Iron in PDB 4u9h: Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
Enzymatic activity of Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
All present enzymatic activity of Ultra 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 Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9h
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)
|
37.64 /
0.89
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.530,
97.950,
125.850,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
9.6 /
10.6
|
Other elements in 4u9h:
The structure of Ultra 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 Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F
(pdb code 4u9h). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the
Ultra High Resolution Structure of the Ni-R State of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F, PDB code: 4u9h:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 1 out
of 12 in the Ultra 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 Ultra 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:Fe1001
b:4.3
occ:1.00
|
FE1
|
S:SF41001
|
0.0
|
4.3
|
1.0
|
|
S4
|
S:SF41001
|
2.2
|
4.6
|
1.0
|
|
SG
|
S:CYS17
|
2.3
|
4.4
|
1.0
|
|
S2
|
S:SF41001
|
2.3
|
4.4
|
1.0
|
|
S3
|
S:SF41001
|
2.3
|
4.8
|
1.0
|
|
FE2
|
S:SF41001
|
2.7
|
4.5
|
1.0
|
|
FE3
|
S:SF41001
|
2.7
|
4.4
|
1.0
|
|
FE4
|
S:SF41001
|
2.7
|
4.5
|
1.0
|
|
H
|
S:CYS17
|
3.0
|
5.1
|
0.9
|
|
HB3
|
S:CYS17
|
3.3
|
5.2
|
1.0
|
|
CB
|
S:CYS17
|
3.4
|
4.6
|
1.0
|
|
HE2
|
L:HIS235
|
3.4
|
4.1
|
1.0
|
|
H
|
S:GLY19
|
3.5
|
2.3
|
0.7
|
|
N
|
S:CYS17
|
3.8
|
4.8
|
1.0
|
|
HG3
|
L:ARG79
|
3.8
|
3.9
|
0.9
|
|
H1
|
S:HOH1169
|
3.8
|
14.5
|
1.0
|
|
S1
|
S:SF41001
|
3.9
|
4.6
|
1.0
|
|
HA3
|
S:GLY19
|
4.0
|
5.4
|
0.9
|
|
H
|
S:CYS20
|
4.0
|
4.6
|
1.0
|
|
CA
|
S:CYS17
|
4.0
|
4.5
|
1.0
|
|
NE2
|
L:HIS235
|
4.2
|
4.6
|
1.0
|
|
HB2
|
S:CYS17
|
4.2
|
5.2
|
1.0
|
|
N
|
S:GLY19
|
4.2
|
4.8
|
1.0
|
|
H
|
S:THR18
|
4.3
|
4.0
|
0.9
|
|
O
|
S:HOH1169
|
4.5
|
5.8
|
1.0
|
|
HB3
|
L:ARG79
|
4.5
|
3.5
|
1.0
|
|
CA
|
S:GLY19
|
4.5
|
4.8
|
1.0
|
|
C
|
S:CYS17
|
4.5
|
4.5
|
1.0
|
|
HA
|
S:GLU16
|
4.5
|
5.8
|
1.0
|
|
N
|
S:THR18
|
4.6
|
4.7
|
1.0
|
|
HD2
|
L:HIS235
|
4.6
|
3.3
|
1.0
|
|
N
|
S:CYS20
|
4.6
|
4.7
|
1.0
|
|
CG
|
L:ARG79
|
4.7
|
4.6
|
1.0
|
|
SG
|
S:CYS114
|
4.7
|
4.9
|
1.0
|
|
SG
|
S:CYS150
|
4.7
|
4.4
|
1.0
|
|
HA
|
L:ARG79
|
4.8
|
3.1
|
0.8
|
|
HB2
|
S:GLU16
|
4.8
|
5.1
|
0.9
|
|
HG2
|
L:ARG79
|
4.8
|
6.2
|
1.0
|
|
CD2
|
L:HIS235
|
4.8
|
4.4
|
1.0
|
|
SG
|
S:CYS20
|
4.9
|
4.8
|
1.0
|
|
C
|
S:GLU16
|
4.9
|
5.1
|
1.0
|
|
HA
|
S:CYS17
|
4.9
|
3.8
|
1.0
|
|
Iron binding site 2 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 2 out
of 12 in the Ultra 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 Ultra 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:Fe1001
b:4.5
occ:1.00
|
FE2
|
S:SF41001
|
0.0
|
4.5
|
1.0
|
|
SG
|
S:CYS114
|
2.3
|
4.9
|
1.0
|
|
S3
|
S:SF41001
|
2.3
|
4.8
|
1.0
|
|
S4
|
S:SF41001
|
2.3
|
4.6
|
1.0
|
|
S1
|
S:SF41001
|
2.3
|
4.6
|
1.0
|
|
FE3
|
S:SF41001
|
2.6
|
4.4
|
1.0
|
|
FE1
|
S:SF41001
|
2.7
|
4.3
|
1.0
|
|
FE4
|
S:SF41001
|
2.7
|
4.5
|
1.0
|
|
HB2
|
S:CYS114
|
3.0
|
4.2
|
1.0
|
|
CB
|
S:CYS114
|
3.3
|
5.0
|
1.0
|
|
H
|
S:CYS114
|
3.4
|
3.8
|
1.0
|
|
H2
|
S:HOH1179
|
3.4
|
8.6
|
1.0
|
|
H1
|
S:HOH1169
|
3.4
|
14.5
|
1.0
|
|
H1
|
S:HOH1172
|
3.4
|
7.9
|
1.0
|
|
S2
|
S:SF41001
|
3.9
|
4.4
|
1.0
|
|
H1
|
S:HOH1179
|
3.9
|
6.9
|
1.0
|
|
HB3
|
S:CYS114
|
3.9
|
4.9
|
1.0
|
|
O
|
S:HOH1179
|
4.0
|
5.9
|
1.0
|
|
N
|
S:CYS114
|
4.0
|
4.7
|
1.0
|
|
O
|
S:HOH1172
|
4.0
|
5.6
|
1.0
|
|
H
|
S:CYS17
|
4.1
|
5.1
|
0.9
|
|
HA
|
S:GLU16
|
4.1
|
5.8
|
1.0
|
|
O
|
S:HOH1169
|
4.1
|
5.8
|
1.0
|
|
CA
|
S:CYS114
|
4.2
|
5.0
|
1.0
|
|
H2
|
S:HOH1169
|
4.4
|
4.8
|
0.9
|
|
SG
|
S:CYS150
|
4.5
|
4.4
|
1.0
|
|
HE22
|
S:GLN121
|
4.5
|
7.8
|
0.9
|
|
HA2
|
S:GLY76
|
4.5
|
5.3
|
0.9
|
|
HG12
|
S:VAL120
|
4.5
|
7.9
|
0.9
|
|
H
|
S:VAL120
|
4.6
|
6.1
|
0.8
|
|
HA
|
S:CYS114
|
4.7
|
4.7
|
1.0
|
|
SG
|
S:CYS20
|
4.7
|
4.8
|
1.0
|
|
H2
|
S:HOH1172
|
4.7
|
10.9
|
1.0
|
|
HA3
|
S:GLY119
|
4.8
|
4.2
|
0.8
|
|
SG
|
S:CYS17
|
4.8
|
4.4
|
1.0
|
|
N
|
S:CYS17
|
4.9
|
4.8
|
1.0
|
|
HA
|
S:CYS150
|
4.9
|
4.5
|
1.0
|
|
HA3
|
S:GLY112
|
4.9
|
4.4
|
1.0
|
|
HB2
|
S:GLU16
|
5.0
|
5.1
|
0.9
|
|
HB3
|
S:GLU16
|
5.0
|
10.3
|
0.9
|
|
CA
|
S:GLU16
|
5.0
|
5.5
|
1.0
|
|
HB3
|
S:CYS17
|
5.0
|
5.2
|
1.0
|
|
Iron binding site 3 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 3 out
of 12 in the Ultra 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 Ultra 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:Fe1001
b:4.4
occ:1.00
|
FE3
|
S:SF41001
|
0.0
|
4.4
|
1.0
|
|
S2
|
S:SF41001
|
2.3
|
4.4
|
1.0
|
|
SG
|
S:CYS150
|
2.3
|
4.4
|
1.0
|
|
S1
|
S:SF41001
|
2.3
|
4.6
|
1.0
|
|
S4
|
S:SF41001
|
2.3
|
4.6
|
1.0
|
|
FE2
|
S:SF41001
|
2.6
|
4.5
|
1.0
|
|
FE1
|
S:SF41001
|
2.7
|
4.3
|
1.0
|
|
FE4
|
S:SF41001
|
2.7
|
4.5
|
1.0
|
|
HA
|
S:CYS150
|
2.8
|
4.5
|
1.0
|
|
H1
|
S:HOH1179
|
3.3
|
6.9
|
1.0
|
|
CB
|
S:CYS150
|
3.4
|
4.6
|
1.0
|
|
CA
|
S:CYS150
|
3.4
|
4.5
|
1.0
|
|
HG3
|
L:ARG79
|
3.5
|
3.9
|
0.9
|
|
H2
|
S:HOH1179
|
3.7
|
8.6
|
1.0
|
|
HB2
|
S:CYS150
|
3.8
|
5.1
|
1.0
|
|
C
|
S:CYS150
|
3.8
|
4.4
|
1.0
|
|
O
|
S:HOH1179
|
3.9
|
5.9
|
1.0
|
|
HG2
|
L:ARG79
|
3.9
|
6.2
|
1.0
|
|
S3
|
S:SF41001
|
3.9
|
4.8
|
1.0
|
|
HD2
|
L:HIS235
|
3.9
|
3.3
|
1.0
|
|
HE
|
L:ARG79
|
3.9
|
5.5
|
1.0
|
|
HA
|
S:PRO151
|
4.1
|
3.9
|
1.0
|
|
CG
|
L:ARG79
|
4.2
|
4.6
|
1.0
|
|
HB3
|
S:CYS150
|
4.2
|
6.2
|
1.0
|
|
HE2
|
L:HIS235
|
4.2
|
4.1
|
1.0
|
|
O
|
S:CYS150
|
4.2
|
4.7
|
1.0
|
|
N
|
S:PRO151
|
4.4
|
4.3
|
1.0
|
|
SG
|
S:CYS114
|
4.4
|
4.9
|
1.0
|
|
H
|
S:CYS114
|
4.6
|
3.8
|
1.0
|
|
CD2
|
L:HIS235
|
4.6
|
4.4
|
1.0
|
|
SG
|
S:CYS17
|
4.6
|
4.4
|
1.0
|
|
NE2
|
L:HIS235
|
4.7
|
4.6
|
1.0
|
|
CA
|
S:PRO151
|
4.7
|
4.4
|
1.0
|
|
HB
|
S:THR113
|
4.7
|
3.9
|
1.0
|
|
NE
|
L:ARG79
|
4.7
|
4.5
|
1.0
|
|
O
|
S:GLY149
|
4.7
|
4.8
|
1.0
|
|
HB3
|
S:PRO151
|
4.7
|
4.4
|
1.0
|
|
HZ2
|
S:TRP258
|
4.7
|
4.2
|
1.0
|
|
SG
|
S:CYS20
|
4.8
|
4.8
|
1.0
|
|
N
|
S:CYS150
|
4.8
|
4.4
|
1.0
|
|
HD3
|
S:PRO151
|
4.8
|
3.8
|
0.9
|
|
HB3
|
L:ARG79
|
4.9
|
3.5
|
1.0
|
|
H
|
S:THR113
|
4.9
|
3.0
|
1.0
|
|
Iron binding site 4 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 4 out
of 12 in the Ultra 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 Ultra 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:Fe1001
b:4.5
occ:1.00
|
FE4
|
S:SF41001
|
0.0
|
4.5
|
1.0
|
|
SG
|
S:CYS20
|
2.3
|
4.8
|
1.0
|
|
S1
|
S:SF41001
|
2.3
|
4.6
|
1.0
|
|
S2
|
S:SF41001
|
2.3
|
4.4
|
1.0
|
|
S3
|
S:SF41001
|
2.3
|
4.8
|
1.0
|
|
FE1
|
S:SF41001
|
2.7
|
4.3
|
1.0
|
|
FE2
|
S:SF41001
|
2.7
|
4.5
|
1.0
|
|
FE3
|
S:SF41001
|
2.7
|
4.4
|
1.0
|
|
H1
|
S:HOH1172
|
3.1
|
7.9
|
1.0
|
|
H
|
S:CYS20
|
3.2
|
4.6
|
1.0
|
|
CB
|
S:CYS20
|
3.5
|
5.3
|
1.0
|
|
HB2
|
S:CYS20
|
3.5
|
6.2
|
1.0
|
|
HB3
|
S:PRO151
|
3.6
|
4.4
|
1.0
|
|
N
|
S:CYS20
|
3.7
|
4.7
|
1.0
|
|
HA
|
S:PRO151
|
3.7
|
3.9
|
1.0
|
|
HA3
|
S:GLY112
|
3.7
|
4.4
|
1.0
|
|
HA
|
S:CYS150
|
3.9
|
4.5
|
1.0
|
|
O
|
S:HOH1172
|
3.9
|
5.6
|
1.0
|
|
S4
|
S:SF41001
|
4.0
|
4.6
|
1.0
|
|
CA
|
S:CYS20
|
4.0
|
4.8
|
1.0
|
|
HA
|
S:CYS20
|
4.2
|
4.0
|
0.9
|
|
HG3
|
S:GLU75
|
4.2
|
9.8
|
1.0
|
|
H2
|
S:HOH1172
|
4.2
|
10.9
|
1.0
|
|
HD3
|
S:PRO152
|
4.3
|
3.6
|
0.9
|
|
HB3
|
S:CYS20
|
4.3
|
4.2
|
0.8
|
|
CA
|
S:PRO151
|
4.4
|
4.4
|
1.0
|
|
CB
|
S:PRO151
|
4.4
|
4.6
|
1.0
|
|
H
|
S:CYS114
|
4.5
|
3.8
|
1.0
|
|
C
|
S:GLY19
|
4.5
|
4.6
|
1.0
|
|
HA3
|
S:GLY19
|
4.5
|
5.4
|
0.9
|
|
CA
|
S:GLY112
|
4.6
|
4.8
|
1.0
|
|
HA2
|
S:GLY112
|
4.6
|
4.5
|
1.0
|
|
H
|
S:GLY19
|
4.6
|
2.3
|
0.7
|
|
HB2
|
S:CYS114
|
4.6
|
4.2
|
1.0
|
|
SG
|
S:CYS17
|
4.7
|
4.4
|
1.0
|
|
OE2
|
S:GLU75
|
4.7
|
7.4
|
1.0
|
|
H
|
S:CYS17
|
4.7
|
5.1
|
0.9
|
|
CA
|
S:CYS150
|
4.8
|
4.5
|
1.0
|
|
O
|
S:GLY149
|
4.8
|
4.8
|
1.0
|
|
N
|
S:PRO151
|
4.8
|
4.3
|
1.0
|
|
HB2
|
S:PRO151
|
4.8
|
3.4
|
1.0
|
|
H
|
S:THR113
|
4.8
|
3.0
|
1.0
|
|
CA
|
S:GLY19
|
4.9
|
4.8
|
1.0
|
|
SG
|
S:CYS114
|
4.9
|
4.9
|
1.0
|
|
SG
|
S:CYS150
|
4.9
|
4.4
|
1.0
|
|
N
|
S:GLY19
|
4.9
|
4.8
|
1.0
|
|
Iron binding site 5 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 5 out
of 12 in the Ultra 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 Ultra 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:Fe1002
b:6.3
occ:1.00
|
FE1
|
S:SF41002
|
0.0
|
6.3
|
1.0
|
|
ND1
|
S:HIS188
|
2.1
|
7.0
|
1.0
|
|
S3
|
S:SF41002
|
2.3
|
6.2
|
1.0
|
|
S4
|
S:SF41002
|
2.3
|
6.1
|
1.0
|
|
S2
|
S:SF41002
|
2.3
|
6.6
|
1.0
|
|
FE3
|
S:SF41002
|
2.6
|
6.0
|
1.0
|
|
FE2
|
S:SF41002
|
2.7
|
5.7
|
1.0
|
|
FE4
|
S:SF41002
|
2.7
|
6.2
|
1.0
|
|
CE1
|
S:HIS188
|
3.0
|
8.0
|
1.0
|
|
HE1
|
S:HIS188
|
3.1
|
7.9
|
0.7
|
|
CG
|
S:HIS188
|
3.2
|
6.9
|
1.0
|
|
HA
|
S:HIS188
|
3.3
|
4.5
|
0.8
|
|
HB2
|
S:HIS188
|
3.3
|
5.0
|
0.7
|
|
HD3
|
S:PRO225
|
3.5
|
5.5
|
0.9
|
|
HG3
|
S:PRO225
|
3.6
|
5.2
|
1.0
|
|
CB
|
S:HIS188
|
3.6
|
6.8
