Iron in PDB 4u9i: High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
Enzymatic activity of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
All present enzymatic activity of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F:
1.12.2.1;
Protein crystallography data
The structure of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9i
was solved by
H.Ogata,
K.Nishikawa,
W.Lubitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.20 /
1.06
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.850,
99.690,
122.190,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
11 /
13.2
|
Other elements in 4u9i:
The structure of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Iron atom in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
(pdb code 4u9i). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the
High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9i:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 1 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2001
b:5.7
occ:1.00
|
FE1
|
S:SF42001
|
0.0
|
5.7
|
1.0
|
|
S4
|
S:SF42001
|
2.2
|
6.1
|
1.0
|
|
SG
|
S:CYS17
|
2.3
|
5.6
|
1.0
|
|
S2
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
S3
|
S:SF42001
|
2.3
|
6.1
|
1.0
|
|
FE2
|
S:SF42001
|
2.7
|
5.8
|
1.0
|
|
FE3
|
S:SF42001
|
2.7
|
5.7
|
1.0
|
|
FE4
|
S:SF42001
|
2.7
|
5.6
|
1.0
|
|
H
|
S:CYS17
|
3.0
|
9.4
|
1.0
|
|
HB3
|
S:CYS17
|
3.3
|
0.3
|
1.0
|
|
CB
|
S:CYS17
|
3.4
|
5.6
|
1.0
|
|
H
|
S:GLY19
|
3.5
|
2.5
|
1.0
|
|
N
|
S:CYS17
|
3.7
|
5.8
|
1.0
|
|
HG3
|
L:ARG79
|
3.8
|
9.0
|
1.0
|
|
S1
|
S:SF42001
|
3.9
|
5.8
|
1.0
|
|
HA3
|
S:GLY19
|
3.9
|
1.5
|
1.0
|
|
H
|
S:CYS20
|
4.0
|
2.8
|
1.0
|
|
CA
|
S:CYS17
|
4.0
|
5.7
|
1.0
|
|
HB2
|
S:CYS17
|
4.2
|
3.0
|
1.0
|
|
NE2
|
L:HIS235
|
4.2
|
6.1
|
1.0
|
|
N
|
S:GLY19
|
4.2
|
5.3
|
1.0
|
|
H
|
S:THR18
|
4.3
|
10.1
|
1.0
|
|
O
|
S:HOH2172
|
4.5
|
6.8
|
1.0
|
|
HB3
|
L:ARG79
|
4.5
|
3.8
|
1.0
|
|
C
|
S:CYS17
|
4.5
|
5.9
|
1.0
|
|
CA
|
S:GLY19
|
4.5
|
5.9
|
1.0
|
|
HA
|
S:GLU16
|
4.5
|
10.8
|
1.0
|
|
N
|
S:THR18
|
4.5
|
5.8
|
1.0
|
|
HD2
|
L:HIS235
|
4.6
|
3.1
|
1.0
|
|
N
|
S:CYS20
|
4.6
|
5.8
|
1.0
|
|
CG
|
L:ARG79
|
4.6
|
6.5
|
1.0
|
|
SG
|
S:CYS114
|
4.7
|
6.1
|
1.0
|
|
SG
|
S:CYS150
|
4.7
|
5.7
|
1.0
|
|
HA
|
L:ARG79
|
4.7
|
2.0
|
1.0
|
