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Iron in PDB 4h0l: Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno

Enzymatic activity of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno

All present enzymatic activity of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno:
1.10.9.1;

Protein crystallography data

The structure of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno, PDB code: 4h0l 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) 48.45 / 3.25
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.133, 159.133, 362.250, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 24.7

Other elements in 4h0l:

The structure of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno (pdb code 4h0l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno, PDB code: 4h0l:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4h0l

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Iron binding site 1 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:47.0
occ:1.00
FE A:HEM302 0.0 47.0 1.0
NA A:HEM302 1.9 60.3 1.0
NE2 A:HIS86 2.0 46.4 1.0
NB A:HEM302 2.0 48.5 1.0
NE2 A:HIS187 2.1 48.4 1.0
NC A:HEM302 2.1 52.0 1.0
ND A:HEM302 2.1 59.0 1.0
CE1 A:HIS187 2.9 54.7 1.0
CE1 A:HIS86 2.9 57.6 1.0
HE1 A:HIS187 2.9 65.7 1.0
C1A A:HEM302 3.0 51.7 1.0
C4A A:HEM302 3.0 66.6 1.0
HE1 A:HIS86 3.0 69.1 1.0
C1B A:HEM302 3.1 54.0 1.0
C4B A:HEM302 3.1 56.8 1.0
C4C A:HEM302 3.1 51.1 1.0
CD2 A:HIS86 3.1 56.2 1.0
C1C A:HEM302 3.1 48.5 1.0
C4D A:HEM302 3.1 54.4 1.0
C1D A:HEM302 3.1 56.6 1.0
CD2 A:HIS187 3.2 46.1 1.0
HD2 A:HIS86 3.3 67.4 1.0
CHB A:HEM302 3.4 58.7 1.0
CHA A:HEM302 3.4 48.3 1.0
CHD A:HEM302 3.5 53.2 1.0
CHC A:HEM302 3.5 57.8 1.0
HD2 A:HIS187 3.5 55.4 1.0
ND1 A:HIS86 4.0 49.8 1.0
ND1 A:HIS187 4.1 56.4 1.0
CG A:HIS86 4.1 56.0 1.0
C2A A:HEM302 4.2 49.5 1.0
C3A A:HEM302 4.2 44.9 1.0
HA3 A:GLY135 4.2 76.6 1.0
CG A:HIS187 4.2 51.1 1.0
C3B A:HEM302 4.3 61.4 1.0
C3C A:HEM302 4.3 58.0 1.0
C2B A:HEM302 4.3 68.5 1.0
C2C A:HEM302 4.3 54.1 1.0
C2D A:HEM302 4.4 46.5 1.0
C3D A:HEM302 4.4 49.4 1.0
HHB A:HEM302 4.4 70.4 1.0
HHA A:HEM302 4.4 57.9 1.0
HHD A:HEM302 4.4 63.8 1.0
HHC A:HEM302 4.4 69.4 1.0
HA2 A:GLY51 4.6 68.7 1.0
HD12 A:LEU138 4.7 60.7 1.0
HD2 A:PHE131 4.7 72.9 1.0
HA2 A:GLY135 4.8 76.6 1.0
HD1 A:HIS86 4.8 59.8 1.0
HA3 A:GLY51 4.8 68.7 1.0
HD1 A:HIS187 4.8 67.7 1.0
HE3 A:MET54 4.9 65.5 1.0
OE1 A:GLN47 4.9 55.7 1.0
CA A:GLY135 5.0 63.8 1.0
HE1 A:MET54 5.0 65.5 1.0

Iron binding site 2 out of 6 in 4h0l

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Iron binding site 2 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:52.0
occ:1.00
FE A:HEM303 0.0 52.0 1.0
NA A:HEM303 2.0 48.2 1.0
NC A:HEM303 2.0 53.3 1.0
ND A:HEM303 2.1 57.6 1.0
NB A:HEM303 2.1 52.5 1.0
NE2 A:HIS202 2.1 62.4 1.0
NE2 A:HIS100 2.1 60.8 1.0
C4C A:HEM303 3.0 54.2 1.0
CE1 A:HIS202 3.0 58.7 1.0
C1A A:HEM303 3.0 50.3 1.0
C1D A:HEM303 3.0 56.1 1.0
C4A A:HEM303 3.0 57.4 1.0
C1C A:HEM303 3.1 50.7 1.0
C4D A:HEM303 3.1 58.0 1.0
CD2 A:HIS100 3.1 59.2 1.0
C4B A:HEM303 3.1 54.8 1.0
C1B A:HEM303 3.1 51.2 1.0
CE1 A:HIS100 3.1 61.7 1.0
HE1 A:HIS202 3.1 70.5 1.0
CD2 A:HIS202 3.2 56.8 1.0
HD2 A:HIS100 3.2 71.1 1.0
HE1 A:HIS100 3.3 74.0 1.0
CHD A:HEM303 3.4 47.7 1.0
HD2 A:HIS202 3.4 68.1 1.0
CHA A:HEM303 3.4 54.5 1.0
CHB A:HEM303 3.4 55.7 1.0
CHC A:HEM303 3.5 51.3 1.0
ND1 A:HIS202 4.1 55.7 1.0
ND1 A:HIS100 4.2 71.8 1.0
C3C A:HEM303 4.2 55.3 1.0
C3A A:HEM303 4.2 57.4 1.0
C2A A:HEM303 4.2 54.9 1.0
CG A:HIS100 4.2 71.5 1.0
CG A:HIS202 4.2 71.6 1.0
C2C A:HEM303 4.3 53.5 1.0
C2D A:HEM303 4.3 66.4 1.0
C3D A:HEM303 4.3 41.1 1.0
C3B A:HEM303 4.3 50.6 1.0
C2B A:HEM303 4.3 47.6 1.0
HHD A:HEM303 4.3 57.2 1.0
HD11 A:ILE206 4.3 55.7 1.0
HHA A:HEM303 4.4 65.4 1.0
HHB A:HEM303 4.4 66.8 1.0
HHC A:HEM303 4.4 61.6 1.0
HG21 A:VAL104 4.5 67.8 1.0
HA3 A:GLY121 4.7 71.4 1.0
HG22 A:THR117 4.7 77.7 1.0
HA2 A:GLY121 4.8 71.4 1.0
HD1 A:HIS202 4.9 66.8 1.0
HD12 A:LEU124 5.0 67.7 1.0
HD1 A:HIS100 5.0 86.1 1.0

Iron binding site 3 out of 6 in 4h0l

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Iron binding site 3 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe304

b:73.8
occ:1.00
FE A:HEM304 0.0 73.8 1.0
O A:HOH402 2.0 58.1 1.0
NA A:HEM304 2.0 94.1 1.0
NB A:HEM304 2.1 89.5 1.0
NC A:HEM304 2.1 86.8 1.0
ND A:HEM304 2.1 82.2 1.0
OH A:QNO308 2.5 84.0 1.0
HZ B:PHE40 2.9 0.9 1.0
C1A A:HEM304 3.0 89.2 1.0
C4B A:HEM304 3.0 85.5 1.0
C1C A:HEM304 3.0 75.8 1.0
C4D A:HEM304 3.1 68.6 1.0
C4A A:HEM304 3.1 90.0 1.0
H61 A:QNO308 3.1 0.4 1.0
C1B A:HEM304 3.1 86.4 1.0
C4C A:HEM304 3.2 78.8 1.0
C1D A:HEM304 3.2 76.4 1.0
HE2 B:PHE40 3.2 0.9 1.0
CHA A:HEM304 3.3 85.8 1.0
CHC A:HEM304 3.4 80.2 1.0
CZ B:PHE40 3.4 95.8 1.0
CHB A:HEM304 3.5 87.0 1.0
CHD A:HEM304 3.6 71.8 1.0
CE2 B:PHE40 3.6 0.2 1.0
N1 A:QNO308 3.7 0.9 1.0
C61 A:QNO308 3.9 97.0 1.0
HAAA A:HEM303 4.1 74.2 1.0
HMA A:HEM303 4.2 75.5 1.0
C2A A:HEM304 4.2 79.6 1.0
C6 A:QNO308 4.2 99.6 1.0
C3B A:HEM304 4.2 85.6 1.0
C3A A:HEM304 4.2 78.3 1.0
C2B A:HEM304 4.3 86.4 1.0
C2C A:HEM304 4.3 66.2 1.0
HHA A:HEM304 4.3 0.0 1.0
C3D A:HEM304 4.3 79.4 1.0
C3C A:HEM304 4.3 76.2 1.0
HHC A:HEM304 4.4 96.2 1.0
HA3 A:GLY38 4.4 72.0 1.0
C2D A:HEM304 4.4 69.4 1.0
O A:TYR34 4.5 87.1 1.0
HHB A:HEM304 4.5 0.4 1.0
H211 A:QNO308 4.5 0.2 1.0
HMAA A:HEM303 4.5 75.5 1.0
HHD A:HEM304 4.5 86.2 1.0
CE1 B:PHE40 4.6 96.6 1.0
C2 A:QNO308 4.6 99.9 1.0
HA A:CYS35 4.7 73.8 1.0
O2A A:HEM303 4.7 65.8 1.0
H A:GLY38 4.7 80.3 1.0
CMA A:HEM303 4.8 62.9 1.0
HE1 B:PHE40 4.8 0.9 1.0
CD2 B:PHE40 4.8 97.8 1.0
HBAA A:HEM303 4.9 81.9 1.0
C62 A:QNO308 5.0 98.5 1.0

