Iron in PDB 9erp: Hydrogenase-2 Ni-Si State
Enzymatic activity of Hydrogenase-2 Ni-Si State
All present enzymatic activity of Hydrogenase-2 Ni-Si State:
1.12.99.6;
Protein crystallography data
The structure of Hydrogenase-2 Ni-Si State, PDB code: 9erp
was solved by
S.B.Carr,
W.Li,
K.L.Wong,
P.A.Ash,
K.A.Vincent,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
64.28 /
1.37
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.18,
100.001,
167.814,
90,
90,
90
|
|
R / Rfree (%)
|
15.7 /
17.4
|
Other elements in 9erp:
The structure of Hydrogenase-2 Ni-Si State 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 Hydrogenase-2 Ni-Si State
(pdb code 9erp). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
Hydrogenase-2 Ni-Si State, PDB code: 9erp:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 1 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe301
b:15.0
occ:1.00
|
FE1
|
S:SF4301
|
0.0
|
15.0
|
1.0
|
|
S3
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
S2
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
SG
|
S:CYS220
|
2.3
|
15.4
|
1.0
|
|
S4
|
S:SF4301
|
2.3
|
15.2
|
1.0
|
|
FE4
|
S:SF4301
|
2.7
|
14.8
|
1.0
|
|
FE3
|
S:SF4301
|
2.8
|
15.0
|
1.0
|
|
FE2
|
S:SF4301
|
2.8
|
14.3
|
1.0
|
|
H
|
S:LEU221
|
3.2
|
16.6
|
1.0
|
|
CB
|
S:CYS220
|
3.4
|
17.3
|
1.0
|
|
HB2
|
S:CYS220
|
3.4
|
20.7
|
1.0
|
|
HB2
|
S:PHE201
|
3.4
|
20.4
|
1.0
|
|
HA
|
S:CYS220
|
3.6
|
18.7
|
1.0
|
|
H
|
S:TYR222
|
3.6
|
18.2
|
1.0
|
|
HB2
|
S:ARG197
|
3.7
|
17.5
|
1.0
|
|
HB2
|
S:TYR222
|
3.8
|
21.1
|
1.0
|
|
HD1
|
S:PHE201
|
3.8
|
21.2
|
1.0
|
|
N
|
S:LEU221
|
3.8
|
13.8
|
1.0
|
|
S1
|
S:SF4301
|
3.9
|
15.4
|
1.0
|
|
CA
|
S:CYS220
|
4.0
|
15.6
|
1.0
|
|
N
|
S:TYR222
|
4.1
|
15.2
|
1.0
|
|
HB3
|
S:CYS220
|
4.2
|
20.7
|
1.0
|
|
HE1
|
S:HIS192
|
4.3
|
19.3
|
1.0
|
|
HB3
|
S:ARG197
|
4.3
|
17.5
|
1.0
|
|
C
|
S:CYS220
|
4.3
|
15.9
|
1.0
|
|
CB
|
S:PHE201
|
4.4
|
17.0
|
1.0
|
|
CD1
|
S:PHE201
|
4.4
|
17.6
|
1.0
|
|
CB
|
S:ARG197
|
4.5
|
14.6
|
1.0
|
|
ND1
|
S:HIS192
|
4.5
|
15.2
|
1.0
|
|
HB3
|
S:CYS226
|
4.5
|
17.3
|
1.0
|
|
HA
|
S:TYR222
|
4.6
|
19.5
|
1.0
|
|
CB
|
S:TYR222
|
4.6
|
17.6
|
1.0
|
|
O
|
S:ARG197
|
4.6
|
15.4
|
1.0
|
|
HA
|
S:ARG198
|
4.7
|
17.8
|
1.0
|
|
CA
|
S:TYR222
|
4.7
|
16.2
|
1.0
|
|
CE1
|
S:HIS192
