Iron in PDB 6nhg: Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex

Enzymatic activity of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex

All present enzymatic activity of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex:
1.10.2.2;

Protein crystallography data

The structure of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex, PDB code: 6nhg was solved by D.Xia, F.Zhou, L.Esser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.181, 154.181, 598.180, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 28.9

Iron Binding Sites:

The binding sites of Iron atom in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex (pdb code 6nhg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex, PDB code: 6nhg:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 6nhg

Go back to Iron Binding Sites List in 6nhg
Iron binding site 1 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:0.9
occ:1.00
FE C:HEM1001 0.0 0.9 1.0
NE2 C:HIS182 2.0 95.5 1.0
NE2 C:HIS83 2.0 95.4 1.0
NA C:HEM1001 2.0 0.8 1.0
ND C:HEM1001 2.0 0.8 1.0
NB C:HEM1001 2.1 0.5 1.0
NC C:HEM1001 2.1 0.5 1.0
CE1 C:HIS83 2.9 0.4 1.0
CE1 C:HIS182 2.9 94.9 1.0
HE1 C:HIS83 3.0 1.0 1.0
C1A C:HEM1001 3.1 0.2 1.0
C4A C:HEM1001 3.1 0.8 1.0
CD2 C:HIS182 3.1 96.2 1.0
C4D C:HEM1001 3.1 0.3 1.0
C1B C:HEM1001 3.1 0.4 1.0
C1D C:HEM1001 3.1 0.2 1.0
C4B C:HEM1001 3.1 0.2 1.0
C4C C:HEM1001 3.1 0.3 1.0
C1C C:HEM1001 3.1 0.3 1.0
CD2 C:HIS83 3.1 96.8 1.0
HE1 C:HIS182 3.1 0.5 1.0
HD2 C:HIS182 3.3 0.1 1.0
HD2 C:HIS83 3.3 0.9 1.0
CHA C:HEM1001 3.4 0.0 1.0
CHB C:HEM1001 3.4 0.6 1.0
CHD C:HEM1001 3.4 0.9 1.0
CHC C:HEM1001 3.4 0.6 1.0
ND1 C:HIS83 4.1 0.2 1.0
ND1 C:HIS182 4.1 95.2 1.0
CG C:HIS182 4.2 96.0 1.0
CG C:HIS83 4.2 96.2 1.0
HA3 C:GLY130 4.2 0.9 1.0
C3A C:HEM1001 4.3 1.0 1.0
C2A C:HEM1001 4.3 1.0 1.0
C3D C:HEM1001 4.3 0.1 1.0
C2D C:HEM1001 4.3 0.5 1.0
C2B C:HEM1001 4.3 0.1 1.0
C3B C:HEM1001 4.3 0.5 1.0
C3C C:HEM1001 4.3 0.6 1.0
C2C C:HEM1001 4.3 0.9 1.0
HHA C:HEM1001 4.4 0.7 1.0
HHB C:HEM1001 4.4 0.8 1.0
HHD C:HEM1001 4.4 0.7 1.0
HHC C:HEM1001 4.4 0.8 1.0
HA2 C:GLY48 4.6 0.8 1.0
HA3 C:GLY48 4.6 0.8 1.0
HA2 C:GLY130 4.6 0.9 1.0
HD12 C:LEU133 4.7 0.4 1.0
HE21 C:GLN44 4.8 0.2 1.0
CA C:GLY130 4.9 99.7 1.0

Iron binding site 2 out of 5 in 6nhg

Go back to Iron Binding Sites List in 6nhg
Iron binding site 2 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1002

b:72.1
occ:1.00
FE C:HEM1002 0.0 72.1 1.0
ND C:HEM1002 2.0 75.2 1.0
NE2 C:HIS196 2.0 73.6 1.0
NE2 C:HIS97 2.0 75.3 1.0
NA C:HEM1002 2.1 82.9 1.0
NC C:HEM1002 2.1 71.3 1.0
NB C:HEM1002 2.1 71.0 1.0
CE1 C:HIS196 3.0 73.6 1.0
CE1 C:HIS97 3.0 75.0 1.0
CD2 C:HIS196 3.0 73.5 1.0
C4D C:HEM1002 3.0 71.7 1.0
C1D C:HEM1002 3.0 84.8 1.0
C4C C:HEM1002 3.0 84.5 1.0
C1A C:HEM1002 3.1 82.7 1.0
C1C C:HEM1002 3.1 76.9 1.0
C4B C:HEM1002 3.1 70.9 1.0
CD2 C:HIS97 3.1 98.8 1.0
C4A C:HEM1002 3.1 78.4 1.0
C1B C:HEM1002 3.1 78.5 1.0
HE1 C:HIS196 3.1 84.9 1.0
HE1 C:HIS97 3.1 89.6 1.0
HD2 C:HIS196 3.2 84.8 1.0
HD2 C:HIS97 3.3 0.2 1.0
CHA C:HEM1002 3.4 71.7 1.0
CHD C:HEM1002 3.4 89.7 1.0
CHC C:HEM1002 3.4 87.7 1.0
CHB C:HEM1002 3.5 84.4 1.0
ND1 C:HIS196 4.1 73.4 1.0
CG C:HIS196 4.1 73.3 1.0
ND1 C:HIS97 4.1 75.8 1.0
CG C:HIS97 4.2 76.8 1.0
C3C C:HEM1002 4.2 86.8 1.0
C3D C:HEM1002 4.2 71.9 1.0
C2C C:HEM1002 4.2 83.6 1.0
C2D C:HEM1002 4.3 92.7 1.0
HH22 C:ARG100 4.3 0.9 1.0
C2A C:HEM1002 4.3 71.5 1.0
C3A C:HEM1002 4.3 71.3 1.0
C3B C:HEM1002 4.3 88.5 1.0
C2B C:HEM1002 4.3 82.1 1.0
HHA C:HEM1002 4.4 86.7 1.0
HHD C:HEM1002 4.4 0.2 1.0
HHC C:HEM1002 4.4 0.9 1.0
HHB C:HEM1002 4.5 1.0 1.0
HD12 C:LEU37 4.6 90.6 1.0
HA2 C:GLY34 4.9 0.9 1.0
NH2 C:ARG100 5.0 95.2 1.0
HH21 C:ARG100 5.0 0.9 1.0
HD13 C:LEU37 5.0 90.6 1.0
HD12 C:LEU119 5.0 88.3 1.0