Iron binding site 4 out of 6 in 4h0l

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Iron binding site 4 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe302

b:75.9
occ:1.00
FE C:HEM302 0.0 75.9 1.0
H1 C:TYR1 1.8 91.1 1.0
NC C:HEM302 2.0 67.4 1.0
NA C:HEM302 2.0 63.2 1.0
ND C:HEM302 2.0 76.0 1.0
NB C:HEM302 2.1 70.6 1.0
H2 C:TYR1 2.1 91.1 1.0
NE2 C:HIS26 2.2 84.7 1.0
N C:TYR1 2.3 75.9 1.0
HA C:TYR1 2.9 97.9 1.0
C4C C:HEM302 2.9 63.8 1.0
C1D C:HEM302 3.0 79.0 1.0
C4A C:HEM302 3.0 68.0 1.0
C1B C:HEM302 3.1 74.5 1.0
C1A C:HEM302 3.1 78.7 1.0
C4D C:HEM302 3.1 90.9 1.0
C1C C:HEM302 3.1 74.2 1.0
CA C:TYR1 3.1 81.6 1.0
H3 C:TYR1 3.1 91.1 1.0
CE1 C:HIS26 3.2 73.7 1.0
C4B C:HEM302 3.2 61.2 1.0
CD2 C:HIS26 3.2 84.1 1.0
CHD C:HEM302 3.3 79.1 1.0
HE1 C:HIS26 3.3 88.5 1.0
CHB C:HEM302 3.4 82.0 1.0
HD2 C:HIS26 3.4 0.9 1.0
CHA C:HEM302 3.4 87.2 1.0
CHC C:HEM302 3.5 59.7 1.0
C C:TYR1 3.8 72.6 1.0
HE3 C:TRP4 3.9 0.5 1.0
C3C C:HEM302 4.1 62.7 1.0
C2C C:HEM302 4.2 72.7 1.0
HHD C:HEM302 4.2 95.0 1.0
C3A C:HEM302 4.3 91.3 1.0
C2D C:HEM302 4.3 84.6 1.0
O C:TYR1 4.3 62.4 1.0
C2A C:HEM302 4.3 81.9 1.0
C3D C:HEM302 4.3 81.8 1.0
ND1 C:HIS26 4.3 69.8 1.0
HD3 C:PRO2 4.3 91.2 1.0
HHA C:HEM302 4.3 0.6 1.0
C2B C:HEM302 4.3 73.6 1.0
CG C:HIS26 4.3 89.6 1.0
HHB C:HEM302 4.3 98.4 1.0
C3B C:HEM302 4.4 68.6 1.0
HHC C:HEM302 4.4 71.6 1.0
CB C:TYR1 4.4 0.3 1.0
N C:PRO2 4.5 63.1 1.0
HB2 C:TRP4 4.6 0.5 1.0
CE3 C:TRP4 4.6 0.6 1.0
HA3 C:GLY158 4.7 0.7 1.0
CG C:TYR1 4.8 92.4 1.0
HZ3 C:TRP4 4.8 0.3 1.0
CD C:PRO2 4.9 76.0 1.0
HB2 C:TYR1 4.9 0.6 1.0
H C:GLY158 4.9 99.1 1.0