|
4.7
|
16.1
|
1.0
|
|
C
|
S:LEU221
|
4.8
|
15.8
|
1.0
|
|
HB3
|
S:PHE201
|
4.8
|
20.4
|
1.0
|
|
CA
|
S:LEU221
|
4.8
|
15.2
|
1.0
|
|
C
|
S:ARG197
|
4.8
|
14.4
|
1.0
|
|
CG
|
S:PHE201
|
4.8
|
17.2
|
1.0
|
|
SG
|
S:CYS226
|
4.8
|
13.9
|
1.0
|
|
SG
|
S:CYS195
|
4.8
|
14.0
|
1.0
|
|
H
|
S:PHE201
|
4.8
|
19.3
|
1.0
|
|
HB2
|
S:LEU221
|
4.9
|
18.7
|
1.0
|
|
HB3
|
S:TYR222
|
4.9
|
21.1
|
1.0
|
|
Iron binding site 2 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 2 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe301
b:14.3
occ:1.00
|
FE2
|
S:SF4301
|
0.0
|
14.3
|
1.0
|
|
S1
|
S:SF4301
|
2.3
|
15.4
|
1.0
|
|
SG
|
S:CYS226
|
2.3
|
13.9
|
1.0
|
|
S4
|
S:SF4301
|
2.3
|
15.2
|
1.0
|
|
S3
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
FE4
|
S:SF4301
|
2.7
|
14.8
|
1.0
|
|
FE3
|
S:SF4301
|
2.7
|
15.0
|
1.0
|
|
FE1
|
S:SF4301
|
2.8
|
15.0
|
1.0
|
|
HB3
|
S:CYS226
|
3.0
|
17.3
|
1.0
|
|
CB
|
S:CYS226
|
3.2
|
14.4
|
1.0
|
|
HB2
|
S:CYS226
|
3.5
|
17.3
|
1.0
|
|
HD3
|
S:PRO229
|
3.5
|
18.9
|
1.0
|
|
HA3
|
S:GLY228
|
3.7
|
19.1
|
1.0
|
|
H
|
S:GLY228
|
3.8
|
18.2
|
1.0
|
|
S2
|
S:SF4301
|
3.9
|
14.6
|
1.0
|
|
HG21
|
S:VAL249
|
3.9
|
17.7
|
1.0
|
|
H
|
S:LEU221
|
4.2
|
16.6
|
1.0
|
|
HB2
|
S:LEU221
|
4.3
|
18.7
|
1.0
|
|
HA
|
S:TYR222
|
4.4
|
19.5
|
1.0
|
|
N
|
S:GLY228
|
4.5
|
15.2
|
1.0
|
|
CD
|
S:PRO229
|
4.5
|
15.8
|
1.0
|
|
CA
|
S:GLY228
|
4.5
|
15.9
|
1.0
|
|
CA
|
S:CYS226
|
4.6
|
14.2
|
1.0
|
|
HG11
|
S:VAL249
|
4.6
|
16.2
|
1.0
|
|
HG22
|
S:VAL249
|
4.6
|
17.7
|
1.0
|
|
ND1
|
S:HIS192
|
4.6
|
15.2
|
1.0
|
|
SG
|
S:CYS195
|
4.7
|
14.0
|
1.0
|
|
CG2
|
S:VAL249
|
4.7
|
14.7
|
1.0
|
|
SG
|
S:CYS220
|
4.7
|
15.4
|
1.0
|
|
H
|
S:TYR222
|
4.8
|
18.2
|
1.0
|
|
N
|
S:TYR222
|
4.8
|
15.2
|
1.0
|
|
C
|
S:CYS226
|
4.8
|
15.2
|
1.0
|
|
HB2
|
S:HIS192
|
4.8
|
18.5
|
1.0
|
|
HD2
|
S:PRO229
|
4.8
|
18.9
|
1.0
|
|
HB2
|
S:TYR222
|
4.9
|
21.1
|
1.0
|
|
HH2
|
S:TRP247
|
4.9
|
16.6
|
1.0
|
|
HG3
|
S:PRO229
|
4.9
|
18.3
|
1.0
|
|
N
|
S:LEU221
|
4.9
|
13.8
|
1.0
|
|
HA
|
S:CYS226
|
4.9
|
17.1
|
1.0
|
|
H
|
S:CYS255
|
4.9
|
15.1
|
1.0
|
|
HA
|
S:HIS192
|
5.0
|
18.0
|
1.0
|
|
C
|
S:LEU221
|
5.0
|
15.8
|
1.0
|
|
O
|
S:CYS226
|
5.0
|
15.5
|
1.0
|
|
Iron binding site 3 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 3 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe301
