Iron in PDB 8qjg: Crystal Structure of Cytochrome Domain 2 From Pgca
Protein crystallography data
The structure of Crystal Structure of Cytochrome Domain 2 From Pgca, PDB code: 8qjg
was solved by
B.W.Nash,
M.J.Edwards,
T.A.Clarke,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.96 /
1.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.104,
74.101,
56.019,
90,
103.92,
90
|
R / Rfree (%)
|
17.5 /
22.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Cytochrome Domain 2 From Pgca
(pdb code 8qjg). 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 Cytochrome Domain 2 From Pgca, PDB code: 8qjg:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 1 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe103
b:8.1
occ:1.00
|
FE
|
A:HEC103
|
0.0
|
8.1
|
1.0
|
NB
|
A:HEC103
|
2.0
|
5.4
|
1.0
|
NA
|
A:HEC103
|
2.0
|
9.5
|
1.0
|
NC
|
A:HEC103
|
2.0
|
15.0
|
1.0
|
ND
|
A:HEC103
|
2.1
|
2.3
|
1.0
|
NE2
|
A:HIS17
|
2.1
|
5.7
|
1.0
|
SD
|
A:MET44
|
2.4
|
8.4
|
1.0
|
CD2
|
A:HIS17
|
2.9
|
9.2
|
1.0
|
C4B
|
A:HEC103
|
3.0
|
7.8
|
1.0
|
C1B
|
A:HEC103
|
3.0
|
7.7
|
1.0
|
C1C
|
A:HEC103
|
3.0
|
10.4
|
1.0
|
C1A
|
A:HEC103
|
3.0
|
12.3
|
1.0
|
C1D
|
A:HEC103
|
3.1
|
3.9
|
1.0
|
C4D
|
A:HEC103
|
3.1
|
9.1
|
1.0
|
C4A
|
A:HEC103
|
3.1
|
6.7
|
1.0
|
C4C
|
A:HEC103
|
3.1
|
11.7
|
1.0
|
CE1
|
A:HIS17
|
3.2
|
7.7
|
1.0
|
CHC
|
A:HEC103
|
3.3
|
10.0
|
1.0
|
CHA
|
A:HEC103
|
3.4
|
8.2
|
1.0
|
CG
|
A:MET44
|
3.4
|
7.2
|
1.0
|
CHB
|
A:HEC103
|
3.4
|
3.6
|
1.0
|
CHD
|
A:HEC103
|
3.5
|
11.0
|
1.0
|
CE
|
A:MET44
|
3.6
|
9.1
|
1.0
|
CG
|
A:HIS17
|
4.2
|
6.6
|
1.0
|
C3B
|
A:HEC103
|
4.2
|
12.2
|
1.0
|
C2B
|
A:HEC103
|
4.2
|
12.1
|
1.0
|
ND1
|
A:HIS17
|
4.2
|
6.3
|
1.0
|
C2C
|
A:HEC103
|
4.2
|
10.2
|
1.0
|
C2A
|
A:HEC103
|
4.3
|
6.1
|
1.0
|
C2D
|
A:HEC103
|
4.3
|
9.0
|
1.0
|
C3C
|
A:HEC103
|
4.3
|
9.2
|
1.0
|
C3D
|
A:HEC103
|
4.3
|
9.9
|
1.0
|
C3A
|
A:HEC103
|
4.3
|
5.1
|
1.0
|
CB
|
A:MET44
|
4.8
|
6.4
|
1.0
|
O
|
A:ARG41
|
4.9
|
6.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 2 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe102
b:7.9
occ:1.00
|
FE
|
B:HEC102
|
0.0
|
7.9
|
1.0
|
NC
|
B:HEC102
|
2.0
|
8.9
|
1.0
|
NE2
|
B:HIS17
|
2.0
|
9.5
|
1.0
|
NA
|
B:HEC102
|
2.0
|
10.1
|
1.0
|
NB
|
B:HEC102
|
2.1
|
5.2
|
1.0
|
ND
|
B:HEC102
|
2.1
|
4.7
|
1.0
|
SD
|
B:MET44
|
2.5
|
6.6
|