Iron binding site 5 out of 6 in 4h0l

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Iron binding site 5 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:0.2
occ:1.00
FE1 D:FES200 0.0 0.2 1.0
SG D:CYS126 2.1 0.3 1.0
SG D:CYS108 2.1 0.9 1.0
S1 D:FES200 2.2 0.1 1.0
S2 D:FES200 2.2 0.6 1.0
HB3 D:HIS110 2.8 0.8 1.0
HB3 D:CYS126 2.9 0.1 1.0
FE2 D:FES200 3.0 0.9 1.0
CB D:CYS126 3.0 0.7 1.0
HB2 D:CYS126 3.2 0.1 1.0
OG D:SER131 3.4 0.1 1.0
HB3 D:CYS108 3.5 0.3 1.0
CB D:CYS108 3.5 0.1 1.0
HB2 D:HIS110 3.6 0.8 1.0
HB2 D:SER131 3.6 0.0 1.0
H D:HIS110 3.6 0.9 1.0
CB D:HIS110 3.6 0.0 1.0
HB2 D:ALA144 3.7 0.4 1.0
HG D:SER131 3.7 0.1 1.0
H D:LEU111 3.9 0.5 1.0
H D:HIS129 3.9 0.8 1.0
HD1 D:HIS110 4.0 0.4 1.0
HB2 D:CYS108 4.0 0.3 1.0
CB D:SER131 4.0 0.3 1.0
HB2 D:CYS128 4.1 0.3 1.0
N D:HIS110 4.3 0.4 1.0
HB2 D:HIS129 4.4 0.1 1.0
CA D:CYS126 4.5 0.6 1.0
H D:SER131 4.5 0.1 1.0
ND1 D:HIS110 4.5 0.5 1.0
CA D:HIS110 4.5 0.2 1.0
CG D:HIS110 4.6 0.4 1.0
H D:THR109 4.6 0.1 1.0
HH D:TYR133 4.6 0.6 1.0
CB D:ALA144 4.6 1.0 1.0
HD1 D:HIS129 4.6 0.3 1.0
HB3 D:SER131 4.7 0.0 1.0
N D:LEU111 4.7 0.7 1.0
CA D:CYS108 4.7 0.1 1.0
HB2 D:CYS113 4.7 0.6 1.0
N D:HIS129 4.7 0.8 1.0
HG2 D:PRO143 4.7 0.9 1.0
HA D:CYS126 4.8 1.0 1.0
N D:SER131 4.8 0.8 1.0
HA D:CYS108 4.8 0.2 1.0
HB1 D:ALA144 4.9 0.4 1.0
N D:THR109 4.9 0.9 1.0
H D:CYS113 4.9 0.4 1.0
H D:CYS128 4.9 0.7 1.0
H D:GLY130 5.0 0.3 1.0
C D:CYS126 5.0 0.7 1.0
OH D:TYR133 5.0 0.6 1.0
C D:CYS108 5.0 0.9 1.0

Iron binding site 6 out of 6 in 4h0l

Go back to Iron Binding Sites List in 4h0l
Iron binding site 6 out of 6 in the Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome B6F Complex Crystal Structure From Mastigocladus Laminosus with N-Side Inhibitor Nqno within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:0.9
occ:1.00
FE2 D:FES200 0.0 0.9 1.0
HD1 D:HIS129 1.6 0.3 1.0
HD1 D:HIS110 2.1 0.4 1.0
S2 D:FES200 2.2 0.6 1.0
S1 D:FES200 2.2 0.1 1.0
ND1 D:HIS129 2.4 91.0 1.0
HB2 D:HIS129 2.5 0.1 1.0
ND1 D:HIS110 2.9 0.5 1.0
FE1 D:FES200 3.0 0.2 1.0
HB2 D:CYS128 3.0 0.3 1.0
HB3 D:HIS110 3.1 0.8 1.0
H D:HIS129 3.1 0.8 1.0
CG D:HIS129 3.1 0.8 1.0
CB D:HIS129 3.2 0.9 1.0
CE1 D:HIS129 3.5 0.8 1.0
N D:HIS129 3.5 0.8 1.0
H D:LEU111 3.6 0.5 1.0
HB3 D:CYS128 3.7 0.3 1.0
HE1 D:HIS129 3.7 0.5 1.0
CG D:HIS110 3.7 0.4 1.0
HB2 D:LEU111 3.8 0.7 1.0
CB D:CYS128 3.8 0.2 1.0
CB D:HIS110 3.8 0.0 1.0
CA D:HIS129 3.9 0.4 1.0
CE1 D:HIS110 3.9 0.1 1.0
HB3 D:HIS129 4.0 0.1 1.0
HG D:LEU111 4.0 0.1 1.0
HE1 D:HIS110 4.0 0.6 1.0
C D:CYS128 4.2 0.8 1.0
HB2 D:HIS110 4.2 0.8 1.0
HD12 D:LEU111 4.2 0.2 1.0
HG2 D:PRO143 4.3 0.9 1.0
SG D:CYS126 4.3 0.3 1.0
CD2 D:HIS129 4.3 0.8 1.0
N D:LEU111 4.3 0.7 1.0
NE2 D:HIS129 4.5 0.7 1.0
CA D:CYS128 4.6 0.9 1.0
CB D:LEU111 4.6 98.9 1.0
C D:HIS129 4.6 0.8 1.0
CG D:LEU111 4.6 0.2 1.0
HA D:HIS129 4.7 0.7 1.0
CD1 D:LEU111 4.9 96.0 1.0
CD2 D:HIS110 4.9 0.8 1.0
HB3 D:CYS126 4.9 0.1 1.0
NE2 D:HIS110 5.0 0.5 1.0
SG D:CYS108 5.0 0.9 1.0
H D:CYS128 5.0 0.7 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 15:35:55 2020

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