b:15.0
occ:1.00
|
FE3
|
S:SF4301
|
0.0
|
15.0
|
1.0
|
|
ND1
|
S:HIS192
|
2.0
|
15.2
|
1.0
|
|
S1
|
S:SF4301
|
2.3
|
15.4
|
1.0
|
|
S4
|
S:SF4301
|
2.3
|
15.2
|
1.0
|
|
S2
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
FE4
|
S:SF4301
|
2.7
|
14.8
|
1.0
|
|
FE2
|
S:SF4301
|
2.7
|
14.3
|
1.0
|
|
FE1
|
S:SF4301
|
2.8
|
15.0
|
1.0
|
|
CE1
|
S:HIS192
|
2.9
|
16.1
|
1.0
|
|
HE1
|
S:HIS192
|
3.0
|
19.3
|
1.0
|
|
CG
|
S:HIS192
|
3.1
|
15.0
|
1.0
|
|
HA
|
S:HIS192
|
3.3
|
18.0
|
1.0
|
|
HB2
|
S:HIS192
|
3.3
|
18.5
|
1.0
|
|
HD3
|
S:PRO229
|
3.5
|
18.9
|
1.0
|
|
HG3
|
S:PRO229
|
3.5
|
18.3
|
1.0
|
|
CB
|
S:HIS192
|
3.6
|
15.4
|
1.0
|
|
S3
|
S:SF4301
|
3.9
|
14.6
|
1.0
|
|
CA
|
S:HIS192
|
3.9
|
15.0
|
1.0
|
|
NE2
|
S:HIS192
|
4.1
|
16.8
|
1.0
|
|
HB3
|
S:CYS195
|
4.1
|
17.6
|
1.0
|
|
CD2
|
S:HIS192
|
4.2
|
17.0
|
1.0
|
|
HA3
|
S:GLY228
|
4.2
|
19.1
|
1.0
|
|
CD
|
S:PRO229
|
4.3
|
15.8
|
1.0
|
|
CG
|
S:PRO229
|
4.3
|
15.2
|
1.0
|
|
HB2
|
S:PHE201
|
4.5
|
20.4
|
1.0
|
|
HD1
|
S:PHE201
|
4.5
|
21.2
|
1.0
|
|
HB3
|
S:HIS192
|
4.6
|
18.5
|
1.0
|
|
HB2
|
S:CYS195
|
4.6
|
17.6
|
1.0
|
|
CB
|
S:CYS195
|
4.6
|
14.7
|
1.0
|
|
SG
|
S:CYS195
|
4.6
|
14.0
|
1.0
|
|
SG
|
S:CYS220
|
4.7
|
15.4
|
1.0
|
|
HD3
|
S:ARG198
|
4.7
|
20.6
|
1.0
|
|
HG2
|
S:PRO229
|
4.7
|
18.3
|
1.0
|
|
O
|
S:HIS192
|
4.7
|
16.0
|
1.0
|
|
CD1
|
S:PHE201
|
4.8
|
17.6
|
1.0
|
|
SG
|
S:CYS226
|
4.8
|
13.9
|
1.0
|
|
HE2
|
S:HIS192
|
4.8
|
20.1
|
1.0
|
|
N
|
S:PRO229
|
4.8
|
15.0
|
1.0
|
|
HA
|
S:ARG198
|
4.8
|
17.8
|
1.0
|
|
HB2
|
S:TYR222
|
4.8
|
21.1
|
1.0
|
|
C
|
S:HIS192
|
4.9
|
15.4
|
1.0
|
|
N
|
S:HIS192
|
4.9
|
14.7
|
1.0
|
|
HB3
|
S:CYS226
|
5.0
|
17.3
|
1.0
|
|
Iron binding site 4 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 4 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe301
b:14.8
occ:1.00
|
FE4
|
S:SF4301
|
0.0
|
14.8
|
1.0
|
|
SG
|
S:CYS195
|
2.2
|
14.0
|
1.0
|
|
S3
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
S2
|
S:SF4301
|
2.3
|
14.6
|
1.0
|
|
S1
|
S:SF4301
|
2.3
|
15.4
|
1.0
|
|
FE2
|
S:SF4301
|
2.7
|
14.3
|
1.0
|
|
FE1
|
S:SF4301
|
2.7
|
15.0
|
1.0
|
|
FE3
|
S:SF4301
|
2.7
|
15.0
|
1.0
|
|
HB3
|
S:CYS195
|
3.0
|
17.6
|
1.0
|
|
HB2
|
S:ARG197
|
3.0
|
17.5
|
1.0