|
HB2
|
S:GLU16
|
4.8
|
4.1
|
1.0
|
|
CD2
|
L:HIS235
|
4.8
|
6.1
|
1.0
|
|
HG2
|
L:ARG79
|
4.8
|
14.3
|
1.0
|
|
SG
|
S:CYS20
|
4.9
|
5.7
|
1.0
|
|
C
|
S:GLU16
|
4.9
|
6.1
|
1.0
|
|
HA
|
S:CYS17
|
4.9
|
1.2
|
1.0
|
|
Iron binding site 2 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 2 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2001
b:5.8
occ:1.00
|
FE2
|
S:SF42001
|
0.0
|
5.8
|
1.0
|
|
S3
|
S:SF42001
|
2.3
|
6.1
|
1.0
|
|
SG
|
S:CYS114
|
2.3
|
6.1
|
1.0
|
|
S4
|
S:SF42001
|
2.3
|
6.1
|
1.0
|
|
S1
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
FE3
|
S:SF42001
|
2.6
|
5.7
|
1.0
|
|
FE1
|
S:SF42001
|
2.7
|
5.7
|
1.0
|
|
FE4
|
S:SF42001
|
2.7
|
5.6
|
1.0
|
|
HB2
|
S:CYS114
|
3.0
|
12.6
|
1.0
|
|
CB
|
S:CYS114
|
3.2
|
6.6
|
1.0
|
|
H
|
S:CYS114
|
3.3
|
1.0
|
1.0
|
|
S2
|
S:SF42001
|
3.9
|
5.8
|
1.0
|
|
HB3
|
S:CYS114
|
3.9
|
2.4
|
1.0
|
|
O
|
S:HOH2171
|
4.0
|
7.3
|
1.0
|
|
O
|
S:HOH2168
|
4.0
|
6.3
|
1.0
|
|
N
|
S:CYS114
|
4.0
|
5.8
|
1.0
|
|
HA
|
S:GLU16
|
4.1
|
10.8
|
1.0
|
|
H
|
S:CYS17
|
4.1
|
9.4
|
1.0
|
|
O
|
S:HOH2172
|
4.1
|
6.8
|
1.0
|
|
CA
|
S:CYS114
|
4.2
|
5.9
|
1.0
|
|
HG12
|
S:VAL120
|
4.4
|
6.7
|
1.0
|
|
HE22
|
S:GLN121
|
4.5
|
6.3
|
1.0
|
|
SG
|
S:CYS150
|
4.5
|
5.7
|
1.0
|
|
HA2
|
S:GLY76
|
4.5
|
5.6
|
1.0
|
|
H
|
S:VAL120
|
4.6
|
5.5
|
1.0
|
|
HA
|
S:CYS114
|
4.7
|
9.9
|
1.0
|
|
SG
|
S:CYS20
|
4.7
|
5.7
|
1.0
|
|
HA3
|
S:GLY119
|
4.8
|
5.5
|
1.0
|
|
SG
|
S:CYS17
|
4.9
|
5.6
|
1.0
|
|
N
|
S:CYS17
|
4.9
|
5.8
|
1.0
|
|
HA3
|
S:GLY112
|
4.9
|
10.1
|
1.0
|
|
HA
|
S:CYS150
|
4.9
|
7.2
|
1.0
|
|
HB3
|
S:CYS17
|
4.9
|
0.3
|
1.0
|
|
HB2
|
S:GLU16
|
5.0
|
4.1
|
1.0
|
|
CA
|
S:GLU16
|
5.0
|
5.8
|
1.0
|
|
HB3
|
S:GLU16
|
5.0
|
6.5
|
1.0
|
|
Iron binding site 3 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 3 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2001
b:5.7
occ:1.00
|
FE3
|
S:SF42001
|
0.0
|
5.7
|
1.0
|
|
S2
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
SG
|
S:CYS150
|
2.3
|
5.7
|
1.0
|
|
S1
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
S4
|
S:SF42001
|
2.3
|
6.1
|
1.0
|
|
FE2
|
S:SF42001
|
2.6
|
5.8
|
1.0
|
|
FE1
|
S:SF42001
|
2.7
|
5.7
|
1.0
|
|
FE4
|
S:SF42001
|
2.7
|
5.6
|
1.0
|
|
HA
|
S:CYS150
|
2.8
|
7.2
|
1.0
|
|
CB
|
S:CYS150
|
3.4
|
5.9
|
1.0
|
|
HG3
|
L:ARG79
|
3.4
|
9.0
|
1.0
|
|
CA
|
S:CYS150
|
3.5
|
6.0
|
1.0
|
|
HB2
|
S:CYS150
|
3.8
|
11.2
|
1.0
|
|
O
|
S:HOH2171
|
3.8
|
7.3
|
1.0
|
|
C
|
S:CYS150
|
3.9
|
6.1
|
1.0
|
|
HG2
|
L:ARG79
|
3.9
|
14.3
|
1.0
|
|
S3
|
S:SF42001
|
3.9
|
6.1
|
1.0
|
|
HD2
|
L:HIS235
|
3.9
|
3.1
|
1.0
|
|
HE
|
L:ARG79
|
3.9
|
3.3
|
1.0
|
|
HA
|
S:PRO151
|
4.1
|
1.8
|
1.0
|
|
CG
|
L:ARG79
|
4.1
|
6.5
|
1.0
|
|
HB3
|
S:CYS150
|
4.1
|
3.4
|
1.0
|
|
O
|
S:CYS150
|
4.2
|
5.9
|
1.0
|
|
N
|
S:PRO151
|
4.4
|
5.7
|
1.0
|
|
SG
|
S:CYS114
|
4.4
|
6.1
|
1.0
|
|
H
|
S:CYS114
|
4.5
|
1.0
|
1.0
|
|
CD2
|
L:HIS235
|
4.6
|
6.1
|
1.0
|
|
SG
|
S:CYS17
|
4.6
|
5.6
|
1.0
|
|
HB
|
S:THR113
|
4.7
|
9.7
|
1.0
|
|
NE
|
L:ARG79
|
4.7
|
6.6
|
1.0
|
|
NE2
|
L:HIS235
|
4.7
|
6.1
|
1.0
|
|
CA
|
S:PRO151
|
4.7
|
5.4
|
1.0
|
|
O
|
S:GLY149
|
4.7
|
6.3
|
1.0
|
|
HZ2
|
S:TRP258
|
4.7
|
6.2
|
1.0
|
|
HB3
|
S:PRO151
|
4.7
|
11.8
|
1.0
|
|
SG
|
S:CYS20
|
4.7
|
5.7
|
1.0
|
|
N
|
S:CYS150
|
4.8
|
6.1
|
1.0
|
|
HB3
|
L:ARG79
|
4.8
|
3.8
|
1.0
|
|
HD3
|
S:PRO151
|
4.9
|
5.0
|
1.0
|
|
H
|
S:THR113
|
5.0
|
3.9
|
1.0
|
|
Iron binding site 4 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 4 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2001
b:5.6
occ:1.00
|
FE4
|
S:SF42001
|
0.0
|
5.6
|
1.0
|
|
SG
|
S:CYS20
|
2.3
|
5.7
|
1.0
|
|
S1
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
S2
|
S:SF42001
|
2.3
|
5.8
|
1.0
|
|
S3
|
S:SF42001
|
2.3
|
6.1
|
1.0
|
|
FE1
|
S:SF42001
|
2.7
|
5.7
|
1.0
|
|
FE2
|
S:SF42001
|
2.7
|
5.8
|
1.0
|
|
FE3
|
S:SF42001
|
2.7
|
5.7
|
1.0
|
|
H
|
S:CYS20
|
3.2
|
2.8
|
1.0
|
|
CB
|
S:CYS20
|
3.5
|
6.1
|
1.0
|
|
HB2
|
S:CYS20
|
3.5
|
5.1
|
1.0
|
|
HB3
|
S:PRO151
|
3.6
|
11.8
|
1.0
|
|
N
|
S:CYS20
|
3.7
|
5.8
|
1.0
|
|
HA
|
S:PRO151
|
3.7
|
1.8
|
1.0
|
|
HA3
|
S:GLY112
|
3.7
|
10.1
|
1.0
|
|
HA
|
S:CYS150
|
3.9
|
7.2
|
1.0
|
|
O
|
S:HOH2168
|
3.9
|
6.3
|
1.0
|
|
S4
|
S:SF42001
|
4.0
|
6.1
|
1.0
|
|
CA
|
S:CYS20
|
4.0
|
5.8
|
1.0
|
|
HA
|
S:CYS20
|
4.2
|
5.3
|
1.0
|
|
HG3
|
S:GLU75
|
4.2
|
10.4
|
1.0
|
|
HD3
|
S:PRO152
|
4.3
|
7.3
|
1.0
|
|
HB3
|
S:CYS20
|
4.3
|
5.3
|
1.0
|
|
CA
|
S:PRO151
|
4.4
|
5.4
|
1.0
|
|
CB
|
S:PRO151
|
4.4
|
6.4
|
1.0
|
|
HA3
|
S:GLY19
|
4.5
|
1.5
|
1.0
|
|
C
|
S:GLY19
|
4.5
|
6.0
|
1.0
|
|
H
|
S:CYS114
|
4.5
|
1.0
