Iron in PDB 9krd: Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
Protein crystallography data
The structure of Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942, PDB code: 9krd
was solved by
B.T.Zhang,
S.W.Liu,
Y.C.Xu,
W.Sheng,
Y.Gong,
P.Cao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.25 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.505,
73.873,
98.781,
90,
90,
90
|
R / Rfree (%)
|
16.7 /
18.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
(pdb code 9krd). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942, PDB code: 9krd:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 9krd
Go back to
Iron Binding Sites List in 9krd
Iron binding site 1 out
of 4 in the Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
 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 Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:11.1
occ:1.00
|
FE
|
A:HEC101
|
0.0
|
11.1
|
1.0
|
NB
|
A:HEC101
|
2.0
|
10.8
|
1.0
|
NC
|
A:HEC101
|
2.0
|
11.4
|
1.0
|
NA
|
A:HEC101
|
2.0
|
12.7
|
1.0
|
NE2
|
A:HIS18
|
2.0
|
9.5
|
1.0
|
ND
|
A:HEC101
|
2.1
|
11.1
|
1.0
|
SD
|
A:MET58
|
2.4
|
11.2
|
1.0
|
CE1
|
A:HIS18
|
3.0
|
11.5
|
1.0
|
C1B
|
A:HEC101
|
3.0
|
10.2
|
1.0
|
C4A
|
A:HEC101
|
3.0
|
10.5
|
1.0
|
CD2
|
A:HIS18
|
3.0
|
11.2
|
1.0
|
C1C
|
A:HEC101
|
3.0
|
12.1
|
1.0
|
C4C
|
A:HEC101
|
3.1
|
10.0
|
1.0
|
C1A
|
A:HEC101
|
3.1
|
12.1
|
1.0
|
C4B
|
A:HEC101
|
3.1
|
11.9
|
1.0
|
C1D
|
A:HEC101
|
3.1
|
9.4
|
1.0
|
C4D
|
A:HEC101
|
3.1
|
11.1
|
1.0
|
CHB
|
A:HEC101
|
3.4
|
11.2
|
1.0
|
CHD
|
A:HEC101
|
3.4
|
9.7
|
1.0
|
CG
|
A:MET58
|
3.4
|
13.9
|
1.0
|
CE
|
A:MET58
|
3.4
|
11.6
|
1.0
|
CHA
|
A:HEC101
|
3.4
|
11.5
|
1.0
|
CHC
|
A:HEC101
|
3.4
|
13.5
|
1.0
|
CB
|
A:MET58
|
4.1
|
11.0
|
1.0
|
ND1
|
A:HIS18
|
4.1
|
11.3
|
1.0
|
CG
|
A:HIS18
|
4.2
|
9.5
|
1.0
|
C2B
|
A:HEC101
|
4.2
|
12.9
|
1.0
|
C3A
|
A:HEC101
|
4.3
|
12.4
|
1.0
|
C2A
|
A:HEC101
|
4.3
|
10.4
|
1.0
|
C2C
|
A:HEC101
|
4.3
|
10.6
|
1.0
|
C3B
|
A:HEC101
|
4.3
|
13.2
|
1.0
|
C3C
|
A:HEC101
|
4.3
|
11.4
|
1.0
|
C2D
|
A:HEC101
|
4.3
|
10.6
|
1.0
|
C3D
|
A:HEC101
|
4.3
|
10.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 9krd
Go back to
Iron Binding Sites List in 9krd
Iron binding site 2 out
of 4 in the Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
 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 Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe101
b:11.6
occ:1.00
|
FE
|
B:HEC101
|
0.0
|
11.6
|
1.0
|
NB
|
B:HEC101
|
2.0
|
10.7
|
1.0
|
NA
|
B:HEC101
|
2.0
|
13.2
|
1.0
|
NC
|
B:HEC101
|
2.0
|
12.5
|
1.0
|
ND
|
B:HEC101
|
2.0
|
11.7
|
1.0
|
NE2
|
B:HIS18
|
2.1
|
11.2
|
1.0
|
SD
|
B:MET58
|
2.3
|
12.2
|
1.0
|
C1D
|
B:HEC101
|
3.0
|
10.6
|
1.0
|
C4A
|
B:HEC101
|
3.0
|
11.3
|
1.0
|
C4D
|
B:HEC101
|
3.0
|
11.3
|
1.0
|
CD2
|
B:HIS18
|
3.0
|
12.2
|
1.0
|
CE1
|
B:HIS18
|
3.0
|
14.1
|
1.0
|
C4B
|
B:HEC101
|
3.0
|
10.6
|
1.0
|
C1B
|
B:HEC101
|
3.0
|
11.0
|
1.0
|
C1A
|
B:HEC101
|
3.1
|
12.1
|
1.0
|
C1C
|
B:HEC101
|
3.1
|
12.5
|
1.0
|
C4C
|
B:HEC101
|
3.1
|
10.9
|
1.0
|
CG
|
B:MET58
|
3.4
|
13.4
|
1.0
|
CHD
|
B:HEC101
|
3.4
|
11.6
|
1.0
|
CHB
|
B:HEC101
|
3.4
|
11.3
|
1.0
|
CHC
|
B:HEC101
|
3.4
|
12.1
|
1.0
|
CHA
|
B:HEC101
|
3.4
|
11.1
|
1.0
|
CE
|
B:MET58
|
3.4
|
11.4
|
1.0
|
CB
|
B:MET58
|
4.1
|
14.8
|
1.0
|
ND1
|
B:HIS18
|
4.1
|
11.8
|
1.0
|
CG
|
B:HIS18
|
4.2
|
10.9
|
1.0
|
C2D
|
B:HEC101
|
4.2
|
13.7
|
1.0
|
C2B
|
B:HEC101
|
4.2
|
11.1
|
1.0
|
C3D
|
B:HEC101
|
4.3
|
13.4
|
1.0
|
C3A
|
B:HEC101
|
4.3
|
11.7
|
1.0
|
C3B
|
B:HEC101
|
4.3
|
10.8
|
1.0
|
C2A
|
B:HEC101
|
4.3
|
13.2
|
1.0
|
C2C
|
B:HEC101
|
4.3
|
11.5
|
1.0
|
C3C
|
B:HEC101
|
4.3
|
12.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 9krd
Go back to
Iron Binding Sites List in 9krd
Iron binding site 3 out
of 4 in the Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
 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 Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:14.2
occ:1.00
|
FE
|
C:HEC101
|
0.0
|
14.2
|
1.0
|
NB
|
C:HEC101
|
2.0
|
13.8
|
1.0
|
NA
|
C:HEC101
|
2.0
|
12.7
|
1.0
|
NC
|
C:HEC101
|
2.0
|
14.1
|
1.0
|
NE2
|
C:HIS18
|
2.0
|
13.1
|
1.0
|
ND
|
C:HEC101
|
2.1
|
13.9
|
1.0
|
SD
|
C:MET58
|
2.4
|
13.4
|
1.0
|
CD2
|
C:HIS18
|
3.0
|
14.1
|
1.0
|
C4B
|
C:HEC101
|
3.0
|
14.2
|
1.0
|
C1B
|
C:HEC101
|
3.0
|
13.2
|
1.0
|
C1C
|
C:HEC101
|
3.0
|
13.4
|
1.0
|
CE1
|
C:HIS18
|
3.0
|
16.0
|
1.0
|
C1A
|
C:HEC101
|
3.0
|
14.9
|
1.0
|
C4A
|
C:HEC101
|
3.0
|
14.3
|
1.0
|
C4C
|
C:HEC101
|
3.1
|
12.8
|
1.0
|
C4D
|
C:HEC101
|
3.1
|
13.7
|
1.0
|
C1D
|
C:HEC101
|
3.1
|
11.2
|
1.0
|
CHC
|
C:HEC101
|
3.4
|
14.8
|
1.0
|
CHB
|
C:HEC101
|
3.4
|
14.9
|
1.0
|
CHA
|
C:HEC101
|
3.4
|
17.1
|
1.0
|
CG
|
C:MET58
|
3.4
|
15.2
|
1.0
|
CHD
|
C:HEC101
|
3.4
|
14.2
|
1.0
|
CE
|
C:MET58
|
3.5
|
13.2
|
1.0
|
ND1
|
C:HIS18
|
4.1
|
14.5
|
1.0
|
CB
|
C:MET58
|
4.1
|
15.1
|
1.0
|
CG
|
C:HIS18
|
4.2
|
13.8
|
1.0
|
C2B
|
C:HEC101
|
4.2
|
13.8
|
1.0
|
C2C
|
C:HEC101
|
4.2
|
11.2
|
1.0
|
C3B
|
C:HEC101
|
4.2
|
16.1
|
1.0
|
C3A
|
C:HEC101
|
4.3
|
15.1
|
1.0
|
C2A
|
C:HEC101
|
4.3
|
16.6
|
1.0
|
C3C
|
C:HEC101
|
4.3
|
11.1
|
1.0
|
C3D
|
C:HEC101
|
4.3
|
13.2
|
1.0
|
C2D
|
C:HEC101
|
4.3
|
14.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 9krd
Go back to
Iron Binding Sites List in 9krd
Iron binding site 4 out
of 4 in the Crystal Structure of Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942
 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 Reduced Cytochrome C6 From Synechococcus Elongatus Pcc 7942 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe101
b:12.7
occ:1.00
|
FE
|
D:HEC101
|
0.0
|
12.7
|
1.0
|
NB
|
D:HEC101
|
2.0
|
11.2
|
1.0
|
NA
|
D:HEC101
|
2.0
|
11.5
|
1.0
|
NC
|
D:HEC101
|
2.0
|
12.6
|
1.0
|
NE2
|
D:HIS18
|
2.1
|
13.1
|
1.0
|
ND
|
D:HEC101
|
2.1
|
11.8
|
1.0
|
SD
|
D:MET58
|
2.4
|
12.2
|
1.0
|
C1B
|
D:HEC101
|
3.0
|
11.7
|
1.0
|
C4A
|
D:HEC101
|
3.0
|
12.6
|
1.0
|
CD2
|
D:HIS18
|
3.0
|
12.3
|
1.0
|
C4B
|
D:HEC101
|
3.0
|
14.3
|
1.0
|
C1A
|
D:HEC101
|
3.1
|
12.3
|
1.0
|
C1D
|
D:HEC101
|
3.1
|
10.7
|
1.0
|
C4C
|
D:HEC101
|
3.1
|
12.2
|
1.0
|
C1C
|
D:HEC101
|
3.1
|
13.6
|
1.0
|
C4D
|
D:HEC101
|
3.1
|
12.1
|
1.0
|
CE1
|
D:HIS18
|
3.1
|
14.6
|
1.0
|
CHB
|
D:HEC101
|
3.4
|
15.0
|
1.0
|
CHD
|
D:HEC101
|
3.4
|
12.8
|
1.0
|
CG
|
D:MET58
|
3.4
|
16.7
|
1.0
|
CHC
|
D:HEC101
|
3.4
|
15.8
|
1.0
|
CHA
|
D:HEC101
|
3.4
|
12.6
|
1.0
|
CE
|
D:MET58
|
3.5
|
12.5
|
1.0
|
CB
|
D:MET58
|
4.1
|
15.0
|
1.0
|
CG
|
D:HIS18
|
4.2
|
11.1
|
1.0
|
ND1
|
D:HIS18
|
4.2
|
12.8
|
1.0
|
C2B
|
D:HEC101
|
4.2
|
12.4
|
1.0
|
C3B
|
D:HEC101
|
4.2
|
12.4
|
1.0
|
C3A
|
D:HEC101
|
4.2
|
12.3
|
1.0
|
C2A
|
D:HEC101
|
4.3
|
15.9
|
1.0
|
C2D
|
D:HEC101
|
4.3
|
11.5
|
1.0
|
C3D
|
D:HEC101
|
4.3
|
11.5
|
1.0
|
C2C
|
D:HEC101
|
4.3
|
12.1
|
1.0
|
C3C
|
D:HEC101
|
4.3
|
11.4
|
1.0
|
|
Reference:
B.Zhang,
Y.Xu,
S.Liu,
S.Chen,
W.Zhao,
Z.Li,
J.Wang,
W.Zhao,
H.Zhang,
Y.Dong,
Y.Gong,
W.Sheng,
P.Cao.
A High-Resolution Crystallographic Study of Cytochrome C6: Structural Basis For Electron Transfer in Cyanobacterial Photosynthesis Int J Mol Sci V. 26 2025.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS26020824
Page generated: Sun Feb 9 07:25:09 2025
|