Iron in PDB 3ze6: 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
Enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
All present enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms:
1.12.7.2;
Protein crystallography data
The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms, PDB code: 3ze6
was solved by
M.C.Marques,
R.Coelho,
I.A.C.Pereira,
P.M.Matias,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
45.51 /
1.50
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.170,
97.350,
102.970,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
13.5 /
15.4
|
Other elements in 3ze6:
The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Iron atom in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
(pdb code 3ze6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the
3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms, PDB code: 3ze6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 1 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe284
b:9.6
occ:1.00
|
FE1
|
A:SF4284
|
0.0
|
9.6
|
1.0
|
|
S2
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
S3
|
A:SF4284
|
2.3
|
9.6
|
1.0
|
|
S4
|
A:SF4284
|
2.3
|
9.8
|
1.0
|
|
SG
|
A:CYS238
|
2.3
|
9.0
|
1.0
|
|
FE3
|
A:SF4284
|
2.7
|
10.3
|
1.0
|
|
FE4
|
A:SF4284
|
2.7
|
10.4
|
1.0
|
|
FE2
|
A:SF4284
|
2.8
|
9.9
|
1.0
|
|
HB3
|
A:CYS238
|
3.0
|
9.9
|
1.0
|
|
CB
|
A:CYS238
|
3.2
|
8.2
|
1.0
|
|
HB2
|
A:CYS238
|
3.5
|
9.9
|
1.0
|
|
HD3
|
A:PRO241
|
3.6
|
12.3
|
1.0
|
|
HB2
|
A:ARG233
|
3.7
|
8.1
|
1.0
|
|
HA3
|
A:GLY240
|
3.8
|
10.6
|
1.0
|
|
H
|
A:GLY240
|
3.8
|
11.2
|
1.0
|
|
S1
|
A:SF4284
|
3.9
|
9.9
|
1.0
|
|
HG11
|
A:VAL260
|
3.9
|
12.8
|
1.0
|
|
H
|
A:ARG233
|
4.1
|
11.8
|
1.0
|
|
HG12
|
A:VAL260
|
4.2
|
12.8
|
1.0
|
|
HG23
|
A:VAL260
|
4.3
|
15.9
|
1.0
|
|
HG22
|
A:VAL260
|
4.5
|
15.9
|
1.0
|
|
N
|
A:GLY240
|
4.5
|
9.4
|
1.0
|
|
CG1
|
A:VAL260
|
4.5
|
10.7
|
1.0
|
|
CD
|
A:PRO241
|
4.5
|
10.2
|
1.0
|
|
CA
|
A:GLY240
|
4.6
|
8.8
|
1.0
|
|
CA
|
A:CYS238
|
4.6
|
7.3
|
1.0
|
|
HA
|
A:TYR234
|
4.6
|
10.8
|
1.0
|
|
CB
|
A:ARG233
|
4.7
|
6.8
|
1.0
|
|
ND1
|
A:HIS208
|
4.7
|
9.8
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
10.8
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
10.3
|
1.0
|
|
C
|
A:CYS238
|
4.7
|
8.5
|
1.0
|
|
H
|
A:TYR234
|
4.8
|
11.6
|
1.0
|
|
N
|
A:TYR234
|
4.8
|
9.7
|
1.0
|
|
HB2
|
A:TYR234
|
4.8
|
12.4
|
1.0
|
|
CG2
|
A:VAL260
|
4.8
|
13.2
|
1.0
|
|
O
|
A:CYS238
|
4.8
|
9.1
|
1.0
|
|
N
|
A:ARG233
|
4.8
|
9.8
|
1.0
|
|
HB2
|
A:HIS208
|
4.9
|
14.4
|
1.0
|
|
HA
|
A:HIS208
|
4.9
|
11.9
|
1.0
|
|
HD3
|
A:ARG233
|
4.9
|
12.2
|
1.0
|
|
C
|
A:ARG233
|
4.9
|
11.1
|
1.0
|
|
HD2
|
A:PRO241
|
4.9
|
12.3
|
1.0
|
|
HB3
|
A:ARG233
|
5.0
|
8.1
|
1.0
|
|
HA
|
A:CYS238
|
5.0
|
8.8
|
1.0
|
|
HG3
|
A:PRO241
|
5.0
|
13.6
|
1.0
|
|
Iron binding site 2 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 2 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe284
b:9.9
occ:1.00
|
FE2
|
A:SF4284
|
0.0
|
9.9
|
1.0
|
|
S1
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
S4
|
A:SF4284
|
2.3
|
9.8
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
10.3
|
1.0
|
|
S3
|
A:SF4284
|
2.3
|
9.6
|
1.0
|
|
FE4
|
A:SF4284
|
2.7
|
10.4
|
1.0
|
|
FE3
|
A:SF4284
|
2.7
|
10.3
|
1.0
|
|
FE1
|
A:SF4284
|
2.8
|
9.6
|
1.0
|
|
H
|
A:ARG233
|
3.0
|
11.8
|
1.0
|
|
HB2
|
A:CYS232
|
3.4
|
13.1
|
1.0
|
|
HB2
|
A:TYR217
|
3.4
|
14.6
|
1.0
|
|
CB
|
A:CYS232
|
3.4
|
10.9
|
1.0
|
|
H
|
A:TYR234
|
3.6
|
11.6
|
1.0
|
|
HD1
|
A:TYR217
|
3.7
|
15.2
|
1.0
|
|
HA
|
A:CYS232
|
3.7
|
13.3
|
1.0
|
|
HB2
|
A:TYR234
|
3.8
|
12.4
|
1.0
|
|
N
|
A:ARG233
|
3.8
|
9.8
|
1.0
|
|
HB2
|
A:TYR213
|
3.8
|
11.5
|
1.0
|
|
S2
|
A:SF4284
|
3.9
|
9.9
|
1.0
|
|
CA
|
A:CYS232
|
4.0
|
11.1
|
1.0
|
|
N
|
A:TYR234
|
4.1
|
9.7
|
1.0
|
|
HB3
|
A:CYS232
|
4.2
|
13.1
|
1.0
|
|
HE1
|
A:HIS208
|
4.3
|
16.4
|
1.0
|
|
HB2
|
A:ARG233
|
4.3
|
8.1
|
1.0
|
|
CD1
|
A:TYR217
|
4.3
|
12.6
|
1.0
|
|
C
|
A:CYS232
|
4.3
|
9.2
|
1.0
|
|
CB
|
A:TYR217
|
4.3
|
12.2
|
1.0
|
|
ND1
|
A:HIS208
|
4.5
|
9.8
|
1.0
|
|
HB3
|
A:CYS238
|
4.5
|
9.9
|
1.0
|
|
CB
|
A:TYR234
|
4.6
|
10.3
|
1.0
|
|
CB
|
A:TYR213
|
4.6
|
9.6
|
1.0
|
|
O
|
A:TYR213
|
4.6
|
11.6
|
1.0
|
|
HB3
|
A:TYR213
|
4.7
|
11.5
|
1.0
|
|
CA
|
A:ARG233
|
4.7
|
8.7
|
1.0
|
|
CE1
|
A:HIS208
|
4.7
|
13.6
|
1.0
|
|
CG
|
A:TYR217
|
4.7
|
13.3
|
1.0
|
|
HA
|
A:TYR234
|
4.7
|
10.8
|
1.0
|
|
C
|
A:ARG233
|
4.8
|
11.1
|
1.0
|
|
HD3
|
A:ARG233
|
4.8
|
12.2
|
1.0
|
|
HA
|
A:LEU214
|
4.8
|
12.4
|
1.0
|
|
CA
|
A:TYR234
|
4.8
|
9.0
|
1.0
|
|
HB3
|
A:TYR234
|
4.8
|
12.4
|
1.0
|
|
HB3
|
A:TYR217
|
4.8
|
14.6
|
1.0
|
|
SG
|
A:CYS211
|
4.9
|
10.8
|
1.0
|
|
H
|
A:TYR217
|
4.9
|
12.6
|
1.0
|
|
SG
|
A:CYS238
|
4.9
|
9.0
|
1.0
|
|
C
|
A:TYR213
|
4.9
|
10.9
|
1.0
|
|
Iron binding site 3 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 3 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe284
b:10.3
occ:1.00
|
FE3
|
A:SF4284
|
0.0
|
10.3
|
1.0
|
|
S1
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
SG
|
A:CYS211
|
2.3
|
10.8
|
1.0
|
|
S4
|
A:SF4284
|
2.3
|
9.8
|
1.0
|
|
S2
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
FE4
|
A:SF4284
|
2.7
|
10.4
|
1.0
|
|
FE1
|
A:SF4284
|
2.7
|
9.6
|
1.0
|
|
FE2
|
A:SF4284
|
2.7
|
9.9
|
1.0
|
|
HB3
|
A:CYS211
|
3.0
|
12.2
|
1.0
|
|
CB
|
A:CYS211
|
3.1
|
10.2
|
1.0
|
|
HB2
|
A:CYS211
|
3.2
|
12.2
|
1.0
|
|
HB2
|
A:TYR213
|
3.2
|
11.5
|
1.0
|
|
HG12
|
A:VAL260
|
3.4
|
12.8
|
1.0
|
|
HD2
|
A:TYR213
|
3.6
|
16.4
|
1.0
|
|
S3
|
A:SF4284
|
3.8
|
9.6
|
1.0
|
|
H
|
A:TYR213
|
3.9
|
13.9
|
1.0
|
|
HA
|
A:HIS208
|
4.0
|
11.9
|
1.0
|
|
HG11
|
A:VAL260
|
4.1
|
12.8
|
1.0
|
|
CB
|
A:TYR213
|
4.2
|
9.6
|
1.0
|
|
CG1
|
A:VAL260
|
4.2
|
10.7
|
1.0
|
|
ND1
|
A:HIS208
|
4.4
|
9.8
|
1.0
|
|
CD2
|
A:TYR213
|
4.5
|
13.7
|
1.0
|
|
CA
|
A:CYS211
|
4.6
|
11.2
|
1.0
|
|
C
|
A:TYR213
|
4.6
|
10.9
|
1.0
|
|
HG22
|
A:VAL260
|
4.6
|
15.9
|
1.0
|
|
N
|
A:TYR213
|
4.6
|
11.6
|
1.0
|
|
HG13
|
A:VAL260
|
4.7
|
12.8
|
1.0
|
|
H
|
A:ARG233
|
4.7
|
11.8
|
1.0
|
|
CA
|
A:TYR213
|
4.7
|
11.5
|
1.0
|
|
N
|
A:LEU214
|
4.7
|
10.8
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
12.4
|
1.0
|
|
HB3
|
A:TYR213
|
4.7
|
11.5
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
9.0
|
1.0
|
|
H
|
A:LEU214
|
4.8
|
12.9
|
1.0
|
|
HG23
|
A:ILE207
|
4.8
|
13.1
|
0.4
|
|
CG
|
A:TYR213
|
4.9
|
12.9
|
1.0
|
|
HG23
|
A:ILE207
|
4.9
|
13.1
|
0.6
|
|
HA
|
A:CYS211
|
4.9
|
13.5
|
1.0
|
|
CA
|
A:HIS208
|
4.9
|
9.9
|
1.0
|
|
HD3
|
A:ARG233
|
4.9
|
12.2
|
1.0
|
|
SG
|
A:CYS232
|
4.9
|
10.3
|
1.0
|
|
O
|
A:TYR213
|
5.0
|
11.6
|
1.0
|
|
Iron binding site 4 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 4 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe284
b:10.4
occ:1.00
|
FE4
|
A:SF4284
|
0.0
|
10.4
|
1.0
|
|
ND1
|
A:HIS208
|
2.1
|
9.8
|
1.0
|
|
S3
|
A:SF4284
|
2.3
|
9.6
|
1.0
|
|
S2
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
S1
|
A:SF4284
|
2.3
|
9.9
|
1.0
|
|
FE3
|
A:SF4284
|
2.7
|
10.3
|
1.0
|
|
FE2
|
A:SF4284
|
2.7
|
9.9
|
1.0
|
|
FE1
|
A:SF4284
|
2.7
|
9.6
|
1.0
|
|
CE1
|
A:HIS208
|
2.9
|
13.6
|
1.0
|
|
HE1
|
A:HIS208
|
3.0
|
16.4
|
1.0
|
|
CG
|
A:HIS208
|
3.2
|
9.0
|
1.0
|
|
HA
|
A:HIS208
|
3.3
|
11.9
|
1.0
|
|
HB2
|
A:HIS208
|
3.3
|
14.4
|
1.0
|
|
HD3
|
A:PRO241
|
3.4
|
12.3
|
1.0
|
|
HG3
|
A:PRO241
|
3.5
|
13.6
|
1.0
|
|
CB
|
A:HIS208
|
3.6
|
12.0
|
1.0
|
|
S4
|
A:SF4284
|
3.9
|
9.8
|
1.0
|
|
CA
|
A:HIS208
|
3.9
|
9.9
|
1.0
|
|
NE2
|
A:HIS208
|
4.1
|
13.0
|
1.0
|
|
HB3
|
A:CYS211
|
4.1
|
12.2
|
1.0
|
|
CD
|
A:PRO241
|
4.2
|
10.2
|
1.0
|
|
CD2
|
A:HIS208
|
4.2
|
10.4
|
1.0
|
|
CG
|
A:PRO241
|
4.2
|
11.3
|
1.0
|
|
HA3
|
A:GLY240
|
4.3
|
10.6
|
1.0
|
|
HB2
|
A:CYS211
|
4.3
|
12.2
|
1.0
|
|
HD1
|
A:TYR217
|
4.4
|
15.2
|
1.0
|
|
HB2
|
A:TYR217
|
4.4
|
14.6
|
1.0
|
|
HD11
|
A:LEU214
|
4.5
|
14.5
|
1.0
|
|
CB
|
A:CYS211
|
4.5
|
10.2
|
1.0
|
|
HB3
|
A:HIS208
|
4.5
|
14.4
|
1.0
|
|
CD1
|
A:TYR217
|
4.6
|
12.6
|
1.0
|
|
O
|
A:HIS208
|
4.6
|
11.3
|
1.0
|
|
SG
|
A:CYS211
|
4.7
|
10.8
|
1.0
|
|
SG
|
A:CYS232
|
4.7
|
10.3
|
1.0
|
|
HG2
|
A:PRO241
|
4.7
|
13.6
|
1.0
|
|
N
|
A:PRO241
|
4.7
|
10.2
|
1.0
|
|
HA
|
A:LEU214
|
4.7
|
12.4
|
1.0
|
|
C
|
A:HIS208
|
4.8
|
11.1
|
1.0
|
|
SG
|
A:CYS238
|
4.8
|
9.0
|
1.0
|
|
HE2
|
A:HIS208
|
4.8
|
15.6
|
1.0
|
|
HB2
|
A:TYR234
|
4.9
|
12.4
|
1.0
|
|
HD13
|
A:LEU214
|
4.9
|
14.5
|
1.0
|
|
CG
|
A:TYR217
|
4.9
|
13.3
|
1.0
|
|
HD2
|
A:PRO241
|
5.0
|
12.3
|
1.0
|
|
Iron binding site 5 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 5 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe285
b:9.7
occ:1.00
|
FE1
|
A:SF4285
|
0.0
|
9.7
|
1.0
|
|
S4
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
S3
|
A:SF4285
|
2.3
|
9.1
|
1.0
|
|
S2
|
A:SF4285
|
2.3
|
10.1
|
1.0
|
|
SG
|
A:CYS268
|
2.3
|
9.7
|
1.0
|
|
FE2
|
A:SF4285
|
2.7
|
10.2
|
1.0
|
|
FE4
|
A:SF4285
|
2.8
|
9.6
|
1.0
|
|
FE3
|
A:SF4285
|
2.8
|
10.3
|
1.0
|
|
H
|
A:CYS268
|
3.0
|
9.5
|
1.0
|
|
HB3
|
A:CYS268
|
3.4
|
11.0
|
1.0
|
|
CB
|
A:CYS268
|
3.4
|
9.1
|
1.0
|
|
HH22
|
B:ARG182
|
3.7
|
13.1
|
1.0
|
|
N
|
A:CYS268
|
3.8
|
7.9
|
1.0
|
|
HG11
|
A:VAL269
|
3.8
|
11.7
|
1.0
|
|
HH12
|
B:ARG182
|
3.8
|
13.0
|
1.0
|
|
S1
|
A:SF4285
|
3.9
|
9.8
|
1.0
|
|
NH2
|
B:ARG182
|
4.0
|
10.9
|
1.0
|
|
NH1
|
B:ARG182
|
4.1
|
10.8
|
1.0
|
|
CA
|
A:CYS268
|
4.1
|
7.7
|
1.0
|
|
H
|
A:VAL269
|
4.1
|
9.2
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
10.0
|
1.0
|
|
HB2
|
A:CYS268
|
4.2
|
11.0
|
1.0
|
|
HH21
|
B:ARG182
|
4.4
|
13.1
|
1.0
|
|
H
|
A:GLY267
|
4.5
|
8.7
|
1.0
|
|
HH2
|
A:TRP165
|
4.5
|
13.2
|
1.0
|
|
N
|
A:VAL269
|
4.6
|
7.7
|
1.0
|
|
HH11
|
B:ARG182
|
4.6
|
13.0
|
1.0
|
|
H
|
A:ILE266
|
4.6
|
8.3
|
1.0
|
|
C
|
A:CYS268
|
4.7
|
7.5
|
1.0
|
|
HG12
|
A:ILE266
|
4.7
|
11.0
|
1.0
|
|
CG1
|
A:VAL269
|
4.7
|
9.8
|
1.0
|
|
HG22
|
A:THR243
|
4.7
|
14.1
|
1.0
|
|
HZ2
|
A:TRP252
|
4.8
|
11.5
|
1.0
|
|
H
|
A:CYS159
|
4.8
|
8.5
|
1.0
|
|
HG23
|
A:VAL269
|
4.8
|
11.2
|
1.0
|
|
SG
|
A:CYS247
|
4.8
|
10.9
|
1.0
|
|
SG
|
A:CYS259
|
4.8
|
9.6
|
1.0
|
|
SG
|
A:CYS265
|
4.9
|
9.3
|
1.0
|
|
C
|
A:GLY267
|
4.9
|
6.9
|
1.0
|
|
N
|
A:GLY267
|
4.9
|
7.2
|
1.0
|
|
HA2
|
A:GLY158
|
5.0
|
10.4
|
1.0
|
|
HA
|
A:CYS268
|
5.0
|
9.3
|
1.0
|
|
HE21
|
B:GLN187
|
5.0
|
11.3
|
1.0
|
|
Iron binding site 6 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 6 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe285
b:10.2
occ:1.00
|
FE2
|
A:SF4285
|
0.0
|
10.2
|
1.0
|
|
S4
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
SG
|
A:CYS259
|
2.3
|
9.6
|
1.0
|
|
S1
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
S3
|
A:SF4285
|
2.3
|
9.1
|
1.0
|
|
FE3
|
A:SF4285
|
2.7
|
10.3
|
1.0
|
|
FE4
|
A:SF4285
|
2.7
|
9.6
|
1.0
|
|
FE1
|
A:SF4285
|
2.7
|
9.7
|
1.0
|
|
HB2
|
A:CYS259
|
2.9
|
9.7
|
1.0
|
|
CB
|
A:CYS259
|
3.1
|
8.1
|
1.0
|
|
HE21
|
B:GLN187
|
3.4
|
11.3
|
1.0
|
|
HB3
|
A:CYS259
|
3.5
|
9.7
|
1.0
|
|
S2
|
A:SF4285
|
3.9
|
10.1
|
1.0
|
|
H
|
A:CYS259
|
3.9
|
9.8
|
1.0
|
|
HA
|
A:CYS265
|
3.9
|
12.0
|
1.0
|
|
CZ
|
B:ARG182
|
4.2
|
10.0
|
1.0
|
|
NE2
|
B:GLN187
|
4.2
|
9.4
|
1.0
|
|
HE1
|
A:TRP252
|
4.3
|
13.6
|
1.0
|
|
NH2
|
B:ARG182
|
4.3
|
10.9
|
1.0
|
|
NE
|
B:ARG182
|
4.3
|
10.3
|
1.0
|
|
HE22
|
B:GLN187
|
4.3
|
11.3
|
1.0
|
|
HD3
|
B:ARG182
|
4.3
|
12.9
|
1.0
|
|
H
|
A:ILE266
|
4.4
|
8.3
|
1.0
|
|
HH21
|
B:ARG182
|
4.4
|
13.1
|
1.0
|
|
CA
|
A:CYS259
|
4.4
|
8.7
|
1.0
|
|
HE
|
B:ARG182
|
4.4
|
12.3
|
1.0
|
|
N
|
A:CYS259
|
4.5
|
8.2
|
1.0
|
|
NH1
|
B:ARG182
|
4.5
|
10.8
|
1.0
|
|
HH22
|
B:ARG182
|
4.5
|
13.1
|
1.0
|
|
SG
|
A:CYS247
|
4.6
|
10.9
|
1.0
|
|
NE1
|
A:TRP252
|
4.7
|
11.4
|
1.0
|
|
SG
|
A:CYS268
|
4.7
|
9.7
|
1.0
|
|
HB2
|
A:CYS265
|
4.7
|
9.8
|
1.0
|
|
HH12
|
B:ARG182
|
4.8
|
13.0
|
1.0
|
|
HH11
|
B:ARG182
|
4.8
|
13.0
|
1.0
|
|
HG3
|
B:GLN187
|
4.8
|
11.9
|
1.0
|
|
SG
|
A:CYS265
|
4.8
|
9.3
|
1.0
|
|
HB3
|
A:CYS247
|
4.8
|
15.1
|
1.0
|
|
CA
|
A:CYS265
|
4.8
|
10.0
|
1.0
|
|
CD
|
B:ARG182
|
4.9
|
10.8
|
1.0
|
|
HG12
|
A:ILE266
|
4.9
|
11.0
|
1.0
|
|
HA
|
A:CYS259
|
4.9
|
10.4
|
1.0
|
|
HG2
|
B:ARG182
|
5.0
|
10.7
|
1.0
|
|
Iron binding site 7 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 7 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe285
b:10.3
occ:1.00
|
FE3
|
A:SF4285
|
0.0
|
10.3
|
1.0
|
|
S1
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
S4
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
SG
|
A:CYS247
|
2.3
|
10.9
|
1.0
|
|
S2
|
A:SF4285
|
2.3
|
10.1
|
1.0
|
|
FE2
|
A:SF4285
|
2.7
|
10.2
|
1.0
|
|
FE4
|
A:SF4285
|
2.7
|
9.6
|
1.0
|
|
FE1
|
A:SF4285
|
2.8
|
9.7
|
1.0
|
|
HB2
|
A:CYS247
|
3.3
|
15.1
|
1.0
|
|
CB
|
A:CYS247
|
3.3
|
12.6
|
1.0
|
|
HD12
|
A:ILE207
|
3.4
|
13.5
|
0.6
|
|
HE1
|
A:TRP252
|
3.5
|
13.6
|
1.0
|
|
HB3
|
A:CYS247
|
3.5
|
15.1
|
1.0
|
|
HD12
|
A:ILE207
|
3.6
|
10.0
|
0.4
|
|
HH2
|
A:TRP165
|
3.7
|
13.2
|
1.0
|
|
S3
|
A:SF4285
|
3.9
|
9.1
|
1.0
|
|
HB1
|
A:ALA245
|
3.9
|
12.1
|
1.0
|
|
HD11
|
A:ILE207
|
4.0
|
13.5
|
0.6
|
|
HD13
|
A:ILE207
|
4.1
|
10.0
|
0.4
|
|
CD1
|
A:ILE207
|
4.1
|
11.2
|
0.6
|
|
HB2
|
A:ALA245
|
4.2
|
12.1
|
1.0
|
|
NE1
|
A:TRP252
|
4.3
|
11.4
|
1.0
|
|
CD1
|
A:ILE207
|
4.3
|
8.3
|
0.4
|
|
H
|
A:CYS247
|
4.4
|
13.0
|
1.0
|
|
CB
|
A:ALA245
|
4.5
|
10.1
|
1.0
|
|
HZ2
|
A:TRP252
|
4.5
|
11.5
|
1.0
|
|
HD13
|
A:ILE207
|
4.6
|
13.5
|
0.6
|
|
CH2
|
A:TRP165
|
4.6
|
11.0
|
1.0
|
|
HE3
|
A:TRP258
|
4.7
|
14.1
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
9.6
|
1.0
|
|
HG11
|
A:VAL269
|
4.7
|
11.7
|
1.0
|
|
CA
|
A:CYS247
|
4.7
|
11.1
|
1.0
|
|
HB2
|
A:CYS259
|
4.7
|
9.7
|
1.0
|
|
HG22
|
A:THR243
|
4.7
|
14.1
|
1.0
|
|
HZ2
|
A:TRP165
|
4.7
|
12.0
|
1.0
|
|
HB3
|
A:ALA245
|
4.8
|
12.1
|
1.0
|
|
SG
|
A:CYS268
|
4.9
|
9.7
|
1.0
|
|
SG
|
A:CYS265
|
4.9
|
9.3
|
1.0
|
|
HD11
|
A:ILE207
|
4.9
|
10.0
|
0.4
|
|
Iron binding site 8 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 8 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe285
b:9.6
occ:1.00
|
FE4
|
A:SF4285
|
0.0
|
9.6
|
1.0
|
|
S1
|
A:SF4285
|
2.3
|
9.8
|
1.0
|
|
S2
|
A:SF4285
|
2.3
|
10.1
|
1.0
|
|
S3
|
A:SF4285
|
2.3
|
9.1
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
9.3
|
1.0
|
|
FE2
|
A:SF4285
|
2.7
|
10.2
|
1.0
|
|
FE3
|
A:SF4285
|
2.7
|
10.3
|
1.0
|
|
FE1
|
A:SF4285
|
2.8
|
9.7
|
1.0
|
|
HA
|
A:CYS265
|
3.3
|
12.0
|
1.0
|
|
HB2
|
A:CYS265
|
3.3
|
9.8
|
1.0
|
|
H
|
A:GLY267
|
3.3
|
8.7
|
1.0
|
|
CB
|
A:CYS265
|
3.3
|
8.1
|
1.0
|
|
HG22
|
A:THR243
|
3.4
|
14.1
|
1.0
|
|
HD11
|
A:ILE207
|
3.5
|
13.5
|
0.6
|
|
HD12
|
A:ILE207
|
3.5
|
13.5
|
0.6
|
|
H
|
A:ILE266
|
3.5
|
8.3
|
1.0
|
|
HD13
|
A:ILE207
|
3.7
|
13.5
|
0.6
|
|
CD1
|
A:ILE207
|
3.8
|
11.2
|
0.6
|
|
CA
|
A:CYS265
|
3.8
|
10.0
|
1.0
|
|
H
|
A:CYS268
|
3.8
|
9.5
|
1.0
|
|
S4
|
A:SF4285
|
3.9
|
9.8
|
1.0
|
|
HB2
|
A:CYS259
|
4.0
|
9.7
|
1.0
|
|
N
|
A:GLY267
|
4.1
|
7.2
|
1.0
|
|
N
|
A:ILE266
|
4.1
|
6.9
|
1.0
|
|
HB3
|
A:CYS265
|
4.2
|
9.8
|
1.0
|
|
HA2
|
A:GLY267
|
4.2
|
9.3
|
1.0
|
|
HD13
|
A:ILE207
|
4.3
|
10.0
|
0.4
|
|
C
|
A:CYS265
|
4.3
|
8.3
|
1.0
|
|
CG2
|
A:THR243
|
4.4
|
11.7
|
1.0
|
|
HD12
|
A:ILE207
|
4.4
|
10.0
|
0.4
|
|
HG13
|
A:ILE207
|
4.4
|
12.7
|
0.4
|
|
N
|
A:CYS268
|
4.6
|
7.9
|
1.0
|
|
CA
|
A:GLY267
|
4.6
|
7.7
|
1.0
|
|
HG23
|
A:THR243
|
4.7
|
14.1
|
1.0
|
|
HG1
|
A:THR243
|
4.7
|
11.8
|
1.0
|
|
SG
|
A:CYS259
|
4.7
|
9.6
|
1.0
|
|
CB
|
A:CYS259
|
4.7
|
8.1
|
1.0
|
|
CD1
|
A:ILE207
|
4.7
|
8.3
|
0.4
|
|
HG21
|
A:THR243
|
4.8
|
14.1
|
1.0
|
|
HB3
|
A:CYS259
|
4.9
|
9.7
|
1.0
|
|
SG
|
A:CYS247
|
4.9
|
10.9
|
1.0
|
|
SG
|
A:CYS268
|
4.9
|
9.7
|
1.0
|
|
HG12
|
A:ILE266
|
5.0
|
11.0
|
1.0
|
|
HG21
|
A:VAL260
|
5.0
|
15.9
|
1.0
|
|
Iron binding site 9 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 9 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe286
b:9.0
occ:0.20
|
FE1
|
A:SF4286
|
0.0
|
9.0
|
0.2
|
|
FE1
|
A:FSX287
|
0.0
|
9.0
|
0.8
|
|
O12
|
A:FSX287
|
1.7
|
11.2
|
0.8
|
|
S2
|
A:SF4286
|
2.2
|
9.3
|
0.2
|
|
S2
|
A:FSX287
|
2.2
|
9.3
|
0.8
|
|
SG
|
A:CYS18
|
2.3
|
9.1
|
1.0
|
|
S4
|
A:SF4286
|
2.3
|
8.5
|
0.2
|
|
S3
|
A:FSX287
|
2.3
|
8.5
|
0.8
|
|
S3
|
A:SF4286
|
2.4
|
4.5
|
0.2
|
|
FE4
|
A:SF4286
|
2.6
|
12.6
|
0.2
|
|
FE3
|
A:SF4286
|
2.7
|
8.3
|
0.2
|
|
FE3
|
A:FSX287
|
2.7
|
8.3
|
0.8
|
|
O1
|
A:FSX287
|
2.9
|
4.8
|
0.8
|
|
H
|
A:CYS18
|
2.9
|
10.0
|
1.0
|
|
FE2
|
A:FSX287
|
3.1
|
13.3
|
0.8
|
|
FE2
|
A:SF4286
|
3.1
|
9.2
|
0.2
|
|
FE4
|
A:FSX287
|
3.1
|
9.2
|
0.8
|
|
HE2
|
B:HIS185
|
3.2
|
9.4
|
1.0
|
|
H
|
A:GLY20
|
3.2
|
10.7
|
1.0
|
|
HB3
|
A:CYS18
|
3.3
|
7.4
|
1.0
|
|
CB
|
A:CYS18
|
3.3
|
6.2
|
1.0
|
|
HA3
|
A:GLY20
|
3.5
|
10.1
|
1.0
|
|
N
|
A:CYS18
|
3.6
|
8.3
|
1.0
|
|
O24
|
A:FSX287
|
3.7
|
13.7
|
0.8
|
|
CA
|
A:CYS18
|
3.9
|
6.2
|
1.0
|
|
N
|
A:GLY20
|
3.9
|
8.9
|
1.0
|
|
S1
|
A:SF4286
|
4.0
|
8.5
|
0.2
|
|
S4
|
A:FSX287
|
4.0
|
8.5
|
0.8
|
|
NE2
|
B:HIS185
|
4.0
|
7.8
|
1.0
|
|
HG3
|
B:ARG73
|
4.1
|
8.3
|
1.0
|
|
HB2
|
A:CYS18
|
4.2
|
7.4
|
1.0
|
|
CA
|
A:GLY20
|
4.2
|
8.4
|
1.0
|
|
C
|
A:CYS18
|
4.3
|
7.7
|
1.0
|
|
SD
|
A:CSS21
|
4.4
|
10.6
|
0.8
|
|
HA
|
B:ARG73
|
4.5
|
7.9
|
1.0
|
|
H
|
A:THR19
|
4.5
|
9.8
|
1.0
|
|
H
|
A:CSS21
|
4.5
|
11.3
|
1.0
|
|
HA2
|
A:GLY17
|
4.5
|
16.9
|
1.0
|
|
OE2
|
A:GLU77
|
4.5
|
22.0
|
1.0
|
|
N
|
A:THR19
|
4.5
|
8.2
|
1.0
|
|
HB3
|
B:ARG73
|
4.7
|
7.3
|
1.0
|
|
C
|
A:GLY17
|
4.7
|
11.5
|
1.0
|
|
SG
|
A:CYS159
|
4.8
|
7.6
|
1.0
|
|
HA
|
A:CYS18
|
4.8
|
7.5
|
1.0
|
|
O
|
A:HOH2007
|
4.8
|
10.9
|
1.0
|
|
HB3
|
A:PRO160
|
4.8
|
9.5
|
1.0
|
|
CG
|
B:ARG73
|
4.8
|
6.9
|
1.0
|
|
O
|
B:ARG73
|
4.9
|
7.0
|
1.0
|
|
HA2
|
A:GLY20
|
4.9
|
10.1
|
1.0
|
|
HA3
|
B:GLY76
|
4.9
|
10.5
|
1.0
|
|
HD2
|
B:HIS185
|
4.9
|
9.6
|
1.0
|
|
HG2
|
B:ARG73
|
4.9
|
8.3
|
1.0
|
|
O
|
A:CYS18
|
4.9
|
9.3
|
1.0
|
|
CD2
|
B:HIS185
|
4.9
|
8.0
|
1.0
|
|
C
|
A:GLY20
|
4.9
|
8.8
|
1.0
|
|
N
|
A:CSS21
|
5.0
|
9.4
|
1.0
|
|
CA
|
A:GLY17
|
5.0
|
14.1
|
1.0
|
|
HA3
|
A:GLY17
|
5.0
|
16.9
|
1.0
|
|
CE1
|
B:HIS185
|
5.0
|
6.9
|
1.0
|
|
HE1
|
B:HIS185
|
5.0
|
8.3
|
1.0
|
|
Iron binding site 10 out
of 18 in 3ze6
Go back to
Iron Binding Sites List in 3ze6
Iron binding site 10 out
of 18 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe286
b:9.2
occ:0.20
|
FE2
|
A:SF4286
|
0.0
|
9.2
|
0.2
|
|
FE4
|
A:FSX287
|
0.0
|
9.2
|
0.8
|
|
O24
|
A:FSX287
|
1.8
|
13.7
|
0.8
|
|
S1
|
A:SF4286
|
2.2
|
8.5
|
0.2
|
|
S4
|
A:FSX287
|
2.2
|
8.5
|
0.8
|
|
S4
|
A:SF4286
|
2.3
|
8.5
|
0.2
|
|
S3
|
A:FSX287
|
2.3
|
8.5
|
0.8
|
|
SG
|
A:CYS121
|
2.3
|
8.5
|
1.0
|
|
S3
|
A:SF4286
|
2.3
|
4.5
|
0.2
|
|
FE3
|
A:SF4286
|
2.7
|
8.3
|
0.2
|
|
FE3
|
A:FSX287
|
2.7
|
8.3
|
0.8
|
|
FE4
|
A:SF4286
|
2.7
|
12.6
|
0.2
|
|
O1
|
A:FSX287
|
2.9
|
4.8
|
0.8
|
|
HB2
|
A:CYS121
|
3.0
|
11.9
|
1.0
|
|
FE2
|
A:FSX287
|
3.1
|
13.3
|
0.8
|
|
FE1
|
A:SF4286
|
3.1
|
9.0
|
0.2
|
|
FE1
|
A:FSX287
|
3.1
|
9.0
|
0.8
|
|
H
|
A:CYS121
|
3.2
|
8.4
|
1.0
|
|
CB
|
A:CYS121
|
3.3
|
9.9
|
1.0
|
|
O12
|
A:FSX287
|
3.5
|
11.2
|
0.8
|
|
O
|
A:HOH2066
|
3.6
|
9.3
|
1.0
|
|
HA2
|
A:GLY17
|
3.7
|
16.9
|
1.0
|
|
N
|
A:CYS121
|
3.9
|
7.0
|
1.0
|
|
HB3
|
A:CYS121
|
4.0
|
11.9
|
1.0
|
|
O
|
A:HOH2121
|
4.0
|
10.2
|
1.0
|
|
O
|
A:HOH2007
|
4.1
|
10.9
|
1.0
|
|
S2
|
A:SF4286
|
4.1
|
9.3
|
0.2
|
|
S2
|
A:FSX287
|
4.1
|
9.3
|
0.8
|
|
H
|
A:CYS18
|
4.1
|
10.0
|
1.0
|
|
HA2
|
A:GLY78
|
4.2
|
12.3
|
1.0
|
|
CA
|
A:CYS121
|
4.2
|
8.4
|
1.0
|
|
HA3
|
A:GLY119
|
4.4
|
8.0
|
1.0
|
|
SD
|
A:CSS21
|
4.4
|
10.6
|
0.8
|
|
CA
|
A:GLY17
|
4.5
|
14.1
|
1.0
|
|
H
|
A:GLY78
|
4.5
|
13.2
|
1.0
|
|
HA3
|
A:GLY17
|
4.5
|
16.9
|
1.0
|
|
SG
|
A:CYS159
|
4.6
|
7.6
|
1.0
|
|
HA
|
A:CYS121
|
4.7
|
10.1
|
1.0
|
|
H
|
A:THR120
|
4.7
|
8.5
|
1.0
|
|
N
|
A:CYS18
|
4.8
|
8.3
|
1.0
|
|
H
|
A:ALA122
|
4.8
|
9.5
|
1.0
|
|
HA
|
A:CYS159
|
4.9
|
6.6
|
1.0
|
|
O
|
A:GLN16
|
4.9
|
11.3
|
1.0
|
|
HG2
|
A:GLU77
|
4.9
|
25.9
|
1.0
|
|
N
|
A:THR120
|
5.0
|
7.1
|
1.0
|
|
Reference:
M.C.Marques,
R.Coelho,
I.A.C.Pereira,
P.M.Matias.
Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Int.J.Hydrogen Energy 2013.
ISSN: ISSN 0360-3199
DOI: 10.1016/J.IJHYDENE.2013.04.132
Page generated: Sun Aug 4 23:00:07 2024
|
