Atomistry » Iron » PDB 4gl7-4h9l » 4h0l
Atomistry »
  Iron »
    PDB 4gl7-4h9l »
      4h0l »

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

Go back to Iron Binding Sites List in 4h0l
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

Go back to Iron Binding Sites List in 4h0l
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

Go back to Iron Binding Sites List in 4h0l
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

Go back to Iron Binding Sites List in 4h0l
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

Go back to Iron Binding Sites List in 4h0l
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: Mon Aug 5 03:06:59 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy