Iron in PDB 2e74: Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Enzymatic activity of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
All present enzymatic activity of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus:
1.10.99.1;
Protein crystallography data
The structure of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus, PDB code: 2e74
was solved by
W.A.Cramer,
E.Yamashita,
H.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.30 /
3.00
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
158.343,
158.343,
361.094,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.2 /
26.8
|
Other elements in 2e74:
The structure of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
(pdb code 2e74). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of the Cytochrome B6F Complex From M.Laminosus, PDB code: 2e74:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 1 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:28.3
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
28.3
|
1.0
|
NA
|
A:HEM301
|
2.0
|
31.1
|
1.0
|
NC
|
A:HEM301
|
2.0
|
31.4
|
1.0
|
NE2
|
A:HIS187
|
2.0
|
34.1
|
1.0
|
NE2
|
A:HIS86
|
2.0
|
22.9
|
1.0
|
NB
|
A:HEM301
|
2.0
|
36.9
|
1.0
|
ND
|
A:HEM301
|
2.1
|
26.3
|
1.0
|
CE1
|
A:HIS187
|
2.7
|
32.2
|
1.0
|
CE1
|
A:HIS86
|
2.8
|
20.5
|
1.0
|
C4A
|
A:HEM301
|
2.9
|
42.3
|
1.0
|
C4C
|
A:HEM301
|
3.0
|
35.2
|
1.0
|
C4B
|
A:HEM301
|
3.0
|
48.1
|
1.0
|
C1C
|
A:HEM301
|
3.0
|
23.7
|
1.0
|
C1A
|
A:HEM301
|
3.0
|
26.4
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
38.6
|
1.0
|
C1D
|
A:HEM301
|
3.1
|
26.2
|
1.0
|
CD2
|
A:HIS86
|
3.1
|
31.6
|
1.0
|
CD2
|
A:HIS187
|
3.2
|
37.0
|
1.0
|
C4D
|
A:HEM301
|
3.2
|
29.0
|
1.0
|
CHC
|
A:HEM301
|
3.3
|
38.0
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
32.3
|
1.0
|
CHB
|
A:HEM301
|
3.4
|
37.5
|
1.0
|
CHA
|
A:HEM301
|
3.5
|
28.0
|
1.0
|
ND1
|
A:HIS187
|
3.9
|
35.2
|
1.0
|
ND1
|
A:HIS86
|
4.0
|
30.0
|
1.0
|
C3A
|
A:HEM301
|
4.2
|
40.2
|
1.0
|
CG
|
A:HIS86
|
4.2
|
31.6
|
1.0
|
CG
|
A:HIS187
|
4.2
|
36.7
|
1.0
|
C3C
|
A:HEM301
|
4.2
|
25.9
|
1.0
|
C2C
|
A:HEM301
|
4.2
|
33.9
|
1.0
|
C3B
|
A:HEM301
|
4.2
|
49.5
|
1.0
|
C2A
|
A:HEM301
|
4.2
|
26.5
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
57.7
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
13.9
|
1.0
|
C3D
|
A:HEM301
|
4.4
|
29.3
|
1.0
|
|
Iron binding site 2 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 2 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:34.5
occ:1.00
|
FE
|
A:HEM302
|
0.0
|
34.5
|
1.0
|
NB
|
A:HEM302
|
2.0
|
31.9
|
1.0
|
NA
|
A:HEM302
|
2.0
|
9.7
|
1.0
|
NC
|
A:HEM302
|
2.0
|
30.4
|
1.0
|
ND
|
A:HEM302
|
2.1
|
13.8
|
1.0
|
NE2
|
A:HIS100
|
2.1
|
36.5
|
1.0
|
NE2
|
A:HIS202
|
2.1
|
42.9
|
1.0
|
CE1
|
A:HIS100
|
2.9
|
25.3
|
1.0
|
C4B
|
A:HEM302
|
3.0
|
34.6
|
1.0
|
C4C
|
A:HEM302
|
3.0
|
33.2
|
1.0
|
C1C
|
A:HEM302
|
3.0
|
30.9
|
1.0
|
C1B
|
A:HEM302
|
3.0
|
36.3
|
1.0
|
C1A
|
A:HEM302
|
3.0
|
29.1
|
1.0
|
CE1
|
A:HIS202
|
3.0
|
44.8
|
1.0
|
C4A
|
A:HEM302
|
3.0
|
34.0
|
1.0
|
C1D
|
A:HEM302
|
3.0
|
37.4
|
1.0
|
CD2
|
A:HIS202
|
3.1
|
28.1
|
1.0
|
C4D
|
A:HEM302
|
3.1
|
32.2
|
1.0
|
CD2
|
A:HIS100
|
3.1
|
51.2
|
1.0
|
CHD
|
A:HEM302
|
3.3
|
34.6
|
1.0
|
CHC
|
A:HEM302
|
3.4
|
39.2
|
1.0
|
CHB
|
A:HEM302
|
3.4
|
33.7
|
1.0
|
CHA
|
A:HEM302
|
3.4
|
34.2
|
1.0
|
ND1
|
A:HIS100
|
4.1
|
54.5
|
1.0
|
ND1
|
A:HIS202
|
4.1
|
44.2
|
1.0
|
CG
|
A:HIS202
|
4.2
|
44.5
|
1.0
|
CG
|
A:HIS100
|
4.2
|
47.4
|
1.0
|
C3B
|
A:HEM302
|
4.2
|
28.1
|
1.0
|
C3C
|
A:HEM302
|
4.2
|
35.5
|
1.0
|
C2C
|
A:HEM302
|
4.2
|
40.9
|
1.0
|
C2B
|
A:HEM302
|
4.2
|
34.1
|
1.0
|
C2A
|
A:HEM302
|
4.2
|
35.8
|
1.0
|
C3A
|
A:HEM302
|
4.2
|
38.1
|
1.0
|
C2D
|
A:HEM302
|
4.3
|
39.8
|
1.0
|
C3D
|
A:HEM302
|
4.3
|
24.3
|
1.0
|
CD1
|
A:ILE206
|
5.0
|
40.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 3 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:53.4
occ:1.00
|
FE
|
A:HEM303
|
0.0
|
53.4
|
1.0
|
O
|
A:HOH1106
|
1.7
|
27.1
|
1.0
|
NA
|
A:HEM303
|
2.0
|
68.3
|
1.0
|
NB
|
A:HEM303
|
2.1
|
57.6
|
1.0
|
NC
|
A:HEM303
|
2.1
|
62.1
|
1.0
|
ND
|
A:HEM303
|
2.1
|
56.5
|
1.0
|
C1A
|
A:HEM303
|
3.0
|
62.8
|
1.0
|
C4A
|
A:HEM303
|
3.0
|
64.1
|
1.0
|
C1B
|
A:HEM303
|
3.1
|
63.7
|
1.0
|
C4D
|
A:HEM303
|
3.1
|
57.6
|
1.0
|
C4B
|
A:HEM303
|
3.1
|
60.4
|
1.0
|
C1C
|
A:HEM303
|
3.1
|
63.5
|
1.0
|
C4C
|
A:HEM303
|
3.1
|
54.8
|
1.0
|
C1D
|
A:HEM303
|
3.2
|
43.7
|
1.0
|
CHA
|
A:HEM303
|
3.3
|
59.0
|
1.0
|
CHC
|
A:HEM303
|
3.4
|
63.8
|
1.0
|
CHB
|
A:HEM303
|
3.4
|
53.2
|
1.0
|
CHD
|
A:HEM303
|
3.5
|
46.0
|
1.0
|
CZ
|
B:PHE40
|
3.6
|
42.5
|
1.0
|
CE2
|
B:PHE40
|
3.7
|
52.9
|
1.0
|
C2A
|
A:HEM303
|
4.2
|
65.3
|
1.0
|
C3A
|
A:HEM303
|
4.2
|
66.5
|
1.0
|
O
|
A:TYR34
|
4.2
|
65.1
|
1.0
|
C2B
|
A:HEM303
|
4.3
|
64.9
|
1.0
|
C3B
|
A:HEM303
|
4.3
|
60.1
|
1.0
|
O2A
|
A:HEM302
|
4.3
|
67.1
|
1.0
|
C2C
|
A:HEM303
|
4.3
|
55.8
|
1.0
|
C3C
|
A:HEM303
|
4.3
|
60.0
|
1.0
|
C3D
|
A:HEM303
|
4.3
|
56.4
|
1.0
|
C2D
|
A:HEM303
|
4.4
|
50.2
|
1.0
|
N
|
A:GLY38
|
4.5
|
46.3
|
1.0
|
CMA
|
A:HEM302
|
4.6
|
26.2
|
1.0
|
CA
|
A:GLY38
|
4.6
|
47.9
|
1.0
|
CE1
|
B:PHE40
|
4.7
|
52.0
|
1.0
|
CAA
|
A:HEM302
|
4.9
|
34.8
|
1.0
|
CD2
|
B:PHE40
|
4.9
|
63.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 4 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:55.8
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
55.8
|
1.0
|
NA
|
C:HEM301
|
1.9
|
29.7
|
1.0
|
N
|
C:TYR1
|
1.9
|
40.5
|
1.0
|
NC
|
C:HEM301
|
2.0
|
29.6
|
1.0
|
ND
|
C:HEM301
|
2.1
|
52.0
|
1.0
|
NB
|
C:HEM301
|
2.1
|
47.2
|
1.0
|
NE2
|
C:HIS26
|
2.2
|
55.6
|
1.0
|
C1A
|
C:HEM301
|
2.9
|
57.2
|
1.0
|
CD2
|
C:HIS26
|
2.9
|
66.2
|
1.0
|
C4A
|
C:HEM301
|
3.0
|
51.9
|
1.0
|
C4C
|
C:HEM301
|
3.0
|
39.1
|
1.0
|
C1C
|
C:HEM301
|
3.0
|
40.6
|
1.0
|
C4D
|
C:HEM301
|
3.0
|
63.9
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
59.0
|
1.0
|
C1D
|
C:HEM301
|
3.1
|
66.2
|
1.0
|
C4B
|
C:HEM301
|
3.1
|
43.8
|
1.0
|
CA
|
C:TYR1
|
3.2
|
41.3
|
1.0
|
CE1
|
C:HIS26
|
3.3
|
59.1
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
58.2
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
58.5
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
58.2
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
37.3
|
1.0
|
C
|
C:TYR1
|
3.8
|
45.8
|
1.0
|
C2A
|
C:HEM301
|
4.2
|
44.8
|
1.0
|
CG
|
C:HIS26
|
4.2
|
57.1
|
1.0
|
C3A
|
C:HEM301
|
4.2
|
56.3
|
1.0
|
O
|
C:TYR1
|
4.2
|
48.9
|
1.0
|
C3C
|
C:HEM301
|
4.2
|
41.3
|
1.0
|
C2C
|
C:HEM301
|
4.2
|
49.1
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
62.6
|
1.0
|
ND1
|
C:HIS26
|
4.3
|
65.8
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
49.8
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
66.8
|
1.0
|
C3B
|
C:HEM301
|
4.4
|
54.5
|
1.0
|
CB
|
C:TYR1
|
4.4
|
46.6
|
1.0
|
N
|
C:PRO2
|
4.6
|
48.3
|
1.0
|
CE3
|
C:TRP4
|
4.7
|
47.3
|
1.0
|
OD1
|
C:ASN154
|
4.8
|
50.6
|
1.0
|
CG
|
C:TYR1
|
4.8
|
50.3
|
1.0
|
CD
|
C:PRO2
|
4.9
|
47.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 5 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:0.5
occ:1.00
|
FE1
|
D:FES200
|
0.0
|
0.5
|
1.0
|
SG
|
D:CYS108
|
1.8
|
0.1
|
1.0
|
S1
|
D:FES200
|
2.2
|
0.2
|
1.0
|
S2
|
D:FES200
|
2.2
|
0.3
|
1.0
|
SG
|
D:CYS126
|
2.4
|
0.1
|
1.0
|
CB
|
D:CYS126
|
2.8
|
92.6
|
1.0
|
OG
|
D:SER131
|
3.0
|
0.1
|
1.0
|
FE2
|
D:FES200
|
3.1
|
96.3
|
1.0
|
CB
|
D:CYS108
|
3.3
|
92.4
|
1.0
|
CB
|
D:HIS110
|
3.8
|
80.0
|
1.0
|
CA
|
D:CYS126
|
4.2
|
94.1
|
1.0
|
O
|
D:CYS126
|
4.4
|
99.8
|
1.0
|
CB
|
D:SER131
|
4.4
|
96.4
|
1.0
|
C
|
D:CYS126
|
4.5
|
95.7
|
1.0
|
ND1
|
D:HIS110
|
4.6
|
77.8
|
1.0
|
CG
|
D:HIS110
|
4.6
|
76.1
|
1.0
|
N
|
D:HIS129
|
4.6
|
86.8
|
1.0
|
CA
|
D:CYS108
|
4.6
|
92.9
|
1.0
|
OH
|
D:TYR133
|
4.7
|
96.9
|
1.0
|
CB
|
D:CYS128
|
4.7
|
90.1
|
1.0
|
CB
|
D:ALA144
|
4.8
|
82.5
|
1.0
|
N
|
D:HIS110
|
4.9
|
84.8
|
1.0
|
CA
|
D:HIS110
|
4.9
|
83.8
|
1.0
|
N
|
D:SER131
|
4.9
|
97.4
|
1.0
|
C
|
D:CYS108
|
5.0
|
90.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 2e74
Go back to
Iron Binding Sites List in 2e74
Iron binding site 6 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Cytochrome B6F Complex From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:96.3
occ:1.00
|
FE2
|
D:FES200
|
0.0
|
96.3
|
1.0
|
S2
|
D:FES200
|
2.2
|
0.3
|
1.0
|
S1
|
D:FES200
|
2.2
|
0.2
|
1.0
|
ND1
|
D:HIS110
|
2.3
|
77.8
|
1.0
|
ND1
|
D:HIS129
|
2.3
|
55.3
|
1.0
|
CG
|
D:HIS129
|
3.0
|
77.7
|
1.0
|
CB
|
D:HIS129
|
3.0
|
85.4
|
1.0
|
CE1
|
D:HIS110
|
3.1
|
65.6
|
1.0
|
FE1
|
D:FES200
|
3.1
|
0.5
|
1.0
|
CG
|
D:HIS110
|
3.2
|
76.1
|
1.0
|
CE1
|
D:HIS129
|
3.4
|
69.3
|
1.0
|
CB
|
D:HIS110
|
3.5
|
80.0
|
1.0
|
N
|
D:HIS129
|
3.7
|
86.8
|
1.0
|
CB
|
D:CYS128
|
4.0
|
90.1
|
1.0
|
CA
|
D:HIS129
|
4.0
|
86.6
|
1.0
|
CD2
|
D:HIS129
|
4.1
|
79.8
|
1.0
|
NE2
|
D:HIS110
|
4.1
|
71.3
|
1.0
|
CD2
|
D:HIS110
|
4.2
|
77.0
|
1.0
|
CG
|
D:PRO143
|
4.2
|
80.2
|
1.0
|
C
|
D:CYS128
|
4.2
|
87.3
|
1.0
|
NE2
|
D:HIS129
|
4.3
|
72.0
|
1.0
|
SG
|
D:CYS108
|
4.4
|
0.1
|
1.0
|
CB
|
D:LEU111
|
4.6
|
81.2
|
1.0
|
N
|
D:LEU111
|
4.6
|
84.0
|
1.0
|
CA
|
D:CYS128
|
4.7
|
89.4
|
1.0
|
SG
|
D:CYS126
|
4.8
|
0.1
|
1.0
|
CA
|
D:HIS110
|
4.8
|
83.8
|
1.0
|
CD1
|
D:LEU111
|
4.9
|
73.4
|
1.0
|
O
|
D:CYS128
|
4.9
|
88.0
|
1.0
|
C
|
D:HIS129
|
4.9
|
88.9
|
1.0
|
C
|
D:HIS110
|
4.9
|
84.5
|
1.0
|
CG
|
D:LEU111
|
4.9
|
76.4
|
1.0
|
CD
|
D:PRO143
|
5.0
|
85.8
|
1.0
|
OG
|
D:SER131
|
5.0
|
0.1
|
1.0
|
|
Reference:
E.Yamashita,
H.Zhang,
W.A.Cramer.
Structure of the Cytochrome B(6)F Complex: Quinone Analogue Inhibitors As Ligands of Heme C(N) J.Mol.Biol. V. 370 39 2007.
ISSN: ISSN 0022-2836
PubMed: 17498743
DOI: 10.1016/J.JMB.2007.04.011
Page generated: Sat Aug 3 20:59:37 2024
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