|
1.0
|
|
HA2
|
S:GLY112
|
4.5
|
8.1
|
1.0
|
|
CA
|
S:GLY112
|
4.5
|
5.7
|
1.0
|
|
HB2
|
S:CYS114
|
4.6
|
12.6
|
1.0
|
|
H
|
S:GLY19
|
4.6
|
2.5
|
1.0
|
|
SG
|
S:CYS17
|
4.7
|
5.6
|
1.0
|
|
H
|
S:CYS17
|
4.7
|
9.4
|
1.0
|
|
OE2
|
S:GLU75
|
4.7
|
8.1
|
1.0
|
|
O
|
S:GLY149
|
4.8
|
6.3
|
1.0
|
|
CA
|
S:CYS150
|
4.8
|
6.0
|
1.0
|
|
N
|
S:PRO151
|
4.8
|
5.7
|
1.0
|
|
HB2
|
S:PRO151
|
4.8
|
9.0
|
1.0
|
|
CA
|
S:GLY19
|
4.9
|
5.9
|
1.0
|
|
H
|
S:THR113
|
4.9
|
3.9
|
1.0
|
|
SG
|
S:CYS150
|
4.9
|
5.7
|
1.0
|
|
SG
|
S:CYS114
|
4.9
|
6.1
|
1.0
|
|
N
|
S:GLY19
|
5.0
|
5.3
|
1.0
|
|
Iron binding site 5 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 5 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2002
b:8.5
occ:1.00
|
FE1
|
S:SF42002
|
0.0
|
8.5
|
1.0
|
|
ND1
|
S:HIS188
|
2.1
|
9.1
|
1.0
|
|
S3
|
S:SF42002
|
2.3
|
9.1
|
1.0
|
|
S4
|
S:SF42002
|
2.3
|
8.3
|
1.0
|
|
S2
|
S:SF42002
|
2.3
|
8.9
|
1.0
|
|
FE3
|
S:SF42002
|
2.6
|
8.4
|
1.0
|
|
FE2
|
S:SF42002
|
2.7
|
8.2
|
1.0
|
|
FE4
|
S:SF42002
|
2.7
|
9.0
|
1.0
|
|
CE1
|
S:HIS188
|
2.9
|
11.6
|
1.0
|
|
HE1
|
S:HIS188
|
3.0
|
20.6
|
1.0
|
|
CG
|
S:HIS188
|
3.2
|
8.7
|
1.0
|
|
HA
|
S:HIS188
|
3.2
|
7.0
|
1.0
|
|
HB2
|
S:HIS188
|
3.3
|
8.4
|
1.0
|
|
HD3
|
S:PRO225
|
3.4
|
5.3
|
1.0
|
|
HG3
|
S:PRO225
|
3.6
|
14.1
|
1.0
|
|
CB
|
S:HIS188
|
3.6
|
8.2
|
1.0
|
|
S1
|
S:SF42002
|
3.9
|
8.5
|
1.0
|
|
CA
|
S:HIS188
|
3.9
|
8.0
|
1.0
|
|
HB3
|
S:CYS191
|
4.0
|
10.4
|
1.0
|
|
NE2
|
S:HIS188
|
4.1
|
11.4
|
1.0
|
|
HA3
|
S:GLY224
|
4.1
|
10.2
|
1.0
|
|
CD
|
S:PRO225
|
4.2
|
8.2
|
1.0
|
|
CD2
|
S:HIS188
|
4.2
|
10.1
|
1.0
|
|
HB2
|
S:PHE197
|
4.3
|
15.7
|
1.0
|
|
HB2
|
S:CYS191
|
4.3
|
34.9
|
1.0
|
|
CG
|
S:PRO225
|
4.3
|
9.0
|
1.0
|
|
HD11
|
S:LEU194
|
4.3
|
36.1
|
1.0
|
|
HD2
|
S:PHE197
|
4.4
|
5.3
|
1.0
|
|
CB
|
S:CYS191
|
4.5
|
8.7
|
1.0
|
|
O
|
S:HIS188
|
4.5
|
8.8
|
1.0
|
|
HB3
|
S:HIS188
|
4.6
|
18.5
|
1.0
|
|
SG
|
S:CYS191
|
4.6
|
8.4
|
1.0
|
|
SG
|
S:CYS216
|
4.6
|
10.0
|
1.0
|
|
HG2
|
S:PRO225
|
4.6
|
5.3
|
1.0
|
|
HA
|
S:LEU194
|
4.7
|
13.6
|
1.0
|
|
CD2
|
S:PHE197
|
4.7
|
13.5
|
1.0
|
|
C
|
S:HIS188
|
4.7
|
7.9
|
1.0
|
|
SG
|
S:CYS222
|
4.7
|
7.8
|
1.0
|
|
N
|
S:PRO225
|
4.8
|
7.5
|
1.0
|
|
HE2
|
S:HIS188
|
4.9
|
8.2
|
1.0
|
|
CB
|
S:PHE197
|
4.9
|
12.9
|
1.0
|
|
CA
|
S:GLY224
|
5.0
|
7.6
|
1.0
|
|
HB3
|
S:CYS222
|
5.0
|
9.2
|
1.0
|
|
N
|
S:HIS188
|
5.0
|
7.8
|
1.0
|
|
HB3
|
S:PHE197
|
5.0
|
13.3
|
1.0
|
|
HD2
|
S:PRO225
|
5.0
|
6.5
|
1.0
|
|
Iron binding site 6 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 6 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2002
b:8.2
occ:1.00
|
FE2
|
S:SF42002
|
0.0
|
8.2
|
1.0
|
|
S4
|
S:SF42002
|
2.3
|
8.3
|
1.0
|
|
S3
|
S:SF42002
|
2.3
|
9.1
|
1.0
|
|
SG
|
S:CYS222
|
2.3
|
7.8
|
1.0
|
|
S1
|
S:SF42002
|
2.3
|
8.5
|
1.0
|
|
FE3
|
S:SF42002
|
2.7
|
8.4
|
1.0
|
|
FE1
|
S:SF42002
|
2.7
|
8.5
|
1.0
|
|
FE4
|
S:SF42002
|
2.8
|
9.0
|
1.0
|
|
HB3
|
S:CYS222
|
3.0
|
9.2
|
1.0
|
|
CB
|
S:CYS222
|
3.2
|
8.1
|
1.0
|
|
HB2
|
S:CYS222
|
3.5
|
3.4
|
1.0
|
|
HD3
|
S:PRO225
|
3.6
|
5.3
|
1.0
|
|
HG21
|
S:VAL243
|
3.6
|
9.7
|
1.0
|
|
HA3
|
S:GLY224
|
3.8
|
10.2
|
1.0
|
|
H
|
S:GLY224
|
3.9
|
5.2
|
1.0
|
|
S2
|
S:SF42002
|
3.9
|
8.9
|
1.0
|
|
HB2
|
S:LEU217
|
4.0
|
2.1
|
1.0
|
|
HG22
|
S:VAL243
|
4.1
|
7.8
|
1.0
|
|
H
|
S:LEU217
|
4.1
|
11.8
|
1.0
|
|
CG2
|
S:VAL243
|
4.3
|
9.3
|
1.0
|
|
N
|
S:GLY224
|
4.5
|
7.5
|
1.0
|
|
CD
|
S:PRO225
|
4.6
|
8.2
|
1.0
|
|
CA
|
S:GLY224
|
4.6
|
7.6
|
1.0
|
|
CA
|
S:CYS222
|
4.6
|
8.0
|
1.0
|
|
HG11
|
S:VAL243
|
4.6
|
8.3
|
1.0
|
|
ND1
|
S:HIS188
|
4.7
|
9.1
|
1.0
|
|
H
|
S:CYS249
|
4.7
|
8.6
|
1.0
|
|
SG
|
S:CYS216
|
4.7
|
10.0
|
1.0
|
|
HA
|
S:TYR218
|
4.8
|
10.5
|
1.0
|
|
SG
|
S:CYS191
|
4.8
|
8.4
|
1.0
|
|
HA
|
S:HIS188
|
4.8
|
7.0
|
1.0
|
|
H
|
S:TYR218
|
4.8
|
25.2
|
1.0
|
|
HG23
|
S:VAL243
|
4.9
|
4.9
|
1.0
|
|
HB2
|
S:TYR218
|
4.9
|
8.8
|
1.0
|
|
HB2
|
S:HIS188
|
4.9
|
8.4
|
1.0
|
|
N
|
S:TYR218
|
4.9
|
9.9
|
1.0
|
|
N
|
S:LEU217
|
4.9
|
9.9
|
1.0
|
|
C
|
S:CYS222
|
4.9
|
8.0
|
1.0
|
|
HB3
|
S:CYS249
|
4.9
|
6.4
|
1.0
|
|
CB
|
S:LEU217
|
4.9
|
8.9
|
1.0
|
|
HD2
|
S:PRO225
|
4.9
|
6.5
|
1.0
|
|
HA
|
S:CYS222
|
4.9
|
5.5
|
1.0
|
|
HA
|
S:PRO248
|
5.0
|
2.9
|
1.0
|
|
Iron binding site 7 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 7 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2002
b:8.4
occ:1.00
|
FE3
|
S:SF42002
|
0.0
|
8.4
|
1.0
|
|
S2
|
S:SF42002
|
2.3
|
8.9
|
1.0
|
|
S1
|
S:SF42002
|
2.3
|
8.5
|
1.0
|
|
SG
|
S:CYS191
|
2.3
|
8.4
|
1.0
|
|
S4
|
S:SF42002
|
2.3
|
8.3
|
1.0
|
|
FE1
|
S:SF42002
|
2.6
|
8.5
|
1.0
|
|
FE2
|
S:SF42002
|
2.7
|
8.2
|
1.0
|
|
FE4
|
S:SF42002
|
2.7
|
9.0
|
1.0
|
|
HB2
|
S:ARG193
|
3.0
|
23.1
|
1.0
|
|
HB3
|
S:CYS191
|
3.1
|
10.4
|
1.0
|
|
CB
|
S:CYS191
|
3.1
|
8.7
|
1.0
|
|
HB2
|
S:CYS191
|
3.2
|
34.9
|
1.0
|
|
HG11
|
S:VAL243
|
3.4
|
8.3
|
1.0
|
|
HG21
|
S:VAL243
|
3.7
|
9.7
|
1.0
|
|
S3
|
S:SF42002
|
3.9
|
9.1
|
1.0
|
|
CB
|
S:ARG193
|
4.0
|
11.3
|
1.0
|
|
H
|
S:ARG193
|
4.0
|
12.3
|
1.0
|
|
HA
|
S:HIS188
|
4.1
|
7.0
|
1.0
|
|
HD2
|
S:ARG193
|
4.2
|
9.2
|
1.0
|
|
HH2
|
S:TRP241
|
4.3
|
4.8
|
1.0
|
|
CG1
|
S:VAL243
|
4.3
|
8.9
|
1.0
|
|
HG3
|
S:ARG193
|
4.4
|
6.4
|
1.0
|
|
ND1
|
S:HIS188
|
4.4
|
9.1
|
1.0
|
|
HB3
|
S:ARG193
|
4.5
|
8.6
|
1.0
|
|
HG13
|
S:VAL243
|
4.5
|
12.3
|
1.0
|
|
CG2
|
S:VAL243
|
4.5
|
9.3
|
1.0
|
|
CA
|
S:CYS191
|
4.6
|
9.7
|
1.0
|
|
N
|
S:ARG193
|
4.6
|
10.9
|
1.0
|
|
CG
|
S:ARG193
|
4.6
|
10.6
|
1.0
|
|
CA
|
S:ARG193
|
4.6
|
10.6
|
1.0
|
|
HG22
|
S:VAL243
|
4.7
|
7.8
|
1.0
|
|
C
|
S:ARG193
|
4.7
|
10.0
|
1.0
|
|
H
|
S:LEU217
|
4.7
|
11.8
|
1.0
|
|
N
|
S:LEU194
|
4.8
|
11.4
|
1.0
|
|
H
|
S:LEU194
|
4.8
|
9.1
|
1.0
|
|
SG
|
S:CYS222
|
4.8
|
7.8
|
1.0
|
|
HA
|
S:LEU194
|
4.8
|
13.6
|
1.0
|
|
HA
|
S:CYS216
|
4.8
|
5.4
|
1.0
|
|
HG12
|
S:VAL243
|
4.9
|
7.3
|
1.0
|
|
HA
|
S:CYS191
|
4.9
|
8.4
|
1.0
|
|
CD
|
S:ARG193
|
4.9
|
11.0
|
1.0
|
|
CB
|
S:VAL243
|
4.9
|
7.5
|
1.0
|
|
SG
|
S:CYS216
|
5.0
|
10.0
|
1.0
|
|
Iron binding site 8 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 8 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2002
b:9.0
occ:1.00
|
FE4
|
S:SF42002
|
0.0
|
9.0
|
1.0
|
|
S2
|
S:SF42002
|
2.3
|
8.9
|
1.0
|
|
SG
|
S:CYS216
|
2.3
|
10.0
|
1.0
|
|
S1
|
S:SF42002
|
2.3
|
8.5
|
1.0
|
|
S3
|
S:SF42002
|
2.3
|
9.1
|
1.0
|
|
FE1
|
S:SF42002
|
2.7
|
8.5
|
1.0
|
|
FE3
|
S:SF42002
|
2.7
|
8.4
|
1.0
|
|
FE2
|
S:SF42002
|
2.8
|
8.2
|
1.0
|
|
H
|
S:LEU217
|
3.1
|
11.8
|
1.0
|
|
HB2
|
S:PHE197
|
3.4
|
15.7
|
1.0
|
|
CB
|
S:CYS216
|
3.4
|
11.3
|
1.0
|
|
HB2
|
S:CYS216
|
3.4
|
13.1
|
1.0
|
|
HA
|
S:CYS216
|
3.4
|
5.4
|
1.0
|
|
HD2
|
S:PHE197
|
3.6
|
5.3
|
1.0
|
|
H
|
S:TYR218
|
3.7
|
25.2
|
1.0
|
|
HB2
|
S:ARG193
|
3.7
|
23.1
|
1.0
|
|
N
|
S:LEU217
|
3.8
|
9.9
|
1.0
|
|
HB2
|
S:TYR218
|
3.8
|
8.8
|
1.0
|
|
CA
|
S:CYS216
|
3.9
|
10.3
|
1.0
|
|
S4
|