|
|
CB
|
S:CYS195
|
3.1
|
14.7
|
1.0
|
|
HB2
|
S:CYS195
|
3.3
|
17.6
|
1.0
|
|
S4
|
S:SF4301
|
3.9
|
15.2
|
1.0
|
|
H
|
S:ARG197
|
3.9
|
17.2
|
1.0
|
|
HG11
|
S:VAL249
|
3.9
|
16.2
|
1.0
|
|
CB
|
S:ARG197
|
4.0
|
14.6
|
1.0
|
|
HA
|
S:HIS192
|
4.1
|
18.0
|
1.0
|
|
HH2
|
S:TRP247
|
4.2
|
16.6
|
1.0
|
|
HB3
|
S:ARG197
|
4.5
|
17.5
|
1.0
|
|
HG21
|
S:VAL249
|
4.5
|
17.7
|
1.0
|
|
ND1
|
S:HIS192
|
4.5
|
15.2
|
1.0
|
|
C
|
S:ARG197
|
4.5
|
14.4
|
1.0
|
|
N
|
S:ARG197
|
4.6
|
14.3
|
1.0
|
|
CA
|
S:CYS195
|
4.6
|
13.9
|
1.0
|
|
HG3
|
S:ARG197
|
4.6
|
17.8
|
1.0
|
|
CA
|
S:ARG197
|
4.6
|
15.2
|
1.0
|
|
H
|
S:ARG198
|
4.6
|
18.4
|
1.0
|
|
N
|
S:ARG198
|
4.6
|
15.3
|
1.0
|
|
HD2
|
S:ARG197
|
4.7
|
18.1
|
1.0
|
|
SG
|
S:CYS226
|
4.8
|
13.9
|
1.0
|
|
HA
|
S:ARG198
|
4.8
|
17.8
|
1.0
|
|
HG22
|
S:ILE191
|
4.8
|
18.1
|
1.0
|
|
H
|
S:LEU221
|
4.8
|
16.6
|
1.0
|
|
CG
|
S:ARG197
|
4.8
|
14.9
|
1.0
|
|
HZ2
|
S:TRP247
|
4.8
|
16.5
|
1.0
|
|
C
|
S:CYS195
|
4.9
|
15.1
|
1.0
|
|
CG1
|
S:VAL249
|
4.9
|
13.5
|
1.0
|
|
SG
|
S:CYS220
|
4.9
|
15.4
|
1.0
|
|
HA
|
S:CYS220
|
5.0
|
18.7
|
1.0
|
|
CH2
|
S:TRP247
|
5.0
|
13.9
|
1.0
|
|
HA
|
S:CYS195
|
5.0
|
16.7
|
1.0
|
|
Iron binding site 5 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 5 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe302
b:12.1
occ:1.00
|
FE1
|
S:F3S302
|
0.0
|
12.1
|
1.0
|
|
S1
|
S:F3S302
|
2.2
|
12.6
|
1.0
|
|
S2
|
S:F3S302
|
2.3
|
13.8
|
1.0
|
|
S3
|
S:F3S302
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS258
|
2.3
|
13.2
|
1.0
|
|
FE3
|
S:F3S302
|
2.7
|
13.2
|
1.0
|
|
FE4
|
S:F3S302
|
2.7
|
13.4
|
1.0
|
|
H
|
S:CYS258
|
3.0
|
16.2
|
1.0
|
|
HB3
|
S:CYS258
|
3.4
|
16.3
|
1.0
|
|
CB
|
S:CYS258
|
3.4
|
13.6
|
1.0
|
|
O
|
L:HOH817
|
3.6
|
12.8
|
1.0
|
|
H
|
S:ASN259
|
3.6
|
16.4
|
1.0
|
|
N
|
S:CYS258
|
3.7
|
13.5
|
1.0
|
|
S4
|
S:F3S302
|
3.8
|
13.9
|
1.0
|
|
CA
|
S:CYS258
|
4.0
|
13.4
|
1.0
|
|
HE2
|
L:LYS211
|
4.0
|
15.3
|
1.0
|
|
N
|
S:ASN259
|
4.2
|
13.7
|
1.0
|
|
OD1
|
S:ASN259
|
4.2
|
14.3
|
1.0
|
|
O
|
S:HOH475
|
4.2
|
14.2
|
1.0
|
|
HB2
|
S:CYS258
|
4.3
|
16.3
|
1.0
|
|
HE22
|
L:GLN216
|
4.4
|
15.4
|
1.0
|
|
C
|
S:CYS258
|
4.4
|
13.9
|
1.0
|
|
H
|
S:GLY257
|
4.5
|
15.9
|
1.0
|
|
H
|
S:CYS154
|
4.6
|
15.0
|
1.0
|
|
H
|
S:TYR256
|
4.6
|
14.3
|
