Iron in PDB 1e3d: [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
Protein crystallography data
The structure of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774, PDB code: 1e3d
was solved by
P.M.Matias,
C.M.Soares,
L.M.Saraiva,
R.Coelho,
J.Morais,
J.Le Gall,
M.A.Carrondo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
25.00 /
1.80
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.090,
169.980,
72.620,
90.00,
92.80,
90.00
|
|
R / Rfree (%)
|
16.7 /
22.3
|
Other elements in 1e3d:
The structure of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Iron atom in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
(pdb code 1e3d). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
[Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774, PDB code: 1e3d:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 1 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe267
b:18.9
occ:1.00
|
FE1
|
A:F3S267
|
0.0
|
18.9
|
1.0
|
|
S2
|
A:F3S267
|
2.3
|
17.6
|
1.0
|
|
S3
|
A:F3S267
|
2.3
|
17.3
|
1.0
|
|
S1
|
A:F3S267
|
2.3
|
15.8
|
1.0
|
|
SG
|
A:CYS248
|
2.3
|
20.1
|
1.0
|
|
FE3
|
A:F3S267
|
2.7
|
17.6
|
1.0
|
|
FE4
|
A:F3S267
|
2.7
|
18.9
|
1.0
|
|
HB2
|
A:CYS248
|
3.3
|
20.3
|
1.0
|
|
CB
|
A:CYS248
|
3.3
|
16.9
|
1.0
|
|
HA
|
A:CYS248
|
3.3
|
23.2
|
1.0
|
|
H
|
A:ILE249
|
3.4
|
19.6
|
1.0
|
|
H
|
A:GLY250
|
3.5
|
23.6
|
1.0
|
|
H
|
A:CYS251
|
3.7
|
24.6
|
1.0
|
|
HG23
|
A:THR226
|
3.7
|
35.2
|
1.0
|
|
CA
|
A:CYS248
|
3.8
|
19.4
|
1.0
|
|
HG22
|
A:VAL186
|
3.8
|
25.6
|
1.0
|
|
S4
|
A:F3S267
|
3.9
|
18.6
|
1.0
|
|
HA2
|
A:GLY250
|
4.0
|
25.4
|
1.0
|
|
N
|
A:ILE249
|
4.0
|
16.3
|
1.0
|
|
HE22
|
B:GLN227
|
4.1
|
25.2
|
1.0
|
|
HG2
|
A:PRO241
|
4.1
|
18.3
|
1.0
|
|
HB3
|
A:CYS248
|
4.1
|
20.3
|
1.0
|
|
N
|
A:GLY250
|
4.2
|
19.6
|
1.0
|
|
C
|
A:CYS248
|
4.3
|
17.6
|
1.0
|
|
HG13
|
A:VAL186
|
4.4
|
28.4
|
1.0
|
|
N
|
A:CYS251
|
4.5
|
20.5
|
1.0
|
|
CA
|
A:GLY250
|
4.6
|
21.1
|
1.0
|
|
CG2
|
A:THR226
|
4.6
|
23.4
|
1.0
|
|
CG2
|
A:VAL186
|
4.7
|
17.1
|
1.0
|
|
HZ3
|
A:TRP240
|
4.8
|
24.8
|
1.0
|
|
HG21
|
A:THR226
|
4.8
|
35.2
|
1.0
|
|
HG12
|
A:ILE249
|
4.8
|
18.8
|
1.0
|
|
SG
|
A:CYS251
|
4.8
|
17.4
|
1.0
|
|
NE2
|
B:GLN227
|
4.9
|
21.0
|
1.0
|
|
SG
|
A:CYS230
|
4.9
|
17.8
|
1.0
|
|
HD21
|
A:ASN228
|
4.9
|
22.7
|
1.0
|
|
HG23
|
A:VAL186
|
4.9
|
25.6
|
1.0
|
|
HB2
|
A:PRO241
|
5.0
|
18.4
|
1.0
|
|
HD2
|
A:PRO241
|
5.0
|
17.9
|
1.0
|
|
Iron binding site 2 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 2 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe267
b:17.6
occ:1.00
|
FE3
|
A:F3S267
|
0.0
|
17.6
|
1.0
|
|
S1
|
A:F3S267
|
2.2
|
15.8
|
1.0
|
|
S4
|
A:F3S267
|
2.3
|
18.6
|
1.0
|
|
S3
|
A:F3S267
|
2.3
|
17.3
|
1.0
|
|
SG
|
A:CYS251
|
2.3
|
17.4
|
1.0
|
|
FE1
|
A:F3S267
|
2.7
|
18.9
|
1.0
|
|
FE4
|
A:F3S267
|
2.7
|
18.9
|
1.0
|
|
H
|
A:CYS251
|
3.0
|
24.6
|
1.0
|
|
HB3
|
A:CYS251
|
3.4
|
22.4
|
1.0
|
|
CB
|
A:CYS251
|
3.5
|
18.6
|
1.0
|
|
O
|
B:HOH2260
|
3.7
|
14.6
|
1.0
|
|
N
|
A:CYS251
|
3.7
|
20.5
|
1.0
|
|
HD21
|
A:ASN228
|
3.8
|
22.7
|
1.0
|
|
S2
|
A:F3S267
|
3.9
|
17.6
|
1.0
|
|
HE2
|
B:LYS222
|
4.0
|
15.4
|
1.0
|
|
CA
|
A:CYS251
|
4.1
|
17.7
|
1.0
|
|
O
|
A:HOH2149
|
4.2
|
15.8
|
1.0
|
|
HB2
|
A:CYS251
|
4.3
|
22.4
|
1.0
|
|
H
|
A:SER252
|
4.3
|
16.4
|
1.0
|
|
ND2
|
A:ASN228
|
4.5
|
18.9
|
1.0
|
|
HD22
|
A:ASN228
|
4.5
|
22.7
|
1.0
|
|
HG2
|
A:PRO241
|
4.6
|
18.3
|
1.0
|
|
H
|
A:ILE249
|
4.6
|
19.6
|
1.0
|
|
H
|
A:CYS150
|
4.6
|
20.3
|
1.0
|
|
HE22
|
B:GLN227
|
4.6
|
25.2
|
1.0
|
|
C
|
A:CYS251
|
4.6
|
17.3
|
1.0
|
|
HG12
|
A:ILE249
|
4.6
|
18.8
|
1.0
|
|
N
|
A:SER252
|
4.7
|
13.7
|
1.0
|
|
H
|
A:GLY250
|
4.7
|
23.6
|
1.0
|
|
HG23
|
A:THR226
|
4.7
|
35.2
|
1.0
|
|
HG13
|
A:ILE249
|
4.8
|
18.8
|
1.0
|
|
SG
|
A:CYS248
|
4.8
|
20.1
|
1.0
|
|
SG
|
A:CYS230
|
4.8
|
17.8
|
1.0
|
|
O
|
B:HOH2256
|
4.8
|
12.7
|
1.0
|
|
C
|
A:GLY250
|
4.8
|
21.7
|
1.0
|
|
HA2
|
A:GLY250
|
5.0
|
25.4
|
1.0
|
|
HA2
|
A:GLY149
|
5.0
|
23.4
|
1.0
|
|
CE
|
B:LYS222
|
5.0
|
12.9
|
1.0
|
|
HA
|
A:CYS251
|
5.0
|
21.2
|
1.0
|
|
HZ
|
A:PHE235
|
5.0
|
24.6
|
1.0
|
|
Iron binding site 3 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 3 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe267
b:18.9
occ:1.00
|
FE4
|
A:F3S267
|
0.0
|
18.9
|
1.0
|
|
S2
|
A:F3S267
|
2.3
|
17.6
|
1.0
|
|
S4
|
A:F3S267
|
2.3
|
18.6
|
1.0
|
|
S3
|
A:F3S267
|
2.3
|
17.3
|
1.0
|
|
SG
|
A:CYS230
|
2.4
|
17.8
|
1.0
|
|
FE1
|
A:F3S267
|
2.7
|
18.9
|
1.0
|
|
FE3
|
A:F3S267
|
2.7
|
17.6
|
1.0
|
|
CB
|
A:CYS230
|
3.4
|
17.1
|
1.0
|
|
HB2
|
A:CYS230
|
3.4
|
20.5
|
1.0
|
|
HD21
|
A:ASN228
|
3.5
|
22.7
|
1.0
|
|
HE2
|
A:PHE235
|
3.5
|
22.4
|
1.0
|
|
HB3
|
A:CYS230
|
3.5
|
20.5
|
1.0
|
|
ND2
|
A:ASN228
|
3.9
|
18.9
|
1.0
|
|
S1
|
A:F3S267
|
3.9
|
15.8
|
1.0
|
|
HZ
|
A:PHE235
|
3.9
|
24.6
|
1.0
|
|
HG22
|
A:VAL186
|
4.0
|
25.6
|
1.0
|
|
HB3
|
A:ASN228
|
4.1
|
25.5
|
1.0
|
|
HG2
|
A:PRO241
|
4.1
|
18.3
|
1.0
|
|
HD22
|
A:ASN228
|
4.1
|
22.7
|
1.0
|
|
HD2
|
A:PRO241
|
4.2
|
17.9
|
1.0
|
|
CE2
|
A:PHE235
|
4.2
|
18.7
|
1.0
|
|
HG23
|
A:VAL186
|
4.3
|
25.6
|
1.0
|
|
HE3
|
A:TRP240
|
4.3
|
20.8
|
1.0
|
|
CZ
|
A:PHE235
|
4.5
|
20.5
|
1.0
|
|
O
|
A:HOH2149
|
4.5
|
15.8
|
1.0
|
|
CG
|
A:ASN228
|
4.6
|
20.0
|
1.0
|
|
HE2
|
B:LYS222
|
4.6
|
15.4
|
1.0
|
|
CG2
|
A:VAL186
|
4.6
|
17.1
|
1.0
|
|
H
|
A:CYS230
|
4.6
|
24.8
|
1.0
|
|
CB
|
A:ASN228
|
4.7
|
21.3
|
1.0
|
|
HB2
|
A:ASN228
|
4.8
|
25.5
|
1.0
|
|
HD3
|
A:PRO241
|
4.8
|
17.9
|
1.0
|
|
SG
|
A:CYS251
|
4.8
|
17.4
|
1.0
|
|
CD
|
A:PRO241
|
4.8
|
14.9
|
1.0
|
|
SG
|
A:CYS248
|
4.8
|
20.1
|
1.0
|
|
CA
|
A:CYS230
|
4.8
|
14.4
|
1.0
|
|
CG
|
A:PRO241
|
4.9
|
15.3
|
1.0
|
|
HZ3
|
A:TRP240
|
5.0
|
24.8
|
1.0
|
|
Iron binding site 4 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 4 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe268
b:20.6
occ:1.00
|
FE1
|
A:SF4268
|
0.0
|
20.6
|
1.0
|
|
S3
|
A:SF4268
|
2.3
|
19.4
|
1.0
|
|
SG
|
A:CYS221
|
2.3
|
20.2
|
1.0
|
|
S2
|
A:SF4268
|
2.3
|
21.2
|
1.0
|
|
S4
|
A:SF4268
|
2.4
|
19.8
|
1.0
|
|
FE4
|
A:SF4268
|
2.7
|
24.5
|
1.0
|
|
FE2
|
A:SF4268
|
2.7
|
22.1
|
1.0
|
|
FE3
|
A:SF4268
|
2.8
|
22.2
|
1.0
|
|
HB3
|
A:CYS221
|
3.1
|
18.7
|
1.0
|
|
CB
|
A:CYS221
|
3.3
|
15.6
|
1.0
|
|
HA3
|
A:GLY223
|
3.5
|
15.5
|
1.0
|
|
HD3
|
A:PRO224
|
3.6
|
21.3
|
1.0
|
|
HG22
|
A:VAL242
|
3.6
|
27.6
|
1.0
|
|
HB2
|
A:CYS221
|
3.7
|
18.7
|
1.0
|
|
HD1
|
A:HIS187
|
3.8
|
30.6
|
1.0
|
|
H
|
A:GLY223
|
3.9
|
18.3
|
1.0
|
|
S1
|
A:SF4268
|
3.9
|
21.5
|
1.0
|
|
H
|
A:LEU216
|
4.1
|
22.1
|
1.0
|
|
HB2
|
A:LEU216
|
4.1
|
23.1
|
1.0
|
|
HG23
|
A:VAL242
|
4.2
|
27.6
|
1.0
|
|
CG2
|
A:VAL242
|
4.4
|
18.4
|
1.0
|
|
CA
|
A:GLY223
|
4.4
|
12.9
|
1.0
|
|
N
|
A:GLY223
|
4.5
|
15.2
|
1.0
|
|
CD
|
A:PRO224
|
4.5
|
17.8
|
1.0
|
|
CA
|
A:CYS221
|
4.6
|
15.7
|
1.0
|
|
ND1
|
A:HIS187
|
4.6
|
25.5
|
1.0
|
|
HG13
|
A:VAL242
|
4.7
|
38.8
|
1.0
|
|
SG
|
A:CYS215
|
4.7
|
22.8
|
1.0
|
|
HA
|
A:HIS187
|
4.7
|
28.5
|
1.0
|
|
H
|
A:CYS248
|
4.8
|
19.7
|
1.0
|
|
SG
|
A:CYS190
|
4.8
|
19.5
|
1.0
|
|
HB2
|
A:HIS187
|
4.8
|
27.9
|
1.0
|
|
C
|
A:CYS221
|
4.8
|
21.0
|
1.0
|
|
HA
|
A:TYR217
|
4.8
|
25.9
|
1.0
|
|
HB3
|
A:CYS248
|
4.8
|
20.3
|
1.0
|
|
N
|
A:LEU216
|
4.8
|
18.4
|
1.0
|
|
H
|
A:TYR217
|
4.9
|
24.3
|
1.0
|
|
HG21
|
A:VAL242
|
4.9
|
27.6
|
1.0
|
|
HD2
|
A:PRO224
|
4.9
|
21.3
|
1.0
|
|
HA2
|
A:GLY223
|
4.9
|
15.5
|
1.0
|
|
HH2
|
A:TRP240
|
4.9
|
24.8
|
1.0
|
|
N
|
A:TYR217
|
4.9
|
20.2
|
1.0
|
|
HB2
|
A:TYR217
|
5.0
|
27.6
|
1.0
|
|
Iron binding site 5 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 5 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe268
b:22.1
occ:1.00
|
FE2
|
A:SF4268
|
0.0
|
22.1
|
1.0
|
|
S4
|
A:SF4268
|
2.2
|
19.8
|
1.0
|
|
SG
|
A:CYS190
|
2.3
|
19.5
|
1.0
|
|
S3
|
A:SF4268
|
2.3
|
19.4
|
1.0
|
|
S1
|
A:SF4268
|
2.3
|
21.5
|
1.0
|
|
FE1
|
A:SF4268
|
2.7
|
20.6
|
1.0
|
|
FE3
|
A:SF4268
|
2.7
|
22.2
|
1.0
|
|
FE4
|
A:SF4268
|
2.7
|
24.5
|
1.0
|
|
HB3
|
A:CYS190
|
3.1
|
25.9
|
1.0
|
|
CB
|
A:CYS190
|
3.2
|
21.6
|
1.0
|
|
HB2
|
A:ARG192
|
3.2
|
30.3
|
1.0
|
|
HB2
|
A:CYS190
|
3.3
|
25.9
|
1.0
|
|
HG13
|
A:VAL242
|
3.6
|
38.8
|
1.0
|
|
HD1
|
A:HIS187
|
3.7
|
30.6
|
1.0
|
|
HG22
|
A:VAL242
|
3.8
|
27.6
|
1.0
|
|
S2
|
A:SF4268
|
3.9
|
21.2
|
1.0
|
|
H
|
A:ARG192
|
4.0
|
24.7
|
1.0
|
|
HH2
|
A:TRP240
|
4.1
|
24.8
|
1.0
|
|
HA
|
A:HIS187
|
4.1
|
28.5
|
1.0
|
|
CB
|
A:ARG192
|
4.2
|
25.3
|
1.0
|
|
ND1
|
A:HIS187
|
4.4
|
25.5
|
1.0
|
|
HG3
|
A:ARG192
|
4.5
|
26.5
|
1.0
|
|
CG1
|
A:VAL242
|
4.5
|
25.9
|
1.0
|
|
HD2
|
A:ARG192
|
4.5
|
26.1
|
1.0
|
|
C
|
A:ARG192
|
4.6
|
22.4
|
1.0
|
|
H
|
A:LEU216
|
4.6
|
22.1
|
1.0
|
|
N
|
A:ARG192
|
4.6
|
20.6
|
1.0
|
|
CA
|
A:CYS190
|
4.6
|
22.7
|
1.0
|
|
N
|
A:ARG193
|
4.6
|
21.2
|
1.0
|
|
HA
|
A:ARG193
|
4.6
|
31.2
|
1.0
|
|
CG2
|
A:VAL242
|
4.7
|
18.4
|
1.0
|
|
CA
|
A:ARG192
|
4.7
|
22.2
|
1.0
|
|
H
|
A:ARG193
|
4.7
|
25.5
|
1.0
|
|
HG12
|
A:VAL242
|
4.7
|
38.8
|
1.0
|
|
HB3
|
A:ARG192
|
4.7
|
30.3
|
1.0
|
|
SG
|
A:CYS221
|
4.8
|
20.2
|
1.0
|
|
HA
|
A:CYS215
|
4.8
|
30.7
|
1.0
|
|
CG
|
A:ARG192
|
4.8
|
22.1
|
1.0
|
|
HZ2
|
A:TRP240
|
4.9
|
21.8
|
1.0
|
|
CH2
|
A:TRP240
|
4.9
|
20.7
|
1.0
|
|
HG23
|
A:VAL242
|
4.9
|
27.6
|
1.0
|
|
SG
|
A:CYS215
|
4.9
|
22.8
|
1.0
|
|
O
|
A:ARG192
|
4.9
|
17.0
|
1.0
|
|
HA
|
A:CYS190
|
5.0
|
27.3
|
1.0
|
|
Iron binding site 6 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 6 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe268
b:22.2
occ:1.00
|
FE3
|
A:SF4268
|
0.0
|
22.2
|
1.0
|
|
S1
|
A:SF4268
|
2.2
|
21.5
|
1.0
|
|
S2
|
A:SF4268
|
2.3
|
21.2
|
1.0
|
|
SG
|
A:CYS215
|
2.3
|
22.8
|
1.0
|
|
S4
|
A:SF4268
|
2.4
|
19.8
|
1.0
|
|
FE4
|
A:SF4268
|
2.6
|
24.5
|
1.0
|
|
FE2
|
A:SF4268
|
2.7
|
22.1
|
1.0
|
|
FE1
|
A:SF4268
|
2.8
|
20.6
|
1.0
|
|
H
|
A:LEU216
|
3.1
|
22.1
|
1.0
|
|
CB
|
A:CYS215
|
3.4
|
27.1
|
1.0
|
|
HD2
|
A:PHE196
|
3.5
|
31.4
|
1.0
|
|
HB2
|
A:CYS215
|
3.5
|
32.5
|
1.0
|
|
HB2
|
A:PHE196
|
3.5
|
25.0
|
1.0
|
|
HA
|
A:CYS215
|
3.6
|
30.7
|
1.0
|
|
HD1
|
A:HIS187
|
3.6
|
30.6
|
1.0
|
|
H
|
A:TYR217
|
3.8
|
24.3
|
1.0
|
|
N
|
A:LEU216
|
3.8
|
18.4
|
1.0
|
|
HB2
|
A:TYR217
|
3.9
|
27.6
|
1.0
|
|
S3
|
A:SF4268
|
3.9
|
19.4
|
1.0
|
|
CA
|
A:CYS215
|
3.9
|
25.6
|
1.0
|
|
HB2
|
A:ARG192
|
4.0
|
30.3
|
1.0
|
|
HE1
|
A:HIS187
|
4.0
|
35.7
|
1.0
|
|
CD2
|
A:PHE196
|
4.2
|
26.2
|
1.0
|
|
HB3
|
A:CYS215
|
4.3
|
32.5
|
1.0
|
|
ND1
|
A:HIS187
|
4.3
|
25.5
|
1.0
|
|
N
|
A:TYR217
|
4.3
|
20.2
|
1.0
|
|
C
|
A:CYS215
|
4.3
|
24.3
|
1.0
|
|
HB3
|
A:CYS221
|
4.4
|
18.7
|
1.0
|
|
CB
|
A:PHE196
|
4.4
|
20.8
|
1.0
|
|
CE1
|
A:HIS187
|
4.5
|
29.7
|
1.0
|
|
HA
|
A:ARG193
|
4.7
|
31.2
|
1.0
|
|
HB2
|
A:LEU216
|
4.7
|
23.1
|
1.0
|
|
O
|
A:ARG192
|
4.7
|
17.0
|
1.0
|
|
CG
|
A:PHE196
|
4.7
|
24.6
|
1.0
|
|
CB
|
A:TYR217
|
4.8
|
23.0
|
1.0
|
|
SG
|
A:CYS221
|
4.8
|
20.2
|
1.0
|
|
CA
|
A:LEU216
|
4.8
|
17.1
|
1.0
|
|
CB
|
A:ARG192
|
4.8
|
25.3
|
1.0
|
|
HB3
|
A:ARG192
|
4.9
|
30.3
|
1.0
|
|
HB3
|
A:PHE196
|
4.9
|
25.0
|
1.0
|
|
SG
|
A:CYS190
|
4.9
|
19.5
|
1.0
|
|
HA
|
A:TYR217
|
4.9
|
25.9
|
1.0
|
|
CA
|
A:TYR217
|
5.0
|
21.6
|
1.0
|
|
C
|
A:LEU216
|
5.0
|
19.0
|
1.0
|
|
Iron binding site 7 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 7 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe268
b:24.5
occ:1.00
|
FE4
|
A:SF4268
|
0.0
|
24.5
|
1.0
|
|
HD1
|
A:HIS187
|
1.2
|
30.6
|
1.0
|
|
ND1
|
A:HIS187
|
2.0
|
25.5
|
1.0
|
|
S2
|
A:SF4268
|
2.3
|
21.2
|
1.0
|
|
S3
|
A:SF4268
|
2.3
|
19.4
|
1.0
|
|
S1
|
A:SF4268
|
2.4
|
21.5
|
1.0
|
|
FE3
|
A:SF4268
|
2.6
|
22.2
|
1.0
|
|
FE1
|
A:SF4268
|
2.7
|
20.6
|
1.0
|
|
FE2
|
A:SF4268
|
2.7
|
22.1
|
1.0
|
|
CE1
|
A:HIS187
|
2.9
|
29.7
|
1.0
|
|
HE1
|
A:HIS187
|
3.0
|
35.7
|
1.0
|
|
CG
|
A:HIS187
|
3.1
|
24.7
|
1.0
|
|
HA
|
A:HIS187
|
3.3
|
28.5
|
1.0
|
|
HB2
|
A:HIS187
|
3.3
|
27.9
|
1.0
|
|
HD3
|
A:PRO224
|
3.4
|
21.3
|
1.0
|
|
HG3
|
A:PRO224
|
3.5
|
26.4
|
1.0
|
|
CB
|
A:HIS187
|
3.6
|
23.3
|
1.0
|
|
S4
|
A:SF4268
|
3.9
|
19.8
|
1.0
|
|
CA
|
A:HIS187
|
3.9
|
23.7
|
1.0
|
|
HB3
|
A:CYS190
|
4.0
|
25.9
|
1.0
|
|
HA3
|
A:GLY223
|
4.0
|
15.5
|
1.0
|
|
NE2
|
A:HIS187
|
4.1
|
26.5
|
1.0
|
|
CD
|
A:PRO224
|
4.1
|
17.8
|
1.0
|
|
HD2
|
A:PHE196
|
4.2
|
31.4
|
1.0
|
|
CD2
|
A:HIS187
|
4.2
|
27.0
|
1.0
|
|
CG
|
A:PRO224
|
4.2
|
22.0
|
1.0
|
|
HB2
|
A:PHE196
|
4.4
|
25.0
|
1.0
|
|
HB2
|
A:CYS190
|
4.4
|
25.9
|
1.0
|
|
CD2
|
A:PHE196
|
4.5
|
26.2
|
1.0
|
|
HB3
|
A:HIS187
|
4.5
|
27.9
|
1.0
|
|
CB
|
A:CYS190
|
4.5
|
21.6
|
1.0
|
|
SG
|
A:CYS215
|
4.6
|
22.8
|
1.0
|
|
HA
|
A:ARG193
|
4.6
|
31.2
|
1.0
|
|
HG2
|
A:PRO224
|
4.6
|
26.4
|
1.0
|
|
SG
|
A:CYS190
|
4.7
|
19.5
|
1.0
|
|
N
|
A:PRO224
|
4.7
|
20.2
|
1.0
|
|
O
|
A:HIS187
|
4.7
|
25.3
|
1.0
|
|
SG
|
A:CYS221
|
4.7
|
20.2
|
1.0
|
|
C
|
A:HIS187
|
4.8
|
26.4
|
1.0
|
|
CA
|
A:GLY223
|
4.8
|
12.9
|
1.0
|
|
HD2
|
A:PRO224
|
4.9
|
21.3
|
1.0
|
|
HG3
|
A:ARG193
|
4.9
|
43.0
|
1.0
|
|
CG
|
A:PHE196
|
4.9
|
24.6
|
1.0
|
|
CE2
|
A:PHE196
|
5.0
|
27.6
|
1.0
|
|
C
|
A:GLY223
|
5.0
|
15.3
|
1.0
|
|
N
|
A:HIS187
|
5.0
|
22.9
|
1.0
|
|
Iron binding site 8 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 8 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe269
b:16.9
occ:1.00
|
FE1
|
A:FSX269
|
0.0
|
16.9
|
1.0
|
|
O12
|
A:FSX269
|
1.8
|
22.8
|
1.0
|
|
S2
|
A:FSX269
|
2.2
|
16.1
|
1.0
|
|
SG
|
A:CYS17
|
2.3
|
16.2
|
1.0
|
|
S3
|
A:FSX269
|
2.3
|
14.5
|
1.0
|
|
FE3
|
A:FSX269
|
2.7
|
16.1
|
1.0
|
|
H
|
A:GLY19
|
3.1
|
18.9
|
1.0
|
|
H
|
A:CYS17
|
3.1
|
16.1
|
1.0
|
|
FE2
|
A:FSX269
|
3.2
|
21.3
|
1.0
|
|
HB3
|
A:CYS17
|
3.2
|
16.3
|
1.0
|
|
HA3
|
A:GLY19
|
3.3
|
19.7
|
1.0
|
|
CB
|
A:CYS17
|
3.3
|
13.6
|
1.0
|
|
FE4
|
A:FSX269
|
3.3
|
17.8
|
1.0
|
|
O24
|
A:FSX269
|
3.6
|
17.5
|
1.0
|
|
N
|
A:GLY19
|
3.8
|
15.8
|
1.0
|
|
N
|
A:CYS17
|
3.8
|
13.4
|
1.0
|
|
HG3
|
B:ARG69
|
3.8
|
17.0
|
1.0
|
|
O1
|
A:FSX269
|
3.8
|
9.7
|
1.0
|
|
CA
|
A:CYS17
|
3.9
|
11.2
|
1.0
|
|
CA
|
A:GLY19
|
4.0
|
16.4
|
1.0
|
|
NE2
|
B:HIS225
|
4.0
|
15.1
|
1.0
|
|
S4
|
A:FSX269
|
4.1
|
18.7
|
1.0
|
|
H
|
A:THR18
|
4.1
|
18.6
|
1.0
|
|
HB2
|
A:CYS17
|
4.1
|
16.3
|
1.0
|
|
C
|
A:CYS17
|
4.2
|
12.4
|
1.0
|
|
H
|
A:CYS20
|
4.3
|
18.3
|
1.0
|
|
N
|
A:THR18
|
4.3
|
15.5
|
1.0
|
|
HG2
|
B:ARG69
|
4.6
|
17.0
|
1.0
|
|
HA
|
B:ARG69
|
4.6
|
16.2
|
1.0
|
|
CG
|
B:ARG69
|
4.6
|
14.2
|
1.0
|
|
OE2
|
A:GLU75
|
4.6
|
20.0
|
1.0
|
|
HA2
|
A:GLY19
|
4.7
|
19.7
|
1.0
|
|
HD2
|
B:HIS225
|
4.7
|
19.5
|
1.0
|
|
SG
|
A:CYS150
|
4.7
|
16.5
|
1.0
|
|
HB2
|
A:GLU16
|
4.7
|
19.8
|
1.0
|
|
CD2
|
B:HIS225
|
4.8
|
16.3
|
1.0
|
|
HA
|
A:CYS17
|
4.8
|
13.5
|
1.0
|
|
N
|
A:CYS20
|
4.8
|
15.2
|
1.0
|
|
HB3
|
A:PRO151
|
4.8
|
18.7
|
1.0
|
|
HA
|
A:GLU16
|
4.8
|
19.4
|
1.0
|
|
C
|
A:GLY19
|
4.9
|
17.4
|
1.0
|
|
O
|
A:CYS17
|
4.9
|
18.2
|
1.0
|
|
C
|
A:THR18
|
4.9
|
16.0
|
1.0
|
|
C
|
A:GLU16
|
5.0
|
13.9
|
1.0
|
|
HA3
|
B:GLY72
|
5.0
|
17.7
|
1.0
|
|
HB3
|
B:ARG69
|
5.0
|
15.6
|
1.0
|
|
O
|
A:HOH2125
|
5.0
|
13.9
|
1.0
|
|
CE1
|
B:HIS225
|
5.0
|
13.9
|
1.0
|
|
Iron binding site 9 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 9 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe269
b:21.3
occ:1.00
|
FE2
|
A:FSX269
|
0.0
|
21.3
|
1.0
|
|
O12
|
A:FSX269
|
1.8
|
22.8
|
1.0
|
|
O24
|
A:FSX269
|
1.8
|
17.5
|
1.0
|
|
O1
|
A:FSX269
|
2.1
|
9.7
|
1.0
|
|
OE2
|
A:GLU75
|
2.2
|
20.0
|
1.0
|
|
H
|
A:CYS20
|
2.9
|
18.3
|
1.0
|
|
HG3
|
A:GLU75
|
2.9
|
19.8
|
1.0
|
|
SG
|
A:CYS20
|
2.9
|
22.9
|
1.0
|
|
CD
|
A:GLU75
|
3.0
|
19.1
|
1.0
|
|
FE4
|
A:FSX269
|
3.1
|
17.8
|
1.0
|
|
HB2
|
A:GLU16
|
3.1
|
19.8
|
1.0
|
|
FE1
|
A:FSX269
|
3.2
|
16.9
|
1.0
|
|
HG2
|
A:GLU75
|
3.2
|
19.8
|
1.0
|
|
CG
|
A:GLU75
|
3.2
|
16.5
|
1.0
|
|
H
|
A:CYS17
|
3.4
|
16.1
|
1.0
|
|
HB2
|
A:CYS20
|
3.5
|
26.1
|
1.0
|
|
N
|
A:CYS20
|
3.6
|
15.2
|
1.0
|
|
H
|
A:GLY19
|
3.6
|
18.9
|
1.0
|
|
H
|
A:THR18
|
3.6
|
18.6
|
1.0
|
|
HB3
|
A:GLU16
|
3.7
|
19.8
|
1.0
|
|
CB
|
A:CYS20
|
3.7
|
21.7
|
1.0
|
|
S4
|
A:FSX269
|
3.8
|
18.7
|
1.0
|
|
CB
|
A:GLU16
|
3.9
|
16.5
|
1.0
|
|
O
|
A:HOH2122
|
3.9
|
13.4
|
1.0
|
|
N
|
A:GLY19
|
4.0
|
15.8
|
1.0
|
|
S2
|
A:FSX269
|
4.0
|
16.1
|
1.0
|
|
N
|
A:CYS17
|
4.2
|
13.4
|
1.0
|
|
OE1
|
A:GLU75
|
4.2
|
19.1
|
1.0
|
|
S3
|
A:FSX269
|
4.2
|
14.5
|
1.0
|
|
N
|
A:THR18
|
4.2
|
15.5
|
1.0
|
|
HA3
|
A:GLY112
|
4.2
|
19.7
|
1.0
|
|
HA3
|
A:GLY19
|
4.3
|
19.7
|
1.0
|
|
CA
|
A:CYS20
|
4.3
|
16.1
|
1.0
|
|
FE3
|
A:FSX269
|
4.3
|
16.1
|
1.0
|
|
HA
|
A:GLU16
|
4.3
|
19.4
|
1.0
|
|
CA
|
A:GLY19
|
4.5
|
16.4
|
1.0
|
|
C
|
A:GLY19
|
4.5
|
17.4
|
1.0
|
|
HA
|
A:THR18
|
4.5
|
18.8
|
1.0
|
|
HB3
|
A:CYS20
|
4.6
|
26.1
|
1.0
|
|
CA
|
A:GLU16
|
4.6
|
16.2
|
1.0
|
|
C
|
A:THR18
|
4.7
|
16.0
|
1.0
|
|
H
|
A:GLY76
|
4.7
|
22.6
|
1.0
|
|
CB
|
A:GLU75
|
4.7
|
14.4
|
1.0
|
|
CA
|
A:THR18
|
4.7
|
15.7
|
1.0
|
|
HB2
|
A:CYS114
|
4.7
|
17.4
|
1.0
|
|
HA
|
A:CYS20
|
4.8
|
19.3
|
1.0
|
|
HA2
|
A:GLY76
|
4.9
|
21.5
|
1.0
|
|
H
|
A:SER21
|
4.9
|
16.4
|
1.0
|
|
HB3
|
A:PRO151
|
4.9
|
18.7
|
1.0
|
|
SG
|
A:CYS17
|
4.9
|
16.2
|
1.0
|
|
C
|
A:GLU16
|
4.9
|
13.9
|
1.0
|
|
N
|
A:GLY76
|
5.0
|
18.9
|
1.0
|
|
C
|
A:CYS17
|
5.0
|
12.4
|
1.0
|
|
HG2
|
A:GLU16
|
5.0
|
21.4
|
1.0
|
|
Iron binding site 10 out
of 24 in 1e3d
Go back to
Iron Binding Sites List in 1e3d
Iron binding site 10 out
of 24 in the [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of [Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe269
b:16.1
occ:1.00
|
FE3
|
A:FSX269
|
0.0
|
16.1
|
1.0
|
|
S4
|
A:FSX269
|
2.2
|
18.7
|
1.0
|
|
S2
|
A:FSX269
|
2.2
|
16.1
|
1.0
|
|
S3
|
A:FSX269
|
2.3
|
14.5
|
1.0
|
|
SG
|
A:CYS150
|
2.3
|
16.5
|
1.0
|
|
FE1
|
A:FSX269
|
2.7
|
16.9
|
1.0
|
|
FE4
|
A:FSX269
|
2.7
|
17.8
|
1.0
|
|
HA
|
A:CYS150
|
2.9
|
20.4
|
1.0
|
|
CB
|
A:CYS150
|
3.4
|
17.2
|
1.0
|
|
HG2
|
B:ARG69
|
3.5
|
17.0
|
1.0
|
|
CA
|
A:CYS150
|
3.5
|
17.0
|
1.0
|
|
HG3
|
B:ARG69
|
3.6
|
17.0
|
1.0
|
|
O
|
A:HOH2234
|
3.8
|
18.9
|
1.0
|
|
HB2
|
A:CYS150
|
3.8
|
20.6
|
1.0
|
|
O1
|
A:FSX269
|
3.9
|
9.7
|
1.0
|
|
HE
|
B:ARG69
|
4.0
|
16.1
|
1.0
|
|
C
|
A:CYS150
|
4.0
|
14.5
|
1.0
|
|
CG
|
B:ARG69
|
4.0
|
14.2
|
1.0
|
|
O12
|
A:FSX269
|
4.0
|
22.8
|
1.0
|
|
O24
|
A:FSX269
|
4.1
|
17.5
|
1.0
|
|
HB3
|
A:CYS150
|
4.2
|
20.6
|
1.0
|
|
HA
|
A:PRO151
|
4.2
|
16.1
|
1.0
|
|
HD2
|
B:HIS225
|
4.2
|
19.5
|
1.0
|
|
FE2
|
A:FSX269
|
4.3
|
21.3
|
1.0
|
|
SG
|
A:CYS114
|
4.4
|
16.2
|
1.0
|
|
O
|
A:CYS150
|
4.4
|
13.8
|
1.0
|
|
N
|
A:PRO151
|
4.5
|
14.1
|
1.0
|
|
HB
|
A:THR113
|
4.6
|
25.5
|
1.0
|
|
NE2
|
B:HIS225
|
4.7
|
15.1
|
1.0
|
|
SG
|
A:CYS17
|
4.7
|
16.2
|
1.0
|
|
NE
|
B:ARG69
|
4.7
|
13.4
|
1.0
|
|
H
|
A:THR113
|
4.7
|
20.1
|
1.0
|
|
O
|
A:GLY149
|
4.7
|
16.1
|
1.0
|
|
H
|
A:CYS114
|
4.8
|
24.0
|
1.0
|
|
CD2
|
B:HIS225
|
4.8
|
16.3
|
1.0
|
|
CA
|
A:PRO151
|
4.8
|
13.5
|
1.0
|
|
N
|
A:CYS150
|
4.8
|
16.9
|
1.0
|
|
HB3
|
A:PRO151
|
4.9
|
18.7
|
1.0
|
|
HZ2
|
A:TRP257
|
4.9
|
20.1
|
1.0
|
|
HA3
|
A:GLY19
|
5.0
|
19.7
|
1.0
|
|
CD
|
B:ARG69
|
5.0
|
14.2
|
1.0
|
|
HB3
|
B:ARG69
|
5.0
|
15.6
|
1.0
|
|
Reference:
P.M.Matias,
C.M.Soares,
L.M.Saraiva,
R.Coelho,
J.Morais,
J.Le Gall,
M.A.Carrondo.
[Nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of Its Interaction with the Tetrahaem Cytochrome C3. J.Biol.Inorg.Chem. V. 6 63 2001.
ISSN: ISSN 0949-8257
PubMed: 11191224
DOI: 10.1007/S007750000167
Page generated: Sat Aug 3 04:12:13 2024
|