Iron binding site 3 out of 5 in 6nhg

Go back to Iron Binding Sites List in 6nhg
Iron binding site 3 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:0.9
occ:1.00
FE D:HEC1001 0.0 0.9 1.0
NE2 D:HIS41 2.0 0.6 1.0
NC D:HEC1001 2.1 0.1 1.0
NB D:HEC1001 2.1 0.5 1.0
NA D:HEC1001 2.1 0.7 1.0
ND D:HEC1001 2.1 0.5 1.0
SD D:MET160 2.2 0.2 1.0
CE1 D:HIS41 3.0 1.0 1.0
CD2 D:HIS41 3.0 0.6 1.0
C4B D:HEC1001 3.1 0.8 1.0
C1C D:HEC1001 3.1 0.6 1.0
C4C D:HEC1001 3.1 0.9 1.0
C4A D:HEC1001 3.1 0.0 1.0
C1D D:HEC1001 3.1 0.6 1.0
C1B D:HEC1001 3.1 0.3 1.0
C1A D:HEC1001 3.1 0.3 1.0
C4D D:HEC1001 3.1 0.0 1.0
HE1 D:HIS41 3.2 0.2 1.0
HD2 D:HIS41 3.2 0.3 1.0
CE D:MET160 3.4 0.7 1.0
CHC D:HEC1001 3.4 0.3 1.0
HG3 D:MET160 3.4 0.9 1.0
CHD D:HEC1001 3.4 0.1 1.0
CHB D:HEC1001 3.5 0.8 1.0
CHA D:HEC1001 3.5 0.3 1.0
CG D:MET160 3.5 0.4 1.0
HE1 D:MET160 3.5 0.7 1.0
HE2 D:MET160 3.5 0.7 1.0
HB2 D:MET160 3.9 0.9 1.0
ND1 D:HIS41 4.1 0.9 1.0
HB3 D:PRO110 4.1 0.6 1.0
CG D:HIS41 4.1 0.3 1.0
HE3 D:MET160 4.2 0.7 1.0
HG2 D:MET160 4.2 0.9 1.0
CB D:MET160 4.3 0.5 1.0
C3B D:HEC1001 4.3 0.2 1.0
C2B D:HEC1001 4.3 0.0 1.0
C2C D:HEC1001 4.3 0.8 1.0
C3A D:HEC1001 4.3 0.4 1.0
C2A D:HEC1001 4.3 0.1 1.0
C3C D:HEC1001 4.3 0.5 1.0
C2D D:HEC1001 4.3 0.9 1.0
C3D D:HEC1001 4.3 0.2 1.0
HHC D:HEC1001 4.4 0.7 1.0
HHD D:HEC1001 4.4 0.9 1.0
HHB D:HEC1001 4.4 0.0 1.0
HHA D:HEC1001 4.4 0.5 1.0
HG3 D:PRO163 4.5 0.3 1.0
HB3 D:MET160 4.6 0.9 1.0
HB2 D:CYS40 4.8 0.9 1.0
HD2 D:PRO111 5.0 0.7 1.0

Iron binding site 4 out of 5 in 6nhg

Go back to Iron Binding Sites List in 6nhg
Iron binding site 4 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:75.8
occ:0.25
FE1 E:FES1001 0.0 75.8 0.2
S1 E:FES1001 2.2 76.7 0.2
S2 E:FES1001 2.2 76.1 0.2
SG E:CYS158 2.3 70.9 0.2
SG E:CYS139 2.3 71.2 0.2
HB3 E:CYS139 2.7 85.3 0.2
HB3 E:HIS141 2.9 90.4 0.2
CB E:CYS139 2.9 70.5 0.2
FE2 E:FES1001 3.1 76.9 0.2
HB2 E:CYS139 3.1 85.3 0.2
HB2 E:CYS144 3.3 87.2 0.2
CB E:CYS158 3.5 71.0 0.2
HB3 E:CYS158 3.5 85.9 0.2
HB2 E:CYS160 3.6 87.8 0.2
HB2 E:CYS158 3.6 85.9 0.2
HB2 E:HIS141 3.7 90.4 0.2
CB E:HIS141 3.7 74.8 0.2
H E:HIS141 3.8 89.6 0.2
H E:LEU142 3.8 92.5 0.2
H E:CYS144 3.9 87.2 0.2
H E:HIS161 4.1 90.5 0.2
CB E:CYS144 4.2 72.1 0.2
H E:GLY143 4.3 86.0 0.2
HB2 E:SER163 4.3 85.4 0.2
CA E:CYS139 4.4 70.2 0.2
CB E:CYS160 4.4 72.6 0.2
HB3 E:CYS160 4.5 87.8 0.2
N E:HIS141 4.5 74.1 0.2
ND1 E:HIS141 4.6 75.5 0.2
OG E:SER163 4.6 70.9 0.2
N E:LEU142 4.6 76.6 0.2
CG E:HIS141 4.6 75.2 0.2
N E:CYS144 4.6 72.1 0.2
CA E:HIS141 4.7 74.4 0.2
SG E:CYS144 4.7 72.8 0.2
HB2 E:HIS161 4.7 91.4 0.2
HH E:TYR165 4.7 83.0 0.2
H E:CYS160 4.7 87.5 0.2
C E:CYS139 4.8 70.4 0.2
HA E:CYS139 4.8 85.0 0.2
HB3 E:CYS144 4.8 87.2 0.2
CA E:CYS158 4.9 70.7 0.2
HG3 E:PRO146 4.9 86.3 0.2
N E:HIS161 4.9 74.8 0.2
CA E:CYS144 4.9 71.7 0.2
ND1 E:HIS161 5.0 75.2 0.2
H E:GLY162 5.0 87.7 0.2
CB E:SER163 5.0 70.6 0.2

Iron binding site 5 out of 5 in 6nhg

Go back to Iron Binding Sites List in 6nhg
Iron binding site 5 out of 5 in the Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rhodobacter Sphaeroides Mitochondrial Respiratory Chain Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:76.9
occ:0.25
FE2 E:FES1001 0.0 76.9 0.2
ND1 E:HIS161 2.1 75.2 0.2
ND1 E:HIS141 2.1 75.5 0.2
S1 E:FES1001 2.2 76.7 0.2
S2 E:FES1001 2.2 76.1 0.2
HB2 E:HIS161 2.5 91.4 0.2
HB3 E:HIS141 2.7 90.4 0.2
CG E:HIS161 3.0 75.5 0.2
CG E:HIS141 3.0 75.2 0.2
FE1 E:FES1001 3.1 75.8 0.2
CE1 E:HIS141 3.1 75.8 0.2
CB E:HIS161 3.2 75.6 0.2
CE1 E:HIS161 3.2 75.2 0.2
CB E:HIS141 3.3 74.8 0.2
HE1 E:HIS141 3.4 91.7 0.2
HE1 E:HIS161 3.5 90.9 0.2
H E:HIS161 3.5 90.5 0.2
HB2 E:HIS141 3.6 90.4 0.2
HB3 E:CYS160 3.8 87.8 0.2
N E:HIS161 3.9 74.8 0.2
HB3 E:HIS161 3.9 91.4 0.2
HB2 E:CYS160 3.9 87.8 0.2
H E:LEU142 4.1 92.5 0.2
CA E:HIS161 4.1 75.5 0.2
HB2 E:LEU142 4.2 92.9 0.2
CD2 E:HIS141 4.2 75.4 0.2
CD2 E:HIS161 4.2 75.8 0.2
NE2 E:HIS141 4.2 75.8 0.2
NE2 E:HIS161 4.2 75.6 0.2
HG E:LEU142 4.3 93.3 0.2
CB E:CYS160 4.3 72.6 0.2
N E:LEU142 4.5 76.6 0.2
CA E:HIS141 4.6 74.4 0.2
SG E:CYS158 4.6 70.9 0.2
HD12 E:LEU142 4.6 93.7 0.2
HG2 E:PRO175 4.7 82.5 0.2
HD13 E:LEU142 4.7 93.7 0.2
C E:CYS160 4.8 73.5 0.2
C E:HIS141 4.8 74.3 0.2
SG E:CYS139 4.8 71.2 0.2
C E:HIS161 4.8 75.6 0.2
H E:GLY162 4.9 87.7 0.2
HA E:HIS161 4.9 91.2 0.2
CG E:LEU142 4.9 77.2 0.2
CB E:LEU142 4.9 76.8 0.2
CD1 E:LEU142 5.0 77.5 0.2
HD2 E:HIS161 5.0 91.6 0.2
HD2 E:HIS141 5.0 91.1 0.2

Reference:

L.Esser, F.Zhou, C.A.Yu, D.Xia. Crystal Structure of Bacterial CYTOCHROMEBC1IN Complex with Azoxystrobin Reveals A Conformational Switch of the Rieske Iron-Sulfur Protein Subunit. J.Biol.Chem. V. 294 12007 2019.
ISSN: ESSN 1083-351X
PubMed: 31182483
DOI: 10.1074/JBC.RA119.008381
Page generated: Sun Dec 13 16:46:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy