50.3 1.0
HHC A:HEM303 4.4 68.2 1.0
HHA A:HEM303 4.4 67.6 1.0
HHD A:HEM303 4.4 57.3 1.0
CMA A:HEM302 4.5 32.5 1.0
O6 A:UMQ307 4.5 0.2 1.0
C5 A:UMQ307 4.5 0.8 1.0
HO61 A:UMQ307 4.6 0.2 1.0
CE1 B:PHE40 4.6 49.8 1.0
HBAA A:HEM302 4.6 56.1 1.0
CA A:GLY38 4.6 37.7 1.0
HA2 A:GLY38 4.7 45.3 1.0
HE1 B:PHE40 4.7 59.8 1.0
CAA A:HEM302 4.7 36.0 1.0
N A:GLY38 4.7 37.6 1.0
H51 A:UMQ307 4.8 0.9 1.0

Iron binding site 4 out of 6 in 4h44

Go back to Iron Binding Sites List in 4h44
Iron binding site 4 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:54.1
occ:1.00
FE C:HEM301 0.0 54.1 1.0
H1 C:TYR1 1.7 79.0 1.0
NA C:HEM301 2.0 48.3 1.0
NB C:HEM301 2.0 45.0 1.0
NC C:HEM301 2.1 36.3 1.0
ND C:HEM301 2.1 54.8 1.0
NE2 C:HIS26 2.3 58.8 1.0
N C:TYR1 2.4 65.8 1.0
H2 C:TYR1 2.4 79.0 1.0
HA C:TYR1 2.8 72.5 1.0
C1A C:HEM301 3.0 59.1 1.0
CA C:TYR1 3.0 60.4 1.0
C4A C:HEM301 3.0 58.0 1.0
C1B C:HEM301 3.1 52.6 1.0
C4D C:HEM301 3.1 57.5 1.0
C1C C:HEM301 3.1 50.9 1.0
C4C C:HEM301 3.1 46.1 1.0
C4B C:HEM301 3.1 37.4 1.0
C1D C:HEM301 3.1 52.6 1.0
H3 C:TYR1 3.2 79.0 1.0
CE1 C:HIS26 3.2 54.6 1.0
HE1 C:HIS26 3.3 65.6 1.0
CD2 C:HIS26 3.4 55.1 1.0
CHA C:HEM301 3.4 54.5 1.0
CHB C:HEM301 3.4 60.5 1.0
CHD C:HEM301 3.4 56.4 1.0
CHC C:HEM301 3.4 44.5 1.0
HD2 C:HIS26 3.6 66.1 1.0
C C:TYR1 3.7 52.4 1.0
O C:TYR1 4.0 50.9 1.0
HE3 C:TRP4 4.1 90.5 1.0
C2A C:HEM301 4.2 53.2 1.0
C3A C:HEM301 4.2 55.0 1.0
HD3 C:PRO2 4.2 50.7 1.0
C2C C:HEM301 4.3 51.6 1.0
C3C C:HEM301 4.3 47.7 1.0
C2B C:HEM301 4.3 34.6 1.0
C3B C:HEM301 4.3 46.1 1.0
C3D C:HEM301 4.3 64.1 1.0
C2D C:HEM301 4.3 56.6 1.0
HHA C:HEM301 4.3 65.3 1.0
ND1 C:HIS26 4.3 62.4 1.0
HHD C:HEM301 4.4 67.7 1.0
CB C:TYR1 4.4 64.5 1.0
HHB C:HEM301 4.4 72.7 1.0
HHC C:HEM301 4.4 53.5 1.0
CG C:HIS26 4.4 68.6 1.0
N C:PRO2 4.5 40.3 1.0
HA3 C:GLY158 4.6 69.6 1.0
HB2 C:TRP4 4.6 83.8 1.0
CG C:TYR1 4.7 58.9 1.0
H C:GLY158 4.8 73.1 1.0
CE3 C:TRP4 4.8 75.4 1.0
CD C:PRO2 4.9 42.2 1.0
HB2 C:TYR1 4.9 77.4 1.0
HB3 C:TYR1 5.0 77.4 1.0

Iron binding site 5 out of 6 in 4h44

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Iron binding site 5 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:95.2
occ:1.00
FE1 D:FES202 0.0 95.2 1.0
S1 D:FES202 2.2 81.3 1.0
S2 D:FES202 2.2 79.9 1.0
SG D:CYS126 2.4 88.4 1.0
SG D:CYS108 2.4 0.0 1.0
HB3 D:CYS108 2.6 0.5 1.0
HB3 D:HIS110 2.9 85.9 1.0
CB D:CYS108 3.0 95.5 1.0
FE2 D:FES202 3.0 82.6 1.0
HB3 D:SER131 3.2 0.1 1.0
HB3 D:CYS126 3.3 0.5 1.0
CB D:CYS126 3.3 0.3 1.0
HB2 D:CYS126 3.4 0.5 1.0
HB2 D:CYS108 3.4 0.5 1.0
HB2 D:HIS110 3.6 85.9 1.0
CB D:HIS110 3.7 71.6 1.0
H D:HIS110 3.7 0.3 1.0
HB2 D:CYS128 3.8 98.2 1.0
HB2 D:SER131 3.9 0.1 1.0
H D:LEU111 3.9 0.9 1.0
CB D:SER131 3.9 87.6 1.0
HB2 D:CYS113 4.0 75.5 1.0
HG D:SER131 4.1 1.0 1.0
HB2 D:ALA144 4.1 0.6 1.0
CA D:CYS108 4.3 85.9 1.0
H D:HIS129 4.4 1.0 1.0
HA D:CYS108 4.4 0.1 1.0
ND1 D:HIS110 4.5 81.6 1.0
H D:CYS113 4.5 0.3 1.0
N D:HIS110 4.5 84.4 1.0
OG D:SER131 4.5 0.6 1.0
CG D:HIS110 4.6 75.4 1.0
H D:THR109 4.6 0.3 1.0
H D:GLY112 4.6 0.9 1.0
H D:SER131 4.6 0.8 1.0
HH D:TYR133 4.6 0.8 1.0
CA D:HIS110 4.7 82.7 1.0
HB2 D:HIS129 4.7 0.1 1.0
N D:LEU111 4.7 92.4 1.0
CB D:CYS128 4.7 81.8 1.0
CA D:CYS126 4.8 0.2 1.0
HG22 D:VAL115 4.8 0.4 1.0
H D:CYS128 4.8 0.4 1.0
HG2 D:PRO143 4.8 0.9 1.0
OH D:TYR133 4.8 0.8 1.0
HE1 D:TYR133 4.9 0.3 1.0
N D:THR109 4.9 0.3 1.0
C D:CYS108 4.9 95.6 1.0
CB D:CYS113 5.0 63.0 1.0

Iron binding site 6 out of 6 in 4h44

Go back to Iron Binding Sites List in 4h44
Iron binding site 6 out of 6 in the 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.70 A Cytochrome B6F Complex Structure From Nostoc Pcc 7120 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:82.6
occ:1.00
FE2 D:FES202 0.0 82.6 1.0
ND1 D:HIS129 2.2 63.4 1.0
S2 D:FES202 2.2 79.9 1.0
S1 D:FES202 2.2 81.3 1.0
ND1 D:HIS110 2.3 81.6 1.0
HB2 D:HIS129 2.6 0.1 1.0
HB3 D:HIS110 2.9 85.9 1.0
FE1 D:FES202 3.0 95.2 1.0
CG D:HIS129 3.1 90.1 1.0
CE1 D:HIS129 3.2 75.6 1.0
CG D:HIS110 3.3 75.4 1.0
CE1 D:HIS110 3.3 66.0 1.0
HB2 D:CYS128 3.3 98.2 1.0
CB D:HIS129 3.3 98.5 1.0
HE1 D:HIS110 3.4 79.3 1.0
HE1 D:HIS129 3.4 90.7 1.0
CB D:HIS110 3.5 71.6 1.0
H D:HIS129 3.6 1.0 1.0
HB3 D:CYS128 3.7 98.2 1.0
HB2 D:HIS110 3.8 85.9 1.0
N D:HIS129 3.8 89.1 1.0
HG2 D:PRO143 3.9 0.9 1.0
CB D:CYS128 3.9 81.8 1.0
HB3 D:HIS129 4.0 0.1 1.0
H D:LEU111 4.0 0.9 1.0
HB2 D:LEU111 4.1 0.4 1.0
CA D:HIS129 4.2 0.5 1.0
HG D:LEU111 4.2 92.0 1.0
HD12 D:LEU111 4.2 0.7 1.0
CD2 D:HIS129 4.2 89.6 1.0
NE2 D:HIS129 4.3 87.8 1.0
NE2 D:HIS110 4.4 83.3 1.0
CD2 D:HIS110 4.4 84.4 1.0
C D:CYS128 4.5 95.3 1.0
HG3 D:PRO143 4.5 0.9 1.0
SG D:CYS126 4.6 88.4 1.0
N D:LEU111 4.6 92.4 1.0
CG D:PRO143 4.6 97.4 1.0
HB2 D:SER131 4.7 0.1 1.0
CA D:CYS128 4.8 92.5 1.0
HB3 D:SER131 4.8 0.1 1.0
CG D:LEU111 4.8 76.7 1.0
CB D:LEU111 4.9 85.3 1.0
CA D:HIS110 4.9 82.7 1.0
HB3 D:CYS108 4.9 0.5 1.0
HA D:HIS129 4.9 0.2 1.0
CD1 D:LEU111 5.0 84.8 1.0
C D:HIS129 5.0 0.7 1.0
H D:SER131 5.0 0.8 1.0

Reference:

S.S.Hasan, E.Yamashita, D.Baniulis, W.A.Cramer. Quinone-Dependent Proton Transfer Pathways in the Photosynthetic Cytochrome B6F Complex Proc.Natl.Acad.Sci.Usa V. 110 4297 2013.
ISSN: ISSN 0027-8424
PubMed: 23440205
DOI: 10.1073/PNAS.1222248110
Page generated: Sun Dec 13 15:36:01 2020

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