Iron in PDB 5ziq: Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
Protein crystallography data
The structure of Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4, PDB code: 5ziq
was solved by
J.Kim,
Y.Fukuda,
T.Inoue,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.01 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.359,
59.185,
67.521,
115.36,
97.98,
97.43
|
R / Rfree (%)
|
14.7 /
19.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
(pdb code 5ziq). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4, PDB code: 5ziq:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 1 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:11.0
occ:0.50
|
FE
|
A:HEM1001
|
0.0
|
11.0
|
0.5
|
FE
|
A:HEM1001
|
0.1
|
11.2
|
0.5
|
ND
|
A:HEM1001
|
1.9
|
12.1
|
0.5
|
ND
|
A:HEM1001
|
1.9
|
11.9
|
0.5
|
NA
|
A:HEM1001
|
2.0
|
12.3
|
0.5
|
NA
|
A:HEM1001
|
2.0
|
12.1
|
0.5
|
NE2
|
A:HIS135
|
2.0
|
10.5
|
1.0
|
NC
|
A:HEM1001
|
2.1
|
9.8
|
0.5
|
NB
|
A:HEM1001
|
2.1
|
11.8
|
0.5
|
NB
|
A:HEM1001
|
2.1
|
10.8
|
0.5
|
NC
|
A:HEM1001
|
2.1
|
11.5
|
0.5
|
NE2
|
A:HIS107
|
2.1
|
9.6
|
1.0
|
C4D
|
A:HEM1001
|
2.9
|
12.9
|
0.5
|
C4D
|
A:HEM1001
|
2.9
|
12.6
|
0.5
|
C1D
|
A:HEM1001
|
2.9
|
10.8
|
0.5
|
C1D
|
A:HEM1001
|
2.9
|
12.5
|
0.5
|
C1A
|
A:HEM1001
|
3.0
|
13.3
|
0.5
|
CE1
|
A:HIS135
|
3.0
|
11.0
|
1.0
|
C4A
|
A:HEM1001
|
3.0
|
12.0
|
0.5
|
C1A
|
A:HEM1001
|
3.0
|
13.0
|
0.5
|
C4B
|
A:HEM1001
|
3.0
|
11.6
|
0.5
|
CD2
|
A:HIS107
|
3.0
|
10.3
|
1.0
|
C1B
|
A:HEM1001
|
3.0
|
12.6
|
0.5
|
C4C
|
A:HEM1001
|
3.0
|
9.9
|
0.5
|
C4A
|
A:HEM1001
|
3.0
|
12.7
|
0.5
|
C1B
|
A:HEM1001
|
3.0
|
11.5
|
0.5
|
CD2
|
A:HIS135
|
3.1
|
11.4
|
1.0
|
C4B
|
A:HEM1001
|
3.1
|
11.0
|
0.5
|
C1C
|
A:HEM1001
|
3.1
|
9.6
|
0.5
|
C4C
|
A:HEM1001
|
3.1
|
11.8
|
0.5
|
CE1
|
A:HIS107
|
3.1
|
11.3
|
1.0
|
C1C
|
A:HEM1001
|
3.1
|
11.0
|
0.5
|
CHA
|
A:HEM1001
|
3.3
|
14.1
|
0.5
|
CHA
|
A:HEM1001
|
3.4
|
13.8
|
0.5
|
CHD
|
A:HEM1001
|
3.4
|
10.2
|
0.5
|
CHB
|
A:HEM1001
|
3.4
|
12.6
|
0.5
|
CHB
|
A:HEM1001
|
3.4
|
11.5
|
0.5
|
CHD
|
A:HEM1001
|
3.4
|
11.9
|
0.5
|
CHC
|
A:HEM1001
|
3.4
|
11.3
|
0.5
|
CHC
|
A:HEM1001
|
3.5
|
11.4
|
0.5
|
ND1
|
A:HIS135
|
4.1
|
11.7
|
1.0
|
ND1
|
A:HIS107
|
4.1
|
11.3
|
1.0
|
CG
|
A:HIS107
|
4.1
|
10.7
|
1.0
|
C2A
|
A:HEM1001
|
4.2
|
13.8
|
0.5
|
C3D
|
A:HEM1001
|
4.2
|
13.4
|
0.5
|
CG
|
A:HIS135
|
4.2
|
10.9
|
1.0
|
C3A
|
A:HEM1001
|
4.2
|
12.8
|
0.5
|
C2D
|
A:HEM1001
|
4.2
|
12.4
|
0.5
|
C3D
|
A:HEM1001
|
4.2
|
12.6
|
0.5
|
C2D
|
A:HEM1001
|
4.2
|
11.3
|
0.5
|
C2A
|
A:HEM1001
|
4.2
|
13.8
|
0.5
|
C3A
|
A:HEM1001
|
4.2
|
12.8
|
0.5
|
C3C
|
A:HEM1001
|
4.2
|
9.5
|
0.5
|
C2B
|
A:HEM1001
|
4.2
|
13.6
|
0.5
|
C2C
|
A:HEM1001
|
4.3
|
9.3
|
0.5
|
C3B
|
A:HEM1001
|
4.3
|
13.0
|
0.5
|
C2B
|
A:HEM1001
|
4.3
|
11.7
|
0.5
|
C2C
|
A:HEM1001
|
4.3
|
11.6
|
0.5
|
C3C
|
A:HEM1001
|
4.3
|
12.3
|
0.5
|
C3B
|
A:HEM1001
|
4.3
|
11.3
|
0.5
|
|
Iron binding site 2 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 2 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:11.2
occ:0.50
|
FE
|
A:HEM1001
|
0.0
|
11.2
|
0.5
|
FE
|
A:HEM1001
|
0.1
|
11.0
|
0.5
|
ND
|
A:HEM1001
|
1.9
|
12.1
|
0.5
|
ND
|
A:HEM1001
|
2.0
|
11.9
|
0.5
|
NA
|
A:HEM1001
|
2.0
|
12.1
|
0.5
|
NA
|
A:HEM1001
|
2.0
|
12.3
|
0.5
|
NB
|
A:HEM1001
|
2.0
|
11.8
|
0.5
|
NE2
|
A:HIS135
|
2.1
|
10.5
|
1.0
|
NC
|
A:HEM1001
|
2.1
|
11.5
|
0.5
|
NC
|
A:HEM1001
|
2.1
|
9.8
|
0.5
|
NB
|
A:HEM1001
|
2.1
|
10.8
|
0.5
|
NE2
|
A:HIS107
|
2.1
|
9.6
|
1.0
|
C4D
|
A:HEM1001
|
2.9
|
12.9
|
0.5
|
C1D
|
A:HEM1001
|
2.9
|
12.5
|
0.5
|
C4D
|
A:HEM1001
|
3.0
|
12.6
|
0.5
|
C1D
|
A:HEM1001
|
3.0
|
10.8
|
0.5
|
C4B
|
A:HEM1001
|
3.0
|
11.6
|
0.5
|
C1B
|
A:HEM1001
|
3.0
|
12.6
|
0.5
|
CD2
|
A:HIS107
|
3.0
|
10.3
|
1.0
|
C1A
|
A:HEM1001
|
3.0
|
13.3
|
0.5
|
C1A
|
A:HEM1001
|
3.0
|
13.0
|
0.5
|
CE1
|
A:HIS135
|
3.0
|
11.0
|
1.0
|
C4A
|
A:HEM1001
|
3.0
|
12.7
|
0.5
|
C4A
|
A:HEM1001
|
3.0
|
12.0
|
0.5
|
C4C
|
A:HEM1001
|
3.0
|
11.8
|
0.5
|
C4C
|
A:HEM1001
|
3.1
|
9.9
|
0.5
|
C4B
|
A:HEM1001
|
3.1
|
11.0
|
0.5
|
C1B
|
A:HEM1001
|
3.1
|
11.5
|
0.5
|
C1C
|
A:HEM1001
|
3.1
|
11.0
|
0.5
|
C1C
|
A:HEM1001
|
3.1
|
9.6
|
0.5
|
CD2
|
A:HIS135
|
3.1
|
11.4
|
1.0
|
CE1
|
A:HIS107
|
3.1
|
11.3
|
1.0
|
CHA
|
A:HEM1001
|
3.4
|
14.1
|
0.5
|
CHB
|
A:HEM1001
|
3.4
|
12.6
|
0.5
|
CHD
|
A:HEM1001
|
3.4
|
11.9
|
0.5
|
CHA
|
A:HEM1001
|
3.4
|
13.8
|
0.5
|
CHC
|
A:HEM1001
|
3.4
|
11.3
|
0.5
|
CHD
|
A:HEM1001
|
3.4
|
10.2
|
0.5
|
CHB
|
A:HEM1001
|
3.4
|
11.5
|
0.5
|
CHC
|
A:HEM1001
|
3.5
|
11.4
|
0.5
|
CG
|
A:HIS107
|
4.1
|
10.7
|
1.0
|
ND1
|
A:HIS107
|
4.1
|
11.3
|
1.0
|
ND1
|
A:HIS135
|
4.2
|
11.7
|
1.0
|
C3D
|
A:HEM1001
|
4.2
|
13.4
|
0.5
|
C2D
|
A:HEM1001
|
4.2
|
12.4
|
0.5
|
C2B
|
A:HEM1001
|
4.2
|
13.6
|
0.5
|
CG
|
A:HIS135
|
4.2
|
10.9
|
1.0
|
C2A
|
A:HEM1001
|
4.2
|
13.8
|
0.5
|
C3B
|
A:HEM1001
|
4.2
|
13.0
|
0.5
|
C3A
|
A:HEM1001
|
4.2
|
12.8
|
0.5
|
C2A
|
A:HEM1001
|
4.2
|
13.8
|
0.5
|
C3A
|
A:HEM1001
|
4.2
|
12.8
|
0.5
|
C3D
|
A:HEM1001
|
4.2
|
12.6
|
0.5
|
C2D
|
A:HEM1001
|
4.2
|
11.3
|
0.5
|
C3C
|
A:HEM1001
|
4.2
|
9.5
|
0.5
|
C2C
|
A:HEM1001
|
4.2
|
11.6
|
0.5
|
C3C
|
A:HEM1001
|
4.2
|
12.3
|
0.5
|
C2C
|
A:HEM1001
|
4.2
|
9.3
|
0.5
|
C2B
|
A:HEM1001
|
4.3
|
11.7
|
0.5
|
C3B
|
A:HEM1001
|
4.3
|
11.3
|
0.5
|
|
Iron binding site 3 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 3 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:10.4
occ:0.50
|
FE
|
B:HEM1001
|
0.0
|
10.4
|
0.5
|
FE
|
B:HEM1001
|
0.1
|
10.6
|
0.5
|
ND
|
B:HEM1001
|
1.9
|
10.7
|
0.5
|
ND
|
B:HEM1001
|
1.9
|
11.1
|
0.5
|
NA
|
B:HEM1001
|
2.0
|
11.1
|
0.5
|
NA
|
B:HEM1001
|
2.0
|
11.3
|
0.5
|
NE2
|
B:HIS135
|
2.0
|
10.5
|
1.0
|
NB
|
B:HEM1001
|
2.1
|
10.0
|
0.5
|
NC
|
B:HEM1001
|
2.1
|
9.8
|
0.5
|
NB
|
B:HEM1001
|
2.1
|
11.0
|
0.5
|
NC
|
B:HEM1001
|
2.1
|
10.9
|
0.5
|
NE2
|
B:HIS107
|
2.2
|
10.0
|
1.0
|
C1D
|
B:HEM1001
|
2.9
|
9.7
|
0.5
|
C4D
|
B:HEM1001
|
2.9
|
10.6
|
0.5
|
C4D
|
B:HEM1001
|
3.0
|
11.8
|
0.5
|
CE1
|
B:HIS135
|
3.0
|
11.2
|
1.0
|
C1D
|
B:HEM1001
|
3.0
|
11.2
|
0.5
|
C1A
|
B:HEM1001
|
3.0
|
11.1
|
0.5
|
C1A
|
B:HEM1001
|
3.0
|
12.5
|
0.5
|
C1B
|
B:HEM1001
|
3.0
|
9.6
|
0.5
|
C4B
|
B:HEM1001
|
3.0
|
9.9
|
0.5
|
C4B
|
B:HEM1001
|
3.0
|
11.2
|
0.5
|
C4A
|
B:HEM1001
|
3.0
|
10.4
|
0.5
|
C4A
|
B:HEM1001
|
3.0
|
12.2
|
0.5
|
C1B
|
B:HEM1001
|
3.0
|
11.9
|
0.5
|
C4C
|
B:HEM1001
|
3.0
|
9.2
|
0.5
|
CD2
|
B:HIS135
|
3.0
|
10.3
|
1.0
|
CD2
|
B:HIS107
|
3.1
|
8.9
|
1.0
|
C1C
|
B:HEM1001
|
3.1
|
11.0
|
0.5
|
C4C
|
B:HEM1001
|
3.1
|
11.6
|
0.5
|
C1C
|
B:HEM1001
|
3.1
|
9.7
|
0.5
|
CE1
|
B:HIS107
|
3.1
|
9.3
|
1.0
|
CHA
|
B:HEM1001
|
3.4
|
11.6
|
0.5
|
CHB
|
B:HEM1001
|
3.4
|
11.9
|
0.5
|
CHD
|
B:HEM1001
|
3.4
|
8.8
|
0.5
|
CHA
|
B:HEM1001
|
3.4
|
11.6
|
0.5
|
CHC
|
B:HEM1001
|
3.4
|
10.6
|
0.5
|
CHB
|
B:HEM1001
|
3.4
|
9.5
|
0.5
|
CHC
|
B:HEM1001
|
3.4
|
10.6
|
0.5
|
CHD
|
B:HEM1001
|
3.4
|
11.0
|
0.5
|
ND1
|
B:HIS135
|
4.1
|
10.4
|
1.0
|
ND1
|
B:HIS107
|
4.1
|
9.2
|
1.0
|
CG
|
B:HIS107
|
4.1
|
8.5
|
1.0
|
CG
|
B:HIS135
|
4.2
|
10.7
|
1.0
|
C2A
|
B:HEM1001
|
4.2
|
11.0
|
0.5
|
C2D
|
B:HEM1001
|
4.2
|
9.3
|
0.5
|
C3A
|
B:HEM1001
|
4.2
|
10.1
|
0.5
|
C3D
|
B:HEM1001
|
4.2
|
10.0
|
0.5
|
C2A
|
B:HEM1001
|
4.2
|
13.3
|
0.5
|
C3A
|
B:HEM1001
|
4.2
|
13.0
|
0.5
|
C3D
|
B:HEM1001
|
4.2
|
11.6
|
0.5
|
C2B
|
B:HEM1001
|
4.2
|
9.3
|
0.5
|
C2D
|
B:HEM1001
|
4.2
|
11.5
|
0.5
|
C3C
|
B:HEM1001
|
4.2
|
9.1
|
0.5
|
C2C
|
B:HEM1001
|
4.2
|
11.7
|
0.5
|
C2B
|
B:HEM1001
|
4.2
|
12.2
|
0.5
|
C2C
|
B:HEM1001
|
4.2
|
9.3
|
0.5
|
C3C
|
B:HEM1001
|
4.3
|
12.1
|
0.5
|
C3B
|
B:HEM1001
|
4.3
|
9.3
|
0.5
|
C3B
|
B:HEM1001
|
4.3
|
12.2
|
0.5
|
|
Iron binding site 4 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 4 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:10.6
occ:0.50
|
FE
|
B:HEM1001
|
0.0
|
10.6
|
0.5
|
FE
|
B:HEM1001
|
0.1
|
10.4
|
0.5
|
ND
|
B:HEM1001
|
1.9
|
11.1
|
0.5
|
ND
|
B:HEM1001
|
1.9
|
10.7
|
0.5
|
NA
|
B:HEM1001
|
2.0
|
11.3
|
0.5
|
NA
|
B:HEM1001
|
2.0
|
11.1
|
0.5
|
NB
|
B:HEM1001
|
2.0
|
11.0
|
0.5
|
NC
|
B:HEM1001
|
2.1
|
10.9
|
0.5
|
NE2
|
B:HIS107
|
2.1
|
10.0
|
1.0
|
NB
|
B:HEM1001
|
2.1
|
10.0
|
0.5
|
NE2
|
B:HIS135
|
2.1
|
10.5
|
1.0
|
NC
|
B:HEM1001
|
2.1
|
9.8
|
0.5
|
C1D
|
B:HEM1001
|
2.9
|
11.2
|
0.5
|
C4D
|
B:HEM1001
|
2.9
|
11.8
|
0.5
|
C4D
|
B:HEM1001
|
3.0
|
10.6
|
0.5
|
C1D
|
B:HEM1001
|
3.0
|
9.7
|
0.5
|
C4A
|
B:HEM1001
|
3.0
|
12.2
|
0.5
|
C1B
|
B:HEM1001
|
3.0
|
11.9
|
0.5
|
C1A
|
B:HEM1001
|
3.0
|
12.5
|
0.5
|
CD2
|
B:HIS107
|
3.0
|
8.9
|
1.0
|
CE1
|
B:HIS107
|
3.0
|
9.3
|
1.0
|
C4B
|
B:HEM1001
|
3.0
|
11.2
|
0.5
|
C1A
|
B:HEM1001
|
3.0
|
11.1
|
0.5
|
C4C
|
B:HEM1001
|
3.0
|
11.6
|
0.5
|
C1B
|
B:HEM1001
|
3.1
|
9.6
|
0.5
|
CE1
|
B:HIS135
|
3.1
|
11.2
|
1.0
|
C4B
|
B:HEM1001
|
3.1
|
9.9
|
0.5
|
C4A
|
B:HEM1001
|
3.1
|
10.4
|
0.5
|
C1C
|
B:HEM1001
|
3.1
|
11.0
|
0.5
|
C4C
|
B:HEM1001
|
3.1
|
9.2
|
0.5
|
CD2
|
B:HIS135
|
3.1
|
10.3
|
1.0
|
C1C
|
B:HEM1001
|
3.1
|
9.7
|
0.5
|
CHB
|
B:HEM1001
|
3.4
|
11.9
|
0.5
|
CHD
|
B:HEM1001
|
3.4
|
11.0
|
0.5
|
CHA
|
B:HEM1001
|
3.4
|
11.6
|
0.5
|
CHA
|
B:HEM1001
|
3.4
|
11.6
|
0.5
|
CHD
|
B:HEM1001
|
3.4
|
8.8
|
0.5
|
CHC
|
B:HEM1001
|
3.4
|
10.6
|
0.5
|
CHC
|
B:HEM1001
|
3.5
|
10.6
|
0.5
|
CHB
|
B:HEM1001
|
3.5
|
9.5
|
0.5
|
ND1
|
B:HIS107
|
4.1
|
9.2
|
1.0
|
CG
|
B:HIS107
|
4.1
|
8.5
|
1.0
|
C3A
|
B:HEM1001
|
4.2
|
13.0
|
0.5
|
ND1
|
B:HIS135
|
4.2
|
10.4
|
1.0
|
C2A
|
B:HEM1001
|
4.2
|
13.3
|
0.5
|
C3D
|
B:HEM1001
|
4.2
|
11.6
|
0.5
|
C2D
|
B:HEM1001
|
4.2
|
11.5
|
0.5
|
C2B
|
B:HEM1001
|
4.2
|
12.2
|
0.5
|
C2A
|
B:HEM1001
|
4.2
|
11.0
|
0.5
|
C3D
|
B:HEM1001
|
4.2
|
10.0
|
0.5
|
C2C
|
B:HEM1001
|
4.2
|
11.7
|
0.5
|
CG
|
B:HIS135
|
4.2
|
10.7
|
1.0
|
C2D
|
B:HEM1001
|
4.2
|
9.3
|
0.5
|
C3A
|
B:HEM1001
|
4.2
|
10.1
|
0.5
|
C3C
|
B:HEM1001
|
4.2
|
12.1
|
0.5
|
C3B
|
B:HEM1001
|
4.3
|
12.2
|
0.5
|
C2B
|
B:HEM1001
|
4.3
|
9.3
|
0.5
|
C3C
|
B:HEM1001
|
4.3
|
9.1
|
0.5
|
C2C
|
B:HEM1001
|
4.3
|
9.3
|
0.5
|
C3B
|
B:HEM1001
|
4.3
|
9.3
|
0.5
|
|
Iron binding site 5 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 5 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1001
b:11.1
occ:0.50
|
FE
|
C:HEM1001
|
0.0
|
11.1
|
0.5
|
FE
|
C:HEM1001
|
0.1
|
11.3
|
0.5
|
ND
|
C:HEM1001
|
1.9
|
11.5
|
0.5
|
ND
|
C:HEM1001
|
1.9
|
10.6
|
0.5
|
NA
|
C:HEM1001
|
2.0
|
12.1
|
0.5
|
NA
|
C:HEM1001
|
2.0
|
11.5
|
0.5
|
NE2
|
C:HIS135
|
2.0
|
10.8
|
1.0
|
NC
|
C:HEM1001
|
2.1
|
10.1
|
0.5
|
NB
|
C:HEM1001
|
2.1
|
11.8
|
0.5
|
NC
|
C:HEM1001
|
2.1
|
11.3
|
0.5
|
NB
|
C:HEM1001
|
2.1
|
10.6
|
0.5
|
NE2
|
C:HIS107
|
2.2
|
10.2
|
1.0
|
C4D
|
C:HEM1001
|
2.9
|
12.4
|
0.5
|
C1D
|
C:HEM1001
|
2.9
|
11.7
|
0.5
|
C1D
|
C:HEM1001
|
2.9
|
10.1
|
0.5
|
C4D
|
C:HEM1001
|
2.9
|
11.0
|
0.5
|
CE1
|
C:HIS135
|
3.0
|
11.1
|
1.0
|
C1A
|
C:HEM1001
|
3.0
|
13.0
|
0.5
|
C1A
|
C:HEM1001
|
3.0
|
12.0
|
0.5
|
C4C
|
C:HEM1001
|
3.0
|
9.9
|
0.5
|
C4A
|
C:HEM1001
|
3.0
|
12.9
|
0.5
|
C4B
|
C:HEM1001
|
3.0
|
12.3
|
0.5
|
C4A
|
C:HEM1001
|
3.0
|
11.4
|
0.5
|
C1B
|
C:HEM1001
|
3.0
|
12.8
|
0.5
|
C1B
|
C:HEM1001
|
3.0
|
10.8
|
0.5
|
CD2
|
C:HIS107
|
3.0
|
9.9
|
1.0
|
C4C
|
C:HEM1001
|
3.1
|
11.8
|
0.5
|
C4B
|
C:HEM1001
|
3.1
|
10.9
|
0.5
|
CD2
|
C:HIS135
|
3.1
|
11.7
|
1.0
|
C1C
|
C:HEM1001
|
3.1
|
11.7
|
0.5
|
C1C
|
C:HEM1001
|
3.1
|
10.5
|
0.5
|
CE1
|
C:HIS107
|
3.1
|
10.7
|
1.0
|
CHA
|
C:HEM1001
|
3.4
|
12.3
|
0.5
|
CHA
|
C:HEM1001
|
3.4
|
12.1
|
0.5
|
CHD
|
C:HEM1001
|
3.4
|
10.3
|
0.5
|
CHD
|
C:HEM1001
|
3.4
|
11.7
|
0.5
|
CHB
|
C:HEM1001
|
3.4
|
13.6
|
0.5
|
CHB
|
C:HEM1001
|
3.4
|
11.7
|
0.5
|
CHC
|
C:HEM1001
|
3.4
|
10.9
|
0.5
|
CHC
|
C:HEM1001
|
3.5
|
11.0
|
0.5
|
ND1
|
C:HIS135
|
4.1
|
11.5
|
1.0
|
ND1
|
C:HIS107
|
4.1
|
10.9
|
1.0
|
CG
|
C:HIS107
|
4.1
|
10.4
|
1.0
|
C2D
|
C:HEM1001
|
4.2
|
12.3
|
0.5
|
CG
|
C:HIS135
|
4.2
|
12.1
|
1.0
|
C3D
|
C:HEM1001
|
4.2
|
12.2
|
0.5
|
C2A
|
C:HEM1001
|
4.2
|
13.6
|
0.5
|
C3A
|
C:HEM1001
|
4.2
|
13.7
|
0.5
|
C2D
|
C:HEM1001
|
4.2
|
10.1
|
0.5
|
C3A
|
C:HEM1001
|
4.2
|
11.7
|
0.5
|
C2A
|
C:HEM1001
|
4.2
|
12.1
|
0.5
|
C3C
|
C:HEM1001
|
4.2
|
9.8
|
0.5
|
C3D
|
C:HEM1001
|
4.2
|
10.4
|
0.5
|
C2C
|
C:HEM1001
|
4.2
|
12.7
|
0.5
|
C3C
|
C:HEM1001
|
4.2
|
12.9
|
0.5
|
C2C
|
C:HEM1001
|
4.2
|
10.0
|
0.5
|
C2B
|
C:HEM1001
|
4.2
|
13.7
|
0.5
|
C2B
|
C:HEM1001
|
4.3
|
10.5
|
0.5
|
C3B
|
C:HEM1001
|
4.3
|
13.8
|
0.5
|
C3B
|
C:HEM1001
|
4.3
|
10.5
|
0.5
|
|
Iron binding site 6 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 6 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 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 Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1001
b:11.3
occ:0.50
|
FE
|
C:HEM1001
|
0.0
|
11.3
|
0.5
|
FE
|
C:HEM1001
|
0.1
|
11.1
|
0.5
|
ND
|
C:HEM1001
|
1.9
|
11.5
|
0.5
|
ND
|
C:HEM1001
|
1.9
|
10.6
|
0.5
|
NA
|
C:HEM1001
|
2.0
|
12.1
|
0.5
|
NA
|
C:HEM1001
|
2.0
|
11.5
|
0.5
|
NB
|
C:HEM1001
|
2.1
|
11.8
|
0.5
|
NC
|
C:HEM1001
|
2.1
|
11.3
|
0.5
|
NC
|
C:HEM1001
|
2.1
|
10.1
|
0.5
|
NB
|
C:HEM1001
|
2.1
|
10.6
|
0.5
|
NE2
|
C:HIS135
|
2.1
|
10.8
|
1.0
|
NE2
|
C:HIS107
|
2.1
|
10.2
|
1.0
|
C1D
|
C:HEM1001
|
2.9
|
11.7
|
0.5
|
C4D
|
C:HEM1001
|
2.9
|
12.4
|
0.5
|
C1D
|
C:HEM1001
|
2.9
|
10.1
|
0.5
|
C4D
|
C:HEM1001
|
3.0
|
11.0
|
0.5
|
C1A
|
C:HEM1001
|
3.0
|
13.0
|
0.5
|
CD2
|
C:HIS107
|
3.0
|
9.9
|
1.0
|
C4A
|
C:HEM1001
|
3.0
|
12.9
|
0.5
|
C1B
|
C:HEM1001
|
3.0
|
12.8
|
0.5
|
CE1
|
C:HIS135
|
3.0
|
11.1
|
1.0
|
C4B
|
C:HEM1001
|
3.0
|
12.3
|
0.5
|
C4C
|
C:HEM1001
|
3.0
|
9.9
|
0.5
|
C1A
|
C:HEM1001
|
3.0
|
12.0
|
0.5
|
C4C
|
C:HEM1001
|
3.0
|
11.8
|
0.5
|
C1B
|
C:HEM1001
|
3.0
|
10.8
|
0.5
|
C4A
|
C:HEM1001
|
3.0
|
11.4
|
0.5
|
CE1
|
C:HIS107
|
3.0
|
10.7
|
1.0
|
C4B
|
C:HEM1001
|
3.1
|
10.9
|
0.5
|
C1C
|
C:HEM1001
|
3.1
|
11.7
|
0.5
|
C1C
|
C:HEM1001
|
3.1
|
10.5
|
0.5
|
CD2
|
C:HIS135
|
3.1
|
11.7
|
1.0
|
CHD
|
C:HEM1001
|
3.4
|
11.7
|
0.5
|
CHB
|
C:HEM1001
|
3.4
|
13.6
|
0.5
|
CHD
|
C:HEM1001
|
3.4
|
10.3
|
0.5
|
CHA
|
C:HEM1001
|
3.4
|
12.1
|
0.5
|
CHA
|
C:HEM1001
|
3.4
|
12.3
|
0.5
|
CHB
|
C:HEM1001
|
3.4
|
11.7
|
0.5
|
CHC
|
C:HEM1001
|
3.4
|
10.9
|
0.5
|
CHC
|
C:HEM1001
|
3.5
|
11.0
|
0.5
|
ND1
|
C:HIS107
|
4.1
|
10.9
|
1.0
|
CG
|
C:HIS107
|
4.1
|
10.4
|
1.0
|
ND1
|
C:HIS135
|
4.2
|
11.5
|
1.0
|
C2D
|
C:HEM1001
|
4.2
|
12.3
|
0.5
|
C3D
|
C:HEM1001
|
4.2
|
12.2
|
0.5
|
C2A
|
C:HEM1001
|
4.2
|
13.6
|
0.5
|
C3A
|
C:HEM1001
|
4.2
|
13.7
|
0.5
|
C3C
|
C:HEM1001
|
4.2
|
9.8
|
0.5
|
C2D
|
C:HEM1001
|
4.2
|
10.1
|
0.5
|
C3A
|
C:HEM1001
|
4.2
|
11.7
|
0.5
|
C2B
|
C:HEM1001
|
4.2
|
13.7
|
0.5
|
C2A
|
C:HEM1001
|
4.2
|
12.1
|
0.5
|
C3C
|
C:HEM1001
|
4.2
|
12.9
|
0.5
|
CG
|
C:HIS135
|
4.2
|
12.1
|
1.0
|
C2C
|
C:HEM1001
|
4.2
|
12.7
|
0.5
|
C3D
|
C:HEM1001
|
4.2
|
10.4
|
0.5
|
C2C
|
C:HEM1001
|
4.2
|
10.0
|
0.5
|
C3B
|
C:HEM1001
|
4.3
|
13.8
|
0.5
|
C2B
|
C:HEM1001
|
4.3
|
10.5
|
0.5
|
C3B
|
C:HEM1001
|
4.3
|
10.5
|
0.5
|
|
Iron binding site 7 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 7 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:13.0
occ:0.50
|
FE
|
D:HEM1001
|
0.0
|
13.0
|
0.5
|
FE
|
D:HEM1001
|
0.1
|
13.3
|
0.5
|
ND
|
D:HEM1001
|
1.9
|
14.9
|
0.5
|
ND
|
D:HEM1001
|
1.9
|
13.0
|
0.5
|
NA
|
D:HEM1001
|
2.0
|
14.0
|
0.5
|
NC
|
D:HEM1001
|
2.0
|
13.3
|
0.5
|
NC
|
D:HEM1001
|
2.1
|
12.2
|
0.5
|
NA
|
D:HEM1001
|
2.1
|
13.3
|
0.5
|
NE2
|
D:HIS135
|
2.1
|
13.0
|
1.0
|
NB
|
D:HEM1001
|
2.1
|
13.3
|
0.5
|
NB
|
D:HEM1001
|
2.1
|
12.3
|
0.5
|
NE2
|
D:HIS107
|
2.1
|
10.9
|
1.0
|
C1D
|
D:HEM1001
|
2.9
|
15.3
|
0.5
|
C1D
|
D:HEM1001
|
2.9
|
12.9
|
0.5
|
C4D
|
D:HEM1001
|
2.9
|
15.7
|
0.5
|
C4D
|
D:HEM1001
|
2.9
|
14.3
|
0.5
|
C4C
|
D:HEM1001
|
3.0
|
14.3
|
0.5
|
CD2
|
D:HIS107
|
3.0
|
11.5
|
1.0
|
C1A
|
D:HEM1001
|
3.0
|
14.5
|
0.5
|
CE1
|
D:HIS135
|
3.0
|
13.3
|
1.0
|
C1C
|
D:HEM1001
|
3.0
|
13.6
|
0.5
|
C4A
|
D:HEM1001
|
3.0
|
14.2
|
0.5
|
C4C
|
D:HEM1001
|
3.0
|
12.4
|
0.5
|
C4B
|
D:HEM1001
|
3.0
|
12.7
|
0.5
|
C1B
|
D:HEM1001
|
3.0
|
13.8
|
0.5
|
C4B
|
D:HEM1001
|
3.0
|
13.6
|
0.5
|
C1B
|
D:HEM1001
|
3.1
|
12.7
|
0.5
|
C1C
|
D:HEM1001
|
3.1
|
13.0
|
0.5
|
C1A
|
D:HEM1001
|
3.1
|
14.9
|
0.5
|
C4A
|
D:HEM1001
|
3.1
|
13.2
|
0.5
|
CD2
|
D:HIS135
|
3.1
|
13.2
|
1.0
|
CE1
|
D:HIS107
|
3.1
|
11.6
|
1.0
|
CHD
|
D:HEM1001
|
3.3
|
14.6
|
0.5
|
CHD
|
D:HEM1001
|
3.4
|
11.8
|
0.5
|
CHA
|
D:HEM1001
|
3.4
|
14.1
|
0.5
|
CHC
|
D:HEM1001
|
3.4
|
13.3
|
0.5
|
CHB
|
D:HEM1001
|
3.4
|
13.9
|
0.5
|
CHC
|
D:HEM1001
|
3.4
|
13.9
|
0.5
|
CHA
|
D:HEM1001
|
3.4
|
15.4
|
0.5
|
CHB
|
D:HEM1001
|
3.5
|
12.1
|
0.5
|
CG
|
D:HIS107
|
4.1
|
11.4
|
1.0
|
ND1
|
D:HIS135
|
4.1
|
13.5
|
1.0
|
ND1
|
D:HIS107
|
4.2
|
12.4
|
1.0
|
C3C
|
D:HEM1001
|
4.2
|
15.3
|
0.5
|
C2D
|
D:HEM1001
|
4.2
|
14.7
|
0.5
|
C3D
|
D:HEM1001
|
4.2
|
15.6
|
0.5
|
C2C
|
D:HEM1001
|
4.2
|
15.0
|
0.5
|
C3D
|
D:HEM1001
|
4.2
|
14.7
|
0.5
|
C2D
|
D:HEM1001
|
4.2
|
13.3
|
0.5
|
C3A
|
D:HEM1001
|
4.2
|
14.1
|
0.5
|
C2A
|
D:HEM1001
|
4.2
|
14.4
|
0.5
|
C3C
|
D:HEM1001
|
4.2
|
12.9
|
0.5
|
CG
|
D:HIS135
|
4.2
|
13.8
|
1.0
|
C2C
|
D:HEM1001
|
4.2
|
13.2
|
0.5
|
C2B
|
D:HEM1001
|
4.3
|
14.7
|
0.5
|
C2B
|
D:HEM1001
|
4.3
|
13.2
|
0.5
|
C3B
|
D:HEM1001
|
4.3
|
14.8
|
0.5
|
C2A
|
D:HEM1001
|
4.3
|
14.9
|
0.5
|
C3A
|
D:HEM1001
|
4.3
|
13.8
|
0.5
|
C3B
|
D:HEM1001
|
4.3
|
12.8
|
0.5
|
|
Iron binding site 8 out
of 8 in 5ziq
Go back to
Iron Binding Sites List in 5ziq
Iron binding site 8 out
of 8 in the Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Hexacoordinated Heme Protein From Anhydrobiotic Tardigrade at pH 4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:13.3
occ:0.50
|
FE
|
D:HEM1001
|
0.0
|
13.3
|
0.5
|
FE
|
D:HEM1001
|
0.1
|
13.0
|
0.5
|
ND
|
D:HEM1001
|
1.9
|
13.0
|
0.5
|
ND
|
D:HEM1001
|
1.9
|
14.9
|
0.5
|
NA
|
D:HEM1001
|
2.0
|
14.0
|
0.5
|
NA
|
D:HEM1001
|
2.0
|
13.3
|
0.5
|
NE2
|
D:HIS135
|
2.1
|
13.0
|
1.0
|
NC
|
D:HEM1001
|
2.1
|
13.3
|
0.5
|
NC
|
D:HEM1001
|
2.1
|
12.2
|
0.5
|
NB
|
D:HEM1001
|
2.1
|
12.3
|
0.5
|
NE2
|
D:HIS107
|
2.1
|
10.9
|
1.0
|
NB
|
D:HEM1001
|
2.1
|
13.3
|
0.5
|
C1D
|
D:HEM1001
|
2.9
|
12.9
|
0.5
|
C4D
|
D:HEM1001
|
2.9
|
14.3
|
0.5
|
C4D
|
D:HEM1001
|
2.9
|
15.7
|
0.5
|
C1D
|
D:HEM1001
|
2.9
|
15.3
|
0.5
|
CE1
|
D:HIS135
|
3.0
|
13.3
|
1.0
|
C1A
|
D:HEM1001
|
3.0
|
14.5
|
0.5
|
C4C
|
D:HEM1001
|
3.0
|
12.4
|
0.5
|
CD2
|
D:HIS107
|
3.0
|
11.5
|
1.0
|
C4C
|
D:HEM1001
|
3.0
|
14.3
|
0.5
|
C1A
|
D:HEM1001
|
3.0
|
14.9
|
0.5
|
C4A
|
D:HEM1001
|
3.0
|
13.2
|
0.5
|
C1B
|
D:HEM1001
|
3.0
|
12.7
|
0.5
|
C4B
|
D:HEM1001
|
3.0
|
12.7
|
0.5
|
C4A
|
D:HEM1001
|
3.1
|
14.2
|
0.5
|
C1C
|
D:HEM1001
|
3.1
|
13.6
|
0.5
|
C1C
|
D:HEM1001
|
3.1
|
13.0
|
0.5
|
C4B
|
D:HEM1001
|
3.1
|
13.6
|
0.5
|
C1B
|
D:HEM1001
|
3.1
|
13.8
|
0.5
|
CD2
|
D:HIS135
|
3.1
|
13.2
|
1.0
|
CE1
|
D:HIS107
|
3.1
|
11.6
|
1.0
|
CHD
|
D:HEM1001
|
3.3
|
11.8
|
0.5
|
CHA
|
D:HEM1001
|
3.3
|
14.1
|
0.5
|
CHD
|
D:HEM1001
|
3.4
|
14.6
|
0.5
|
CHA
|
D:HEM1001
|
3.4
|
15.4
|
0.5
|
CHB
|
D:HEM1001
|
3.4
|
12.1
|
0.5
|
CHC
|
D:HEM1001
|
3.4
|
13.3
|
0.5
|
CHB
|
D:HEM1001
|
3.5
|
13.9
|
0.5
|
CHC
|
D:HEM1001
|
3.5
|
13.9
|
0.5
|
ND1
|
D:HIS135
|
4.1
|
13.5
|
1.0
|
C3D
|
D:HEM1001
|
4.1
|
14.7
|
0.5
|
C2D
|
D:HEM1001
|
4.1
|
13.3
|
0.5
|
CG
|
D:HIS107
|
4.2
|
11.4
|
1.0
|
ND1
|
D:HIS107
|
4.2
|
12.4
|
1.0
|
C3D
|
D:HEM1001
|
4.2
|
15.6
|
0.5
|
C2D
|
D:HEM1001
|
4.2
|
14.7
|
0.5
|
C3C
|
D:HEM1001
|
4.2
|
12.9
|
0.5
|
CG
|
D:HIS135
|
4.2
|
13.8
|
1.0
|
C2A
|
D:HEM1001
|
4.2
|
14.4
|
0.5
|
C3A
|
D:HEM1001
|
4.2
|
14.1
|
0.5
|
C3C
|
D:HEM1001
|
4.2
|
15.3
|
0.5
|
C2A
|
D:HEM1001
|
4.2
|
14.9
|
0.5
|
C3A
|
D:HEM1001
|
4.2
|
13.8
|
0.5
|
C2C
|
D:HEM1001
|
4.2
|
15.0
|
0.5
|
C2C
|
D:HEM1001
|
4.3
|
13.2
|
0.5
|
C2B
|
D:HEM1001
|
4.3
|
13.2
|
0.5
|
C3B
|
D:HEM1001
|
4.3
|
12.8
|
0.5
|
C2B
|
D:HEM1001
|
4.3
|
14.7
|
0.5
|
C3B
|
D:HEM1001
|
4.3
|
14.8
|
0.5
|
|
Reference:
J.Kim,
Y.Fukuda,
T.Inoue.
Crystal Structure of Kumaglobin: A Hexacoordinated Heme Protein From An Anhydrobiotic Tardigrade, Ramazzottius Varieornatus. Febs J. V. 286 1287 2019.
ISSN: ISSN 1742-4658
PubMed: 30506636
DOI: 10.1111/FEBS.14713
Page generated: Tue Aug 6 13:11:40 2024
|