S:SF42002
|
4.0
|
8.3
|
1.0
|
|
HE1
|
S:HIS188
|
4.2
|
20.6
|
1.0
|
|
N
|
S:TYR218
|
4.2
|
9.9
|
1.0
|
|
HB3
|
S:CYS216
|
4.2
|
26.6
|
1.0
|
|
C
|
S:CYS216
|
4.3
|
10.0
|
1.0
|
|
CB
|
S:PHE197
|
4.3
|
12.9
|
1.0
|
|
CD2
|
S:PHE197
|
4.4
|
13.5
|
1.0
|
|
ND1
|
S:HIS188
|
4.4
|
9.1
|
1.0
|
|
HB3
|
S:ARG193
|
4.4
|
8.6
|
1.0
|
|
HB3
|
S:CYS222
|
4.5
|
9.2
|
1.0
|
|
CB
|
S:ARG193
|
4.5
|
11.3
|
1.0
|
|
HB2
|
S:LEU217
|
4.6
|
2.1
|
1.0
|
|
CE1
|
S:HIS188
|
4.6
|
11.6
|
1.0
|
|
CB
|
S:TYR218
|
4.7
|
10.1
|
1.0
|
|
HD2
|
S:ARG193
|
4.7
|
9.2
|
1.0
|
|
HB3
|
S:PHE197
|
4.7
|
13.3
|
1.0
|
|
CA
|
S:LEU217
|
4.8
|
9.5
|
1.0
|
|
CG
|
S:PHE197
|
4.8
|
12.9
|
1.0
|
|
O
|
S:ARG193
|
4.8
|
12.6
|
1.0
|
|
C
|
S:LEU217
|
4.8
|
9.8
|
1.0
|
|
H
|
S:PHE197
|
4.9
|
15.7
|
1.0
|
|
SG
|
S:CYS222
|
4.9
|
7.8
|
1.0
|
|
HA
|
S:TYR218
|
4.9
|
10.5
|
1.0
|
|
HA
|
S:LEU194
|
4.9
|
13.6
|
1.0
|
|
CA
|
S:TYR218
|
4.9
|
10.1
|
1.0
|
|
SG
|
S:CYS191
|
4.9
|
8.4
|
1.0
|
|
HB2
|
S:CYS222
|
5.0
|
3.4
|
1.0
|
|
Iron binding site 9 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 9 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2003
b:6.6
occ:1.00
|
FE1
|
S:F3S2003
|
0.0
|
6.6
|
1.0
|
|
S1
|
S:F3S2003
|
2.2
|
7.5
|
1.0
|
|
S2
|
S:F3S2003
|
2.3
|
7.0
|
1.0
|
|
S3
|
S:F3S2003
|
2.3
|
6.7
|
1.0
|
|
SG
|
S:CYS249
|
2.3
|
6.9
|
1.0
|
|
FE4
|
S:F3S2003
|
2.7
|
6.3
|
1.0
|
|
FE3
|
S:F3S2003
|
2.7
|
6.8
|
1.0
|
|
HA
|
S:CYS249
|
3.2
|
5.4
|
1.0
|
|
HB2
|
S:CYS249
|
3.2
|
11.8
|
1.0
|
|
CB
|
S:CYS249
|
3.2
|
7.6
|
1.0
|
|
H
|
S:GLY251
|
3.4
|
14.4
|
1.0
|
|
H
|
S:ILE250
|
3.5
|
1.4
|
1.0
|
|
HG21
|
S:THR227
|
3.6
|
8.8
|
1.0
|
|
CA
|
S:CYS249
|
3.7
|
6.8
|
1.0
|
|
H
|
S:CYS252
|
3.7
|
5.2
|
1.0
|
|
HG21
|
S:VAL187
|
3.8
|
8.7
|
1.0
|
|
S4
|
S:F3S2003
|
3.9
|
6.9
|
1.0
|
|
HE22
|
L:GLN237
|
4.1
|
8.9
|
1.0
|
|
N
|
S:ILE250
|
4.1
|
7.1
|
1.0
|
|
HG2
|
S:PRO242
|
4.1
|
7.8
|
1.0
|
|
HB3
|
S:CYS249
|
4.1
|
6.4
|
1.0
|
|
N
|
S:GLY251
|
4.2
|
7.2
|
1.0
|
|
HG11
|
S:VAL187
|
4.2
|
11.1
|
1.0
|
|
C
|
S:CYS249
|
4.3
|
7.3
|
1.0
|
|
HA2
|
S:GLY251
|
4.5
|
9.6
|
1.0
|
|
N
|
S:CYS252
|
4.5
|
6.1
|
1.0
|
|
CG2
|
S:THR227
|
4.6
|
7.6
|
1.0
|
|
CG2
|
S:VAL187
|
4.7
|
8.8
|
1.0
|
|
HB2
|
S:PRO242
|
4.8
|
6.0
|
1.0
|
|
SG
|
S:CYS231
|
4.8
|
6.8
|
1.0
|
|
CA
|
S:GLY251
|
4.8
|
7.4
|
1.0
|
|
HZ3
|
S:TRP241
|
4.8
|
15.7
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
6.5
|
1.0
|
|
HG22
|
S:VAL187
|
4.8
|
4.3
|
1.0
|
|
NE2
|
L:GLN237
|
4.8
|
7.7
|
1.0
|
|
HG22
|
S:THR227
|
4.9
|
12.6
|
1.0
|
|
HD22
|
S:ASN229
|
4.9
|
11.8
|
1.0
|
|
N
|
S:CYS249
|
5.0
|
7.3
|
1.0
|
|
Iron binding site 10 out
of 12 in 4u9i
Go back to
Iron Binding Sites List in 4u9i
Iron binding site 10 out
of 12 in the High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Fe2003
b:6.8
occ:1.00
|
FE3
|
S:F3S2003
|
0.0
|
6.8
|
1.0
|
|
S1
|
S:F3S2003
|
2.2
|
7.5
|
1.0
|
|
S4
|
S:F3S2003
|
2.3
|
6.9
|
1.0
|
|
SG
|
S:CYS231
|
2.3
|
6.8
|
1.0
|
|
S3
|
S:F3S2003
|
2.3
|
6.7
|
1.0
|
|
FE4
|
S:F3S2003
|
2.7
|
6.3
|
1.0
|
|
FE1
|
S:F3S2003
|
2.7
|
6.6
|
1.0
|
|
CB
|
S:CYS231
|
3.3
|
7.3
|
1.0
|
|
HB3
|
S:CYS231
|
3.4
|
6.1
|
1.0
|
|
HB2
|
S:CYS231
|
3.4
|
9.8
|
1.0
|
|
HD22
|
S:ASN229
|
3.6
|
11.8
|
1.0
|
|
HE2
|
S:PHE236
|
3.6
|
8.3
|
1.0
|
|
ND2
|
S:ASN229
|
3.9
|
6.9
|
1.0
|
|
S2
|
S:F3S2003
|
4.0
|
7.0
|
1.0
|
|
HB3
|
S:ASN229
|
4.0
|
8.1
|
1.0
|
|
HZ
|
S:PHE236
|
4.0
|
9.3
|
1.0
|
|
HG2
|
S:PRO242
|
4.0
|
7.8
|
1.0
|
|
HD21
|
S:ASN229
|
4.0
|
2.3
|
1.0
|
|
HD2
|
S:PRO242
|
4.1
|
4.7
|
1.0
|
|
HG21
|
S:VAL187
|
4.1
|
8.7
|
1.0
|
|
HG22
|
S:VAL187
|
4.2
|
4.3
|
1.0
|
|
HE3
|
S:TRP241
|
4.3
|
4.7
|
1.0
|
|
CE2
|
S:PHE236
|
4.4
|
7.9
|
1.0
|
|
O
|
S:HOH2193
|
4.4
|
7.9
|
1.0
|
|
CG
|
S:ASN229
|
4.5
|
6.4
|
1.0
|
|
CZ
|
S:PHE236
|
4.5
|
7.4
|
1.0
|
|
CB
|
S:ASN229
|
4.6
|
6.7
|
1.0
|
|
HB2
|
S:ASN229
|
4.6
|
7.5
|
1.0
|
|
CG2
|
S:VAL187
|
4.6
|
8.8
|
1.0
|
|
H
|
S:CYS231
|
4.7
|
26.3
|
1.0
|
|
HE2
|
L:LYS232
|
4.7
|
6.7
|
1.0
|
|
CA
|
S:CYS231
|
4.8
|
7.1
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
6.5
|
1.0
|
|
CD
|
S:PRO242
|
4.8
|
6.7
|
1.0
|
|
SG
|
S:CYS249
|
4.8
|
6.9
|
1.0
|
|
CG
|
S:PRO242
|
4.8
|
7.6
|
1.0
|
|
HG11
|
S:VAL187
|
4.9
|
11.1
|
1.0
|
|
HG21
|
S:THR227
|
4.9
|
8.8
|
1.0
|
|
HA
|
S:CYS231
|
5.0
|
7.8
|
1.0
|
|
HZ3
|
S:TRP241
|
5.0
|
15.7
|
1.0
|
|
Reference:
H.Ogata,
K.Nishikawa,
W.Lubitz.
Hydrogens Detected By Subatomic Resolution Protein Crystallography in A [Nife] Hydrogenase. Nature 2015.
ISSN: ESSN 1476-4687
PubMed: 25624102
DOI: 10.1038/NATURE14110
Page generated: Mon Aug 5 11:57:43 2024
|