1.0
|
CD2
|
B:HIS17
|
3.0
|
6.9
|
1.0
|
C1C
|
B:HEC102
|
3.0
|
8.8
|
1.0
|
C4B
|
B:HEC102
|
3.0
|
9.0
|
1.0
|
C1A
|
B:HEC102
|
3.0
|
10.5
|
1.0
|
CE1
|
B:HIS17
|
3.0
|
9.3
|
1.0
|
C1D
|
B:HEC102
|
3.0
|
4.2
|
1.0
|
C4C
|
B:HEC102
|
3.1
|
11.6
|
1.0
|
C4D
|
B:HEC102
|
3.1
|
8.4
|
1.0
|
C1B
|
B:HEC102
|
3.1
|
6.2
|
1.0
|
C4A
|
B:HEC102
|
3.1
|
5.5
|
1.0
|
CE
|
B:MET44
|
3.2
|
11.3
|
1.0
|
CHC
|
B:HEC102
|
3.4
|
10.7
|
1.0
|
CHA
|
B:HEC102
|
3.4
|
11.4
|
1.0
|
CHD
|
B:HEC102
|
3.4
|
8.4
|
1.0
|
CHB
|
B:HEC102
|
3.5
|
5.0
|
1.0
|
CG
|
B:MET44
|
3.5
|
9.1
|
1.0
|
ND1
|
B:HIS17
|
4.1
|
10.8
|
1.0
|
CG
|
B:HIS17
|
4.1
|
11.9
|
1.0
|
C2C
|
B:HEC102
|
4.2
|
10.5
|
1.0
|
C3B
|
B:HEC102
|
4.3
|
9.5
|
1.0
|
C2B
|
B:HEC102
|
4.3
|
13.8
|
1.0
|
C3C
|
B:HEC102
|
4.3
|
10.0
|
1.0
|
C2A
|
B:HEC102
|
4.3
|
6.0
|
1.0
|
C2D
|
B:HEC102
|
4.3
|
5.7
|
1.0
|
C3A
|
B:HEC102
|
4.3
|
4.0
|
1.0
|
C3D
|
B:HEC102
|
4.3
|
7.0
|
1.0
|
CB
|
B:MET44
|
4.9
|
9.2
|
1.0
|
O
|
B:ARG41
|
5.0
|
8.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 3 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe104
b:9.3
occ:1.00
|
FE
|
C:HEC104
|
0.0
|
9.3
|
1.0
|
NE2
|
C:HIS17
|
2.0
|
10.0
|
1.0
|
NC
|
C:HEC104
|
2.0
|
8.0
|
1.0
|
NB
|
C:HEC104
|
2.0
|
10.3
|
1.0
|
ND
|
C:HEC104
|
2.0
|
4.9
|
1.0
|
NA
|
C:HEC104
|
2.1
|
12.1
|
1.0
|
SD
|
C:MET44
|
2.4
|
8.6
|
1.0
|
CE1
|
C:HIS17
|
3.0
|
7.7
|
1.0
|
C4C
|
C:HEC104
|
3.0
|
8.3
|
1.0
|
CD2
|
C:HIS17
|
3.0
|
9.5
|
1.0
|
C4B
|
C:HEC104
|
3.0
|
9.5
|
1.0
|
C1D
|
C:HEC104
|
3.0
|
8.9
|
1.0
|
C1B
|
C:HEC104
|
3.0
|
13.2
|
1.0
|
C4D
|
C:HEC104
|
3.1
|
5.8
|
1.0
|
C4A
|
C:HEC104
|
3.1
|
8.4
|
1.0
|
C1C
|
C:HEC104
|
3.1
|
9.7
|
1.0
|
C1A
|
C:HEC104
|
3.1
|
11.9
|
1.0
|
CHD
|
C:HEC104
|
3.4
|
10.5
|
1.0
|
CG
|
C:MET44
|
3.4
|
6.4
|
1.0
|
CHB
|
C:HEC104
|
3.4
|
8.0
|
1.0
|
CHC
|
C:HEC104
|
3.4
|
14.1
|
1.0
|
CHA
|
C:HEC104
|
3.4
|
10.4
|
1.0
|
CE
|
C:MET44
|
3.5
|
7.9
|
1.0
|
ND1
|
C:HIS17
|
4.1
|
9.7
|
1.0
|
CG
|
C:HIS17
|
4.1
|
10.1
|
1.0
|
C3B
|
C:HEC104
|
4.2
|
11.1
|
1.0
|
C2B
|
C:HEC104
|
4.2
|
12.1
|
1.0
|
C3C
|
C:HEC104
|
4.3
|
10.4
|
1.0
|
C2D
|
C:HEC104
|
4.3
|
6.8
|
1.0
|
C2C
|
C:HEC104
|
4.3
|
10.2
|
1.0
|
C3D
|
C:HEC104
|
4.3
|
5.6
|
1.0
|
C3A
|
C:HEC104
|
4.3
|
9.2
|
1.0
|
C2A
|
C:HEC104
|
4.3
|
9.1
|
1.0
|
CB
|
C:MET44
|
4.8
|
7.0
|
1.0
|
O
|
C:ARG41
|
4.9
|
8.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 4 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe104
b:9.1
occ:1.00
|
FE
|
D:HEC104
|
0.0
|
9.1
|
1.0
|
NE2
|
D:HIS17
|
2.0
|
9.1
|
1.0
|
NB
|
D:HEC104
|
2.0
|
6.2
|
1.0
|
NA
|
D:HEC104
|
2.0
|
12.1
|
1.0
|
NC
|
D:HEC104
|
2.1
|
16.2
|
1.0
|
ND
|
D:HEC104
|
2.1
|
7.6
|
1.0
|
SD
|
D:MET44
|
2.5
|
9.1
|
1.0
|
CD2
|
D:HIS17
|
3.0
|
10.7
|
1.0
|
CE1
|
D:HIS17
|
3.0
|
6.9
|
1.0
|
C1B
|
D:HEC104
|
3.0
|
8.5
|
1.0
|
C4B
|
D:HEC104
|
3.0
|
7.8
|
1.0
|
C1C
|
D:HEC104
|
3.0
|
9.7
|
1.0
|
C1A
|
D:HEC104
|
3.1
|
7.4
|
1.0
|
C4A
|
D:HEC104
|
3.1
|
8.8
|
1.0
|
C1D
|
D:HEC104
|
3.1
|
6.2
|
1.0
|
C4D
|
D:HEC104
|
3.1
|
11.2
|
1.0
|
C4C
|
D:HEC104
|
3.1
|
12.7
|
1.0
|
CE
|
D:MET44
|
3.2
|
10.3
|
1.0
|
CG
|
D:MET44
|
3.4
|
7.8
|
1.0
|
CHC
|
D:HEC104
|
3.4
|
6.2
|
1.0
|
CHB
|
D:HEC104
|
3.4
|
5.5
|
1.0
|
CHA
|
D:HEC104
|
3.4
|
10.3
|
1.0
|
CHD
|
D:HEC104
|
3.5
|
10.2
|
1.0
|
ND1
|
D:HIS17
|
4.1
|
9.7
|
1.0
|
CG
|
D:HIS17
|
4.1
|
11.5
|
1.0
|
C2B
|
D:HEC104
|
4.2
|
7.5
|
1.0
|
C3B
|
D:HEC104
|
4.2
|
8.5
|
1.0
|
C2C
|
D:HEC104
|
4.3
|
11.2
|
1.0
|
C3A
|
D:HEC104
|
4.3
|
6.6
|
1.0
|
C2A
|
D:HEC104
|
4.3
|
7.0
|
1.0
|
C3C
|
D:HEC104
|
4.3
|
8.7
|
1.0
|
C3D
|
D:HEC104
|
4.3
|
8.3
|
1.0
|
C2D
|
D:HEC104
|
4.4
|
5.7
|
1.0
|
CB
|
D:MET44
|
4.8
|
8.9
|
1.0
|
O
|
D:ARG41
|
4.9
|
8.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 5 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe103
b:9.3
occ:1.00
|
FE
|
E:HEC103
|
0.0
|
9.3
|
1.0
|
NB
|
E:HEC103
|
2.0
|
9.5
|
1.0
|
NE2
|
E:HIS17
|
2.0
|
9.3
|
1.0
|
NC
|
E:HEC103
|
2.1
|
8.6
|
1.0
|
ND
|
E:HEC103
|
2.1
|
5.6
|
1.0
|
NA
|
E:HEC103
|
2.1
|
11.0
|
1.0
|
SD
|
E:MET44
|
2.4
|
7.4
|
1.0
|
CE1
|
E:HIS17
|
3.0
|
7.8
|
1.0
|
C4B
|
E:HEC103
|
3.0
|
7.7
|
1.0
|
C1B
|
E:HEC103
|
3.0
|
18.5
|
1.0
|
CD2
|
E:HIS17
|
3.0
|
12.2
|
1.0
|
C1D
|
E:HEC103
|
3.1
|
11.3
|
1.0
|
C4A
|
E:HEC103
|
3.1
|
10.7
|
1.0
|
C1C
|
E:HEC103
|
3.1
|
10.7
|
1.0
|
C4D
|
E:HEC103
|
3.1
|
5.8
|
1.0
|
C4C
|
E:HEC103
|
3.1
|
9.1
|
1.0
|
C1A
|
E:HEC103
|
3.2
|
10.4
|
1.0
|
CG
|
E:MET44
|
3.4
|
6.8
|
1.0
|
CHC
|
E:HEC103
|
3.4
|
12.2
|
1.0
|
CHB
|
E:HEC103
|
3.4
|
13.7
|
1.0
|
CHD
|
E:HEC103
|
3.4
|
9.4
|
1.0
|
CE
|
E:MET44
|
3.5
|
6.1
|
1.0
|
CHA
|
E:HEC103
|
3.5
|
5.8
|
1.0
|
ND1
|
E:HIS17
|
4.1
|
9.7
|
1.0
|
CG
|
E:HIS17
|
4.2
|
8.8
|
1.0
|
C2B
|
E:HEC103
|
4.2
|
11.8
|
1.0
|
C3B
|
E:HEC103
|
4.2
|
9.7
|
1.0
|
C2C
|
E:HEC103
|
4.3
|
7.2
|
1.0
|
C2D
|
E:HEC103
|
4.3
|
5.1
|
1.0
|
C3D
|
E:HEC103
|
4.3
|
9.5
|
1.0
|
C3A
|
E:HEC103
|
4.3
|
12.1
|
1.0
|
C3C
|
E:HEC103
|
4.3
|
7.3
|
1.0
|
C2A
|
E:HEC103
|
4.4
|
8.6
|
1.0
|
CB
|
E:MET44
|
4.8
|
6.5
|
1.0
|
O
|
E:ARG41
|
4.9
|
7.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 8qjg
Go back to
Iron Binding Sites List in 8qjg
Iron binding site 6 out
of 6 in the Crystal Structure of Cytochrome Domain 2 From Pgca
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 Cytochrome Domain 2 From Pgca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe104
b:9.0
occ:1.00
|
FE
|
F:HEC104
|
0.0
|
9.0
|
1.0
|
NB
|
F:HEC104
|
2.0
|
9.6
|
1.0
|
NE2
|
F:HIS17
|
2.0
|
7.4
|
1.0
|
ND
|
F:HEC104
|
2.0
|
9.7
|
1.0
|
NC
|
F:HEC104
|
2.1
|
9.7
|
1.0
|
NA
|
F:HEC104
|
2.1
|
10.1
|
1.0
|
SD
|
F:MET44
|
2.4
|
8.4
|
1.0
|
CE1
|
F:HIS17
|
2.9
|
6.5
|
1.0
|
C1B
|
F:HEC104
|
3.0
|
13.2
|
1.0
|
C4B
|
F:HEC104
|
3.0
|
5.4
|
1.0
|
C1D
|
F:HEC104
|
3.0
|
10.3
|
1.0
|
C4D
|
F:HEC104
|
3.1
|
8.9
|
1.0
|
CD2
|
F:HIS17
|
3.1
|
9.1
|
1.0
|
C4A
|
F:HEC104
|
3.1
|
5.3
|
1.0
|
C4C
|
F:HEC104
|
3.1
|
7.5
|
1.0
|
C1C
|
F:HEC104
|
3.1
|
7.1
|
1.0
|
C1A
|
F:HEC104
|
3.1
|
8.3
|
1.0
|
CE
|
F:MET44
|
3.4
|
4.6
|
1.0
|
CHD
|
F:HEC104
|
3.4
|
7.9
|
1.0
|
CHB
|
F:HEC104
|
3.4
|
10.3
|
1.0
|
CG
|
F:MET44
|
3.4
|
8.8
|
1.0
|
CHC
|
F:HEC104
|
3.5
|
9.9
|
1.0
|
CHA
|
F:HEC104
|
3.5
|
4.6
|
1.0
|
ND1
|
F:HIS17
|
4.0
|
8.2
|
1.0
|
CG
|
F:HIS17
|
4.2
|
7.7
|
1.0
|
C2B
|
F:HEC104
|
4.2
|
12.4
|
1.0
|
C3B
|
F:HEC104
|
4.2
|
12.0
|
1.0
|
C2D
|
F:HEC104
|
4.3
|
8.9
|
1.0
|
C3D
|
F:HEC104
|
4.3
|
10.8
|
1.0
|
C3A
|
F:HEC104
|
4.3
|
8.4
|
1.0
|
C3C
|
F:HEC104
|
4.3
|
5.6
|
1.0
|
C2C
|
F:HEC104
|
4.3
|
10.0
|
1.0
|
C2A
|
F:HEC104
|
4.3
|
8.0
|
1.0
|
CB
|
F:MET44
|
4.8
|
9.8
|
1.0
|
O
|
F:ARG41
|
4.9
|
8.6
|
1.0
|
|
Reference:
B.W.Nash,
T.M.Fernandes,
J.A.J.Burton,
L.Morgado,
J.H.Van Wonderen,
D.A.Svistunenko,
M.J.Edwards,
C.A.Salgueiro,
J.N.Butt,
T.A.Clarke.
Tethered Heme Domains in A Triheme Cytochrome Allow For Increased Electron Transport Distances. Protein Sci. V. 33 E5200 2024.
ISSN: ESSN 1469-896X
PubMed: 39470321
DOI: 10.1002/PRO.5200
Page generated: Wed Nov 13 09:48:24 2024
|