Atomistry » Iron » PDB 4gl7-4h9l » 4h44
Atomistry »
  Iron »
    PDB 4gl7-4h9l »
      4h44 »

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

Go back to Iron Binding Sites List in 4h44
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

Go back to Iron Binding Sites List in 4h44
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

Go back to Iron Binding Sites List in 4h44
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: Mon Aug 5 03:09:10 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy