Iron in PDB 3nbt: Crystal Structure of Trimeric Cytochrome C From Horse Heart
Protein crystallography data
The structure of Crystal Structure of Trimeric Cytochrome C From Horse Heart, PDB code: 3nbt
was solved by
M.Taketa,
H.Komori,
S.Hirota,
Y.Higuchi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.54 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.204,
95.661,
130.935,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
25.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
(pdb code 3nbt). 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 Trimeric Cytochrome C From Horse Heart, PDB code: 3nbt:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 1 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe105
b:24.1
occ:1.00
|
FE
|
A:HEC105
|
0.0
|
24.1
|
1.0
|
NE2
|
A:HIS18
|
2.0
|
25.7
|
1.0
|
NB
|
A:HEC105
|
2.0
|
24.9
|
1.0
|
NC
|
A:HEC105
|
2.0
|
25.1
|
1.0
|
NA
|
A:HEC105
|
2.0
|
24.7
|
1.0
|
ND
|
A:HEC105
|
2.0
|
23.7
|
1.0
|
O
|
A:HOH201
|
2.1
|
22.2
|
1.0
|
CD2
|
A:HIS18
|
2.9
|
24.1
|
1.0
|
C1B
|
A:HEC105
|
3.0
|
23.7
|
1.0
|
C1C
|
A:HEC105
|
3.0
|
22.3
|
1.0
|
C4A
|
A:HEC105
|
3.0
|
24.4
|
1.0
|
C4B
|
A:HEC105
|
3.0
|
24.8
|
1.0
|
C4C
|
A:HEC105
|
3.0
|
23.2
|
1.0
|
CE1
|
A:HIS18
|
3.0
|
26.9
|
1.0
|
C1D
|
A:HEC105
|
3.0
|
24.0
|
1.0
|
C1A
|
A:HEC105
|
3.0
|
24.2
|
1.0
|
C4D
|
A:HEC105
|
3.0
|
21.1
|
1.0
|
CHB
|
A:HEC105
|
3.3
|
22.5
|
1.0
|
CHC
|
A:HEC105
|
3.4
|
23.6
|
1.0
|
CHD
|
A:HEC105
|
3.4
|
21.9
|
1.0
|
CHA
|
A:HEC105
|
3.4
|
25.0
|
1.0
|
CG
|
A:HIS18
|
4.0
|
27.6
|
1.0
|
ND1
|
A:HIS18
|
4.1
|
28.6
|
1.0
|
C2B
|
A:HEC105
|
4.2
|
24.1
|
1.0
|
C3B
|
A:HEC105
|
4.2
|
23.7
|
1.0
|
C2C
|
A:HEC105
|
4.2
|
22.8
|
1.0
|
C3C
|
A:HEC105
|
4.2
|
21.6
|
1.0
|
C3A
|
A:HEC105
|
4.2
|
23.4
|
1.0
|
C2D
|
A:HEC105
|
4.2
|
24.5
|
1.0
|
C2A
|
A:HEC105
|
4.2
|
22.9
|
1.0
|
C3D
|
A:HEC105
|
4.2
|
23.8
|
1.0
|
OH
|
A:TYR67
|
4.4
|
22.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 2 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe105
b:23.1
occ:1.00
|
FE
|
B:HEC105
|
0.0
|
23.1
|
1.0
|
NA
|
B:HEC105
|
2.0
|
23.1
|
1.0
|
NB
|
B:HEC105
|
2.0
|
24.0
|
1.0
|
NC
|
B:HEC105
|
2.0
|
23.6
|
1.0
|
ND
|
B:HEC105
|
2.0
|
22.1
|
1.0
|
NE2
|
B:HIS18
|
2.0
|
24.4
|
1.0
|
O
|
B:HOH202
|
2.1
|
23.2
|
1.0
|
CE1
|
B:HIS18
|
2.9
|
24.1
|
1.0
|
C4A
|
B:HEC105
|
3.0
|
24.6
|
1.0
|
C1B
|
B:HEC105
|
3.0
|
22.2
|
1.0
|
C4B
|
B:HEC105
|
3.0
|
23.6
|
1.0
|
C1A
|
B:HEC105
|
3.0
|
23.5
|
1.0
|
C1C
|
B:HEC105
|
3.0
|
23.2
|
1.0
|
C4D
|
B:HEC105
|
3.0
|
22.5
|
1.0
|
CD2
|
B:HIS18
|
3.0
|
25.3
|
1.0
|
C1D
|
B:HEC105
|
3.0
|
23.0
|
1.0
|
C4C
|
B:HEC105
|
3.0
|
22.6
|
1.0
|
CHB
|
B:HEC105
|
3.3
|
22.3
|
1.0
|
CHC
|
B:HEC105
|
3.4
|
23.8
|
1.0
|
CHA
|
B:HEC105
|
3.4
|
21.0
|
1.0
|
CHD
|
B:HEC105
|
3.4
|
20.1
|
1.0
|
ND1
|
B:HIS18
|
4.1
|
26.1
|
1.0
|
CG
|
B:HIS18
|
4.1
|
27.3
|
1.0
|
C2B
|
B:HEC105
|
4.2
|
23.8
|
1.0
|
C3A
|
B:HEC105
|
4.2
|
22.9
|
1.0
|
C3B
|
B:HEC105
|
4.2
|
22.7
|
1.0
|
C2A
|
B:HEC105
|
4.2
|
23.8
|
1.0
|
C2C
|
B:HEC105
|
4.2
|
24.1
|
1.0
|
C2D
|
B:HEC105
|
4.2
|
21.7
|
1.0
|
C3D
|
B:HEC105
|
4.2
|
22.8
|
1.0
|
C3C
|
B:HEC105
|
4.2
|
22.7
|
1.0
|
OH
|
B:TYR67
|
4.5
|
21.6
|
1.0
|
SD
|
B:MET80
|
4.8
|
30.4
|
1.0
|
|
Iron binding site 3 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 3 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe105
b:24.2
occ:1.00
|
FE
|
C:HEC105
|
0.0
|
24.2
|
1.0
|
ND
|
C:HEC105
|
1.9
|
20.0
|
1.0
|
NB
|
C:HEC105
|
1.9
|
22.6
|
1.0
|
NC
|
C:HEC105
|
2.0
|
22.3
|
1.0
|
NE2
|
C:HIS18
|
2.0
|
23.1
|
1.0
|
NA
|
C:HEC105
|
2.0
|
21.5
|
1.0
|
O
|
C:HOH203
|
2.1
|
27.6
|
1.0
|
C1D
|
C:HEC105
|
2.9
|
19.2
|
1.0
|
CE1
|
C:HIS18
|
3.0
|
26.4
|
1.0
|
C1B
|
C:HEC105
|
3.0
|
23.6
|
1.0
|
CD2
|
C:HIS18
|
3.0
|
23.7
|
1.0
|
C4C
|
C:HEC105
|
3.0
|
21.1
|
1.0
|
C4B
|
C:HEC105
|
3.0
|
24.2
|
1.0
|
C4D
|
C:HEC105
|
3.0
|
19.4
|
1.0
|
C4A
|
C:HEC105
|
3.0
|
19.9
|
1.0
|
C1C
|
C:HEC105
|
3.0
|
21.1
|
1.0
|
C1A
|
C:HEC105
|
3.0
|
20.6
|
1.0
|
CHD
|
C:HEC105
|
3.3
|
20.4
|
1.0
|
CHB
|
C:HEC105
|
3.3
|
22.7
|
1.0
|
CHC
|
C:HEC105
|
3.4
|
24.1
|
1.0
|
CHA
|
C:HEC105
|
3.4
|
19.0
|
1.0
|
ND1
|
C:HIS18
|
4.1
|
24.9
|
1.0
|
CG
|
C:HIS18
|
4.1
|
26.4
|
1.0
|
C2D
|
C:HEC105
|
4.2
|
19.1
|
1.0
|
C2B
|
C:HEC105
|
4.2
|
24.5
|
1.0
|
C3D
|
C:HEC105
|
4.2
|
17.7
|
1.0
|
C3B
|
C:HEC105
|
4.2
|
23.7
|
1.0
|
C3C
|
C:HEC105
|
4.2
|
23.1
|
1.0
|
C3A
|
C:HEC105
|
4.2
|
17.5
|
1.0
|
C2C
|
C:HEC105
|
4.2
|
23.4
|
1.0
|
C2A
|
C:HEC105
|
4.3
|
19.6
|
1.0
|
OH
|
C:TYR67
|
4.4
|
25.0
|
1.0
|
CE
|
C:MET80
|
4.7
|
31.4
|
1.0
|
|
Iron binding site 4 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 4 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe105
b:22.9
occ:1.00
|
FE
|
D:HEC105
|
0.0
|
22.9
|
1.0
|
NC
|
D:HEC105
|
2.0
|
23.2
|
1.0
|
ND
|
D:HEC105
|
2.0
|
22.2
|
1.0
|
NA
|
D:HEC105
|
2.0
|
23.2
|
1.0
|
NB
|
D:HEC105
|
2.0
|
22.2
|
1.0
|
NE2
|
D:HIS18
|
2.0
|
23.2
|
1.0
|
O
|
D:HOH204
|
2.1
|
26.4
|
1.0
|
C4C
|
D:HEC105
|
3.0
|
23.1
|
1.0
|
CE1
|
D:HIS18
|
3.0
|
25.2
|
1.0
|
C1D
|
D:HEC105
|
3.0
|
23.2
|
1.0
|
C1C
|
D:HEC105
|
3.0
|
23.9
|
1.0
|
C4A
|
D:HEC105
|
3.0
|
22.3
|
1.0
|
C1B
|
D:HEC105
|
3.0
|
23.3
|
1.0
|
C4D
|
D:HEC105
|
3.0
|
22.5
|
1.0
|
CD2
|
D:HIS18
|
3.0
|
20.6
|
1.0
|
C1A
|
D:HEC105
|
3.0
|
22.9
|
1.0
|
C4B
|
D:HEC105
|
3.0
|
23.1
|
1.0
|
CHD
|
D:HEC105
|
3.3
|
21.8
|
1.0
|
CHB
|
D:HEC105
|
3.4
|
21.2
|
1.0
|
CHC
|
D:HEC105
|
3.4
|
23.6
|
1.0
|
CHA
|
D:HEC105
|
3.4
|
21.3
|
1.0
|
ND1
|
D:HIS18
|
4.1
|
23.7
|
1.0
|
CG
|
D:HIS18
|
4.1
|
23.5
|
1.0
|
C3C
|
D:HEC105
|
4.2
|
23.6
|
1.0
|
C2C
|
D:HEC105
|
4.2
|
23.4
|
1.0
|
C2D
|
D:HEC105
|
4.2
|
23.4
|
1.0
|
C3D
|
D:HEC105
|
4.2
|
23.1
|
1.0
|
C3A
|
D:HEC105
|
4.2
|
22.3
|
1.0
|
C2B
|
D:HEC105
|
4.2
|
25.2
|
1.0
|
C2A
|
D:HEC105
|
4.2
|
23.0
|
1.0
|
C3B
|
D:HEC105
|
4.2
|
25.1
|
1.0
|
OH
|
D:TYR67
|
4.4
|
22.1
|
1.0
|
SD
|
D:MET80
|
4.8
|
40.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 5 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe105
b:24.1
occ:1.00
|
FE
|
E:HEC105
|
0.0
|
24.1
|
1.0
|
NE2
|
E:HIS18
|
2.0
|
26.0
|
1.0
|
NB
|
E:HEC105
|
2.0
|
23.9
|
1.0
|
ND
|
E:HEC105
|
2.0
|
23.7
|
1.0
|
NA
|
E:HEC105
|
2.0
|
23.8
|
1.0
|
NC
|
E:HEC105
|
2.0
|
24.0
|
1.0
|
O
|
E:HOH205
|
2.1
|
22.6
|
1.0
|
CD2
|
E:HIS18
|
2.9
|
24.2
|
1.0
|
CE1
|
E:HIS18
|
3.0
|
28.8
|
1.0
|
C1B
|
E:HEC105
|
3.0
|
24.6
|
1.0
|
C4A
|
E:HEC105
|
3.0
|
23.6
|
1.0
|
C4D
|
E:HEC105
|
3.0
|
20.8
|
1.0
|
C1D
|
E:HEC105
|
3.0
|
24.1
|
1.0
|
C1C
|
E:HEC105
|
3.0
|
24.7
|
1.0
|
C4B
|
E:HEC105
|
3.0
|
25.5
|
1.0
|
C1A
|
E:HEC105
|
3.0
|
22.5
|
1.0
|
C4C
|
E:HEC105
|
3.0
|
24.9
|
1.0
|
CHB
|
E:HEC105
|
3.3
|
23.6
|
1.0
|
CHC
|
E:HEC105
|
3.4
|
23.4
|
1.0
|
CHD
|
E:HEC105
|
3.4
|
24.2
|
1.0
|
CHA
|
E:HEC105
|
3.4
|
22.7
|
1.0
|
ND1
|
E:HIS18
|
4.0
|
26.9
|
1.0
|
CG
|
E:HIS18
|
4.0
|
27.7
|
1.0
|
C3D
|
E:HEC105
|
4.2
|
23.4
|
1.0
|
C3A
|
E:HEC105
|
4.2
|
25.9
|
1.0
|
C2D
|
E:HEC105
|
4.2
|
23.8
|
1.0
|
C2B
|
E:HEC105
|
4.2
|
22.6
|
1.0
|
C2A
|
E:HEC105
|
4.2
|
26.9
|
1.0
|
C3B
|
E:HEC105
|
4.2
|
22.8
|
1.0
|
C2C
|
E:HEC105
|
4.2
|
25.2
|
1.0
|
C3C
|
E:HEC105
|
4.2
|
25.0
|
1.0
|
OH
|
E:TYR67
|
4.3
|
22.7
|
1.0
|
CE
|
E:MET80
|
4.8
|
36.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 3nbt
Go back to
Iron Binding Sites List in 3nbt
Iron binding site 6 out
of 6 in the Crystal Structure of Trimeric Cytochrome C From Horse Heart
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 Trimeric Cytochrome C From Horse Heart within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe105
b:21.9
occ:1.00
|
FE
|
F:HEC105
|
0.0
|
21.9
|
1.0
|
ND
|
F:HEC105
|
1.9
|
20.6
|
1.0
|
NA
|
F:HEC105
|
2.0
|
22.8
|
1.0
|
NB
|
F:HEC105
|
2.0
|
20.5
|
1.0
|
NC
|
F:HEC105
|
2.0
|
20.9
|
1.0
|
NE2
|
F:HIS18
|
2.0
|
23.4
|
1.0
|
O
|
F:HOH206
|
2.1
|
23.9
|
1.0
|
CE1
|
F:HIS18
|
2.9
|
23.9
|
1.0
|
C1D
|
F:HEC105
|
3.0
|
20.8
|
1.0
|
C4A
|
F:HEC105
|
3.0
|
22.6
|
1.0
|
C4D
|
F:HEC105
|
3.0
|
20.6
|
1.0
|
C1B
|
F:HEC105
|
3.0
|
20.1
|
1.0
|
C1C
|
F:HEC105
|
3.0
|
21.0
|
1.0
|
C4C
|
F:HEC105
|
3.0
|
18.4
|
1.0
|
CD2
|
F:HIS18
|
3.0
|
21.8
|
1.0
|
C1A
|
F:HEC105
|
3.0
|
21.4
|
1.0
|
C4B
|
F:HEC105
|
3.0
|
20.0
|
1.0
|
CHB
|
F:HEC105
|
3.3
|
19.3
|
1.0
|
CHD
|
F:HEC105
|
3.3
|
18.3
|
1.0
|
CHC
|
F:HEC105
|
3.4
|
20.2
|
1.0
|
CHA
|
F:HEC105
|
3.4
|
23.3
|
1.0
|
ND1
|
F:HIS18
|
4.1
|
24.0
|
1.0
|
CG
|
F:HIS18
|
4.1
|
23.9
|
1.0
|
C3D
|
F:HEC105
|
4.1
|
20.4
|
1.0
|
C3C
|
F:HEC105
|
4.2
|
22.1
|
1.0
|
C2D
|
F:HEC105
|
4.2
|
18.7
|
1.0
|
C3A
|
F:HEC105
|
4.2
|
22.2
|
1.0
|
C2C
|
F:HEC105
|
4.2
|
19.9
|
1.0
|
C3B
|
F:HEC105
|
4.2
|
19.2
|
1.0
|
C2B
|
F:HEC105
|
4.2
|
19.6
|
1.0
|
C2A
|
F:HEC105
|
4.2
|
21.9
|
1.0
|
OH
|
F:TYR67
|
4.4
|
26.5
|
1.0
|
CE
|
F:MET80
|
4.8
|
39.9
|
1.0
|
|
Reference:
S.Hirota,
Y.Hattori,
S.Nagao,
M.Taketa,
H.Komori,
H.Kamikubo,
Z.Wang,
I.Takahashi,
S.Negi,
Y.Sugiura,
M.Kataoka,
Y.Higuchi.
Cytochrome C Polymerization By Successive Domain Swapping at the C-Terminal Helix Proc.Natl.Acad.Sci.Usa V. 107 12854 2010.
ISSN: ISSN 0027-8424
PubMed: 20615990
DOI: 10.1073/PNAS.1001839107
Page generated: Sun Aug 4 16:24:56 2024
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