1.0
|
|
HG2
|
S:PRO248
|
4.6
|
15.5
|
1.0
|
|
SG
|
S:CYS235
|
4.7
|
13.8
|
1.0
|
|
HA2
|
S:GLY153
|
4.7
|
16.5
|
1.0
|
|
C
|
S:GLY257
|
4.8
|
13.5
|
1.0
|
|
CG
|
S:ASN259
|
4.8
|
14.5
|
1.0
|
|
O
|
S:HOH422
|
4.8
|
13.8
|
1.0
|
|
SG
|
S:CYS255
|
4.8
|
13.3
|
1.0
|
|
HA
|
S:CYS258
|
4.9
|
16.1
|
1.0
|
|
OE1
|
L:GLN216
|
4.9
|
13.6
|
1.0
|
|
HG21
|
S:THR231
|
4.9
|
17.2
|
1.0
|
|
HB3
|
S:TYR256
|
4.9
|
16.8
|
1.0
|
|
CE
|
L:LYS211
|
4.9
|
12.8
|
1.0
|
|
N
|
S:GLY257
|
5.0
|
13.3
|
1.0
|
|
HZ
|
S:PHE240
|
5.0
|
15.7
|
1.0
|
|
HZ3
|
L:LYS211
|
5.0
|
15.9
|
1.0
|
|
Iron binding site 6 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 6 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe302
b:13.2
occ:1.00
|
FE3
|
S:F3S302
|
0.0
|
13.2
|
1.0
|
|
S4
|
S:F3S302
|
2.2
|
13.9
|
1.0
|
|
S1
|
S:F3S302
|
2.2
|
12.6
|
1.0
|
|
S3
|
S:F3S302
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS235
|
2.3
|
13.8
|
1.0
|
|
FE1
|
S:F3S302
|
2.7
|
12.1
|
1.0
|
|
FE4
|
S:F3S302
|
2.7
|
13.4
|
1.0
|
|
HB3
|
S:CYS235
|
3.3
|
15.2
|
1.0
|
|
CB
|
S:CYS235
|
3.3
|
12.7
|
1.0
|
|
HB2
|
S:CYS235
|
3.4
|
15.2
|
1.0
|
|
HD11
|
S:ILE191
|
3.7
|
17.1
|
1.0
|
|
HZ
|
S:PHE240
|
3.8
|
15.7
|
1.0
|
|
HD13
|
S:ILE191
|
3.8
|
17.1
|
1.0
|
|
HE1
|
S:PHE240
|
3.8
|
16.0
|
1.0
|
|
S2
|
S:F3S302
|
4.0
|
13.8
|
1.0
|
|
O
|
S:HOH475
|
4.0
|
14.2
|
1.0
|
|
CD1
|
S:ILE191
|
4.2
|
14.2
|
1.0
|
|
HG2
|
S:PRO248
|
4.2
|
15.5
|
1.0
|
|
HD2
|
S:PRO248
|
4.2
|
16.0
|
1.0
|
|
HE3
|
S:TRP247
|
4.4
|
14.4
|
1.0
|
|
CZ
|
S:PHE240
|
4.4
|
13.1
|
1.0
|
|
CE1
|
S:PHE240
|
4.5
|
13.3
|
1.0
|
|
HD12
|
S:ILE191
|
4.5
|
17.1
|
1.0
|
|
CA
|
S:CYS235
|
4.7
|
13.8
|
1.0
|
|
SG
|
S:CYS255
|
4.7
|
13.3
|
1.0
|
|
HE2
|
L:LYS211
|
4.7
|
15.3
|
1.0
|
|
OD1
|
S:ASN259
|
4.7
|
14.3
|
1.0
|
|
SG
|
S:CYS258
|
4.8
|
13.2
|
1.0
|
|
HD21
|
S:ASN259
|
4.8
|
17.0
|
1.0
|
|
H
|
S:CYS235
|
4.8
|
15.2
|
1.0
|
|
HA
|
S:CYS235
|
4.9
|
16.5
|
1.0
|
|
O
|
S:HOH539
|
4.9
|
13.9
|
1.0
|
|
CD
|
S:PRO248
|
4.9
|
13.3
|
1.0
|
|
CG
|
S:PRO248
|
5.0
|
12.9
|
1.0
|
|
CG
|
S:ASN259
|
5.0
|
14.5
|
1.0
|
|
Iron binding site 7 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 7 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe302
b:13.4
occ:1.00
|
FE4
|
S:F3S302
|
0.0
|
13.4
|
1.0
|
|
S4
|
S:F3S302
|
2.2
|
13.9
|
1.0
|
|
S3
|
S:F3S302
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS255
|
2.3
|
13.3
|
1.0
|
|
S2
|
S:F3S302
|
2.3
|
13.8
|
1.0
|
|
FE3
|
S:F3S302
|
2.7
|
13.2
|
1.0
|
|
FE1
|
S:F3S302
|
2.7
|
12.1
|
1.0
|
|
H
|
S:GLY257
|
3.1
|
15.9
|
1.0
|
|
HA
|
S:CYS255
|
3.1
|
16.9
|
1.0
|
|
H
|
S:TYR256
|
3.3
|
14.3
|
1.0
|
|
CB
|
S:CYS255
|
3.3
|
14.2
|
1.0
|
|
HB2
|
S:CYS255
|
3.3
|
17.1
|
1.0
|
|
H
|
S:CYS258
|
3.6
|
16.2
|
1.0
|
|
CA
|
S:CYS255
|
3.7
|
14.1
|
1.0
|
|
HE22
|
L:GLN216
|
3.8
|
15.4
|
1.0
|
|
N
|
S:TYR256
|
3.8
|
11.9
|
1.0
|
|
HD13
|
S:ILE191
|
3.9
|
17.1
|
1.0
|
|
N
|
S:GLY257
|
3.9
|
13.3
|
1.0
|
|
S1
|
S:F3S302
|
3.9
|
12.6
|
1.0
|
|
HG21
|
S:THR231
|
4.0
|
17.2
|
1.0
|
|
HD12
|
S:ILE191
|
4.1
|
17.1
|
1.0
|
|
HB3
|
S:CYS255
|
4.2
|
17.1
|
1.0
|
|
C
|
S:CYS255
|
4.2
|
13.2
|
1.0
|
|
HA2
|
S:GLY257
|
4.2
|
16.2
|
1.0
|
|
HD11
|
S:ILE191
|
4.2
|
17.1
|
1.0
|
|
CD1
|
S:ILE191
|
4.3
|
14.2
|
1.0
|
|
N
|
S:CYS258
|
4.3
|
13.5
|
1.0
|
|
HG2
|
S:PRO248
|
4.4
|
15.5
|
1.0
|
|
CA
|
S:GLY257
|
4.5
|
13.5
|
1.0
|
|
NE2
|
L:GLN216
|
4.6
|
12.8
|
1.0
|
|
H
|
S:ASN259
|
4.7
|
16.4
|
1.0
|
|
SG
|
S:CYS235
|
4.7
|
13.8
|
1.0
|
|
HB3
|
S:TYR256
|
4.8
|
16.8
|
1.0
|
|
C
|
S:TYR256
|
4.8
|
12.9
|
1.0
|
|
C
|
S:GLY257
|
4.9
|
13.5
|
1.0
|
|
SG
|
S:CYS258
|
4.9
|
13.2
|
1.0
|
|
CA
|
S:TYR256
|
4.9
|
13.0
|
1.0
|
|
CG2
|
S:THR231
|
4.9
|
14.3
|
1.0
|
|
HZ3
|
S:TRP247
|
4.9
|
15.0
|
1.0
|
|
HE21
|
L:GLN216
|
5.0
|
15.4
|
1.0
|
|
N
|
S:CYS255
|
5.0
|
12.6
|
1.0
|
|
HB2
|
S:PRO248
|
5.0
|
15.6
|
1.0
|
|
HG22
|
S:THR231
|
5.0
|
17.2
|
1.0
|
|
HB2
|
S:CYS235
|
5.0
|
15.2
|
1.0
|
|
Iron binding site 8 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 8 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe303
b:13.2
occ:1.00
|
FE1
|
S:SF4303
|
0.0
|
13.2
|
1.0
|
|
S4
|
S:SF4303
|
2.2
|
13.7
|
1.0
|
|
SG
|
S:CYS22
|
2.3
|
13.0
|
1.0
|
|
S3
|
S:SF4303
|
2.3
|
14.3
|
1.0
|
|
S2
|
S:SF4303
|
2.3
|
13.0
|
1.0
|
|
FE3
|
S:SF4303
|
2.7
|
13.1
|
1.0
|
|
FE2
|
S:SF4303
|
2.7
|
13.7
|
1.0
|
|
FE4
|
S:SF4303
|
2.7
|
14.2
|
1.0
|
|
H
|
S:CYS22
|
3.0
|
16.8
|
0.6
|
|
H
|
S:CYS22
|
3.0
|
16.8
|
0.4
|
|
HB3
|
S:CYS22
|
3.1
|
15.7
|
1.0
|
|
CB
|
S:CYS22
|
3.3
|
13.1
|
1.0
|
|
HE2
|
L:HIS214
|
3.5
|
15.7
|
1.0
|
|
H
|
S:GLY24
|
3.5
|
16.0
|
1.0
|
|
N
|
S:CYS22
|
3.8
|
14.0
|
1.0
|
|
S1
|
S:SF4303
|
3.8
|
14.3
|
1.0
|
|
HA3
|
S:GLY24
|
4.0
|
16.0
|
1.0
|
|
CA
|
S:CYS22
|
4.0
|
13.5
|
1.0
|
|
HB2
|
S:CYS22
|
4.1
|
15.7
|
1.0
|
|
H
|
S:CYS25
|
4.2
|
14.8
|
1.0
|
|
O
|
S:HOH423
|
4.2
|
14.5
|
1.0
|
|
HG3
|
L:ARG59
|
4.2
|
16.1
|
1.0
|
|
N
|
S:GLY24
|
4.2
|
13.3
|
1.0
|
|
NE2
|
L:HIS214
|
4.3
|
13.1
|
1.0
|
|
H
|
S:THR23
|
4.3
|
16.4
|
1.0
|
|
O
|
S:HOH484
|
4.5
|
15.5
|
1.0
|
|
C
|
S:CYS22
|
4.5
|
14.0
|
1.0
|
|
CA
|
S:GLY24
|
4.5
|
13.3
|
1.0
|
|
HA
|
S:GLU21
|
4.6
|
18.0
|
0.4
|
|
N
|
S:THR23
|
4.6
|
13.7
|
1.0
|
|
HA
|
S:GLU21
|
4.6
|
17.9
|
0.6
|
|
HD2
|
L:HIS214
|
4.6
|
15.8
|
1.0
|
|
SG
|
S:CYS154
|
4.7
|
12.9
|
1.0
|
|
SG
|
S:CYS120
|
4.7
|
13.7
|
1.0
|
|
N
|
S:CYS25
|
4.8
|
12.3
|
1.0
|
|
HB3
|
L:ARG59
|
4.8
|
16.0
|
1.0
|
|
CD2
|
L:HIS214
|
4.9
|
13.2
|
1.0
|
|
SG
|
S:CYS25
|
4.9
|
13.3
|
1.0
|
|
HA
|
S:CYS22
|
4.9
|
16.2
|
1.0
|
|
C
|
S:GLU21
|
4.9
|
15.2
|
0.4
|
|
C
|
S:GLU21
|
4.9
|
15.2
|
0.6
|
|
Iron binding site 9 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 9 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe303
b:13.7
occ:1.00
|
FE2
|
S:SF4303
|
0.0
|
13.7
|
1.0
|
|
S3
|
S:SF4303
|
2.2
|
14.3
|
1.0
|
|
S4
|
S:SF4303
|
2.3
|
13.7
|
1.0
|
|
SG
|
S:CYS120
|
2.3
|
13.7
|
1.0
|
|
S1
|
S:SF4303
|
2.3
|
14.3
|
1.0
|
|
FE3
|
S:SF4303
|
2.7
|
13.1
|
1.0
|
|
FE1
|
S:SF4303
|
2.7
|
13.2
|
1.0
|
|
FE4
|
S:SF4303
|
2.8
|
14.2
|
1.0
|
|
HB2
|
S:CYS120
|
2.9
|
18.9
|
1.0
|
|
CB
|
S:CYS120
|
3.2
|
15.8
|
1.0
|
|
H
|
S:CYS120
|
3.3
|
16.6
|
1.0
|
|
O
|
S:HOH551
|
3.8
|
14.4
|
1.0
|
|
HB3
|
S:CYS120
|
3.9
|
18.9
|
1.0
|
|
O
|
S:HOH428
|
3.9
|
14.0
|
1.0
|
|
S2
|
S:SF4303
|
3.9
|
13.0
|
1.0
|
|
O
|
S:HOH484
|
3.9
|
15.5
|
1.0
|
|
N
|
S:CYS120
|
4.0
|
13.9
|
1.0
|
|
HA2
|
S:GLY82
|
4.1
|
16.9
|
1.0
|
|
H
|
S:CYS22
|
4.2
|
16.8
|
0.6
|
|
CA
|
S:CYS120
|
4.2
|
14.7
|
1.0
|
|
HG12
|
S:VAL126
|
4.2
|
17.6
|
1.0
|
|
H
|
S:CYS22
|
4.2
|
16.8
|
0.4
|
|
HA
|
S:GLU21
|
4.4
|
18.0
|
0.4
|
|
SG
|
S:CYS154
|
4.4
|
12.9
|
1.0
|
|
H
|
S:GLY82
|
4.4
|
16.9
|
1.0
|
|
HA
|
S:GLU21
|
4.4
|
17.9
|
0.6
|
|
HA
|
S:CYS120
|
4.6
|
17.6
|
1.0
|
|
HB3
|
S:CYS22
|
4.8
|
15.7
|
1.0
|
|
HA3
|
S:GLY118
|
4.8
|
16.5
|
1.0
|
|
SG
|
S:CYS22
|
4.9
|
13.0
|
1.0
|
|
SG
|
S:CYS25
|
4.9
|
13.3
|
1.0
|
|
HA
|
S:CYS154
|
4.9
|
15.9
|
1.0
|
|
HG11
|
S:VAL126
|
5.0
|
17.6
|
1.0
|
|
N
|
S:CYS22
|
5.0
|
14.0
|
1.0
|
|
H
|
S:VAL126
|
5.0
|
17.1
|
1.0
|
|
CA
|
S:GLY82
|
5.0
|
14.1
|
1.0
|
|
Iron binding site 10 out
of 24 in 9erp
Go back to
Iron Binding Sites List in 9erp
Iron binding site 10 out
of 24 in the Hydrogenase-2 Ni-Si State
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Hydrogenase-2 Ni-Si State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe303
b:13.1
occ:1.00
|
FE3
|
S:SF4303
|
0.0
|
13.1
|
1.0
|
|
S2
|
S:SF4303
|
2.3
|
13.0
|
1.0
|
|
SG
|
S:CYS154
|
2.3
|
12.9
|
1.0
|
|
S4
|
S:SF4303
|
2.3
|
13.7
|
1.0
|
|
S1
|
S:SF4303
|
2.3
|
14.3
|
1.0
|
|
FE2
|
S:SF4303
|
2.7
|
13.7
|
1.0
|
|
FE1
|
S:SF4303
|
2.7
|
13.2
|
1.0
|
|
FE4
|
S:SF4303
|
2.8
|
14.2
|
1.0
|
|
HA
|
S:CYS154
|
2.8
|
15.9
|
1.0
|
|
CB
|
S:CYS154
|
3.4
|
12.9
|
1.0
|
|
CA
|
S:CYS154
|
3.4
|
13.2
|
1.0
|
|
HG3
|
L:ARG59
|
3.7
|
16.1
|
1.0
|
|
HD2
|
L:HIS214
|
3.7
|
15.8
|
1.0
|
|
HB2
|
S:CYS154
|
3.8
|
15.5
|
1.0
|
|
C
|
S:CYS154
|
3.8
|
12.8
|
1.0
|
|
O
|
S:HOH551
|
3.8
|
14.4
|
1.0
|
|
S3
|
S:SF4303
|
3.8
|
14.3
|
1.0
|
|
HE
|
L:ARG59
|
4.1
|
14.8
|
1.0
|
|
HE2
|
L:HIS214
|
4.1
|
15.7
|
1.0
|
|
HB3
|
S:CYS154
|
4.1
|
15.5
|
1.0
|
|
HA
|
S:PRO155
|
4.2
|
15.7
|
1.0
|
|
HG2
|
L:ARG59
|
4.2
|
16.1
|
1.0
|
|
O
|
S:CYS154
|
4.2
|
13.2
|
1.0
|
|
N
|
S:PRO155
|
4.3
|
12.1
|
1.0
|
|
CG
|
L:ARG59
|
4.4
|
13.4
|
1.0
|
|
CD2
|
L:HIS214
|
4.4
|
13.2
|
1.0
|
|
SG
|
S:CYS120
|
4.4
|
13.7
|
1.0
|
|
SG
|
S:CYS22
|
4.5
|
13.0
|
1.0
|
|
O
|
S:GLY153
|
4.6
|
13.4
|
1.0
|
|
NE2
|
L:HIS214
|
4.6
|
13.1
|
1.0
|
|
H
|
S:CYS120
|
4.6
|
16.6
|
1.0
|
|
HB3
|
S:PRO155
|
4.7
|
16.9
|
1.0
|
|
CA
|
S:PRO155
|
4.7
|
13.1
|
1.0
|
|
H
|
S:SER119
|
4.7
|
16.5
|
1.0
|
|
N
|
S:CYS154
|
4.7
|
12.5
|
1.0
|
|
HB2
|
S:SER119
|
4.8
|
18.3
|
1.0
|
|
SG
|
S:CYS25
|
4.8
|
13.3
|
1.0
|
|
HD3
|
S:PRO155
|
4.8
|
15.4
|
1.0
|
|
NE
|
L:ARG59
|
4.9
|
12.3
|
1.0
|
|
HG12
|
S:VAL126
|
4.9
|
17.6
|
1.0
|
|
Reference:
S.B.Carr,
W.Li,
K.L.Wong,
R.M.Evans,
S.E.T.Kendall-Price,
P.A.Ash,
K.A.Vincent.
Glutamate Flick Enables Proton Tunnelling During Fast Redox Biocatalysis To Be Published.
Page generated: Fri Aug 8 04:43:48 2025
|