|
1.0
|
|
S1
|
S:SF41002
|
3.9
|
6.0
|
1.0
|
|
CA
|
S:HIS188
|
3.9
|
6.2
|
1.0
|
|
HB3
|
S:CYS191
|
4.0
|
7.5
|
0.7
|
|
HA3
|
S:GLY224
|
4.1
|
5.5
|
0.7
|
|
NE2
|
S:HIS188
|
4.1
|
8.7
|
1.0
|
|
CD
|
S:PRO225
|
4.2
|
6.8
|
1.0
|
|
HB2
|
S:CYS191
|
4.3
|
5.9
|
1.0
|
|
CD2
|
S:HIS188
|
4.3
|
8.0
|
1.0
|
|
CG
|
S:PRO225
|
4.3
|
7.1
|
1.0
|
|
HB2
|
S:PHE197
|
4.4
|
9.8
|
1.0
|
|
HD2
|
S:PHE197
|
4.4
|
9.6
|
1.0
|
|
CB
|
S:CYS191
|
4.4
|
7.0
|
1.0
|
|
HD12
|
S:LEU194
|
4.5
|
15.2
|
1.0
|
|
O
|
S:HIS188
|
4.5
|
7.0
|
1.0
|
|
HB3
|
S:HIS188
|
4.6
|
6.2
|
1.0
|
|
SG
|
S:CYS191
|
4.6
|
6.2
|
1.0
|
|
SG
|
S:CYS216
|
4.6
|
6.4
|
1.0
|
|
HG2
|
S:PRO225
|
4.7
|
7.1
|
1.0
|
|
C
|
S:HIS188
|
4.7
|
6.6
|
1.0
|
|
CD2
|
S:PHE197
|
4.7
|
10.4
|
1.0
|
|
SG
|
S:CYS222
|
4.7
|
5.5
|
1.0
|
|
HA
|
S:LEU194
|
4.8
|
6.2
|
1.0
|
|
N
|
S:PRO225
|
4.9
|
6.3
|
1.0
|
|
HE2
|
S:HIS188
|
4.9
|
9.6
|
1.0
|
|
HB2
|
S:TYR218
|
4.9
|
5.4
|
0.3
|
|
CA
|
S:GLY224
|
5.0
|
6.2
|
1.0
|
|
HB3
|
S:CYS222
|
5.0
|
6.5
|
1.0
|
|
Iron binding site 6 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 6 out
of 12 in the Ultra 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 Ultra 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:Fe1002
b:5.7
occ:1.00
|
FE2
|
S:SF41002
|
0.0
|
5.7
|
1.0
|
|
S4
|
S:SF41002
|
2.3
|
6.1
|
1.0
|
|
S3
|
S:SF41002
|
2.3
|
6.2
|
1.0
|
|
SG
|
S:CYS222
|
2.3
|
5.5
|
1.0
|
|
S1
|
S:SF41002
|
2.3
|
6.0
|
1.0
|
|
FE3
|
S:SF41002
|
2.7
|
6.0
|
1.0
|
|
FE1
|
S:SF41002
|
2.7
|
6.3
|
1.0
|
|
FE4
|
S:SF41002
|
2.8
|
6.2
|
1.0
|
|
HB3
|
S:CYS222
|
3.0
|
6.5
|
1.0
|
|
CB
|
S:CYS222
|
3.2
|
5.7
|
1.0
|
|
HB2
|
S:CYS222
|
3.5
|
4.7
|
0.9
|
|
HD3
|
S:PRO225
|
3.6
|
5.5
|
0.9
|
|
HG21
|
S:VAL243
|
3.7
|
5.5
|
1.0
|
|
HA3
|
S:GLY224
|
3.8
|
5.5
|
0.7
|
|
H
|
S:GLY224
|
3.9
|
7.0
|
0.9
|
|
S2
|
S:SF41002
|
3.9
|
6.6
|
1.0
|
|
HB2
|
S:LEU217
|
4.0
|
4.7
|
1.0
|
|
HG22
|
S:VAL243
|
4.1
|
7.5
|
1.0
|
|
H
|
S:LEU217
|
4.1
|
10.7
|
1.0
|
|
CG2
|
S:VAL243
|
4.4
|
6.5
|
1.0
|
|
N
|
S:GLY224
|
4.5
|
5.8
|
1.0
|
|
CD
|
S:PRO225
|
4.6
|
6.8
|
1.0
|
|
CA
|
S:CYS222
|
4.6
|
5.5
|
1.0
|
|
CA
|
S:GLY224
|
4.6
|
6.2
|
1.0
|
|
HG11
|
S:VAL243
|
4.6
|
10.4
|
1.0
|
|
ND1
|
S:HIS188
|
4.6
|
7.0
|
1.0
|
|
H
|
S:CYS249
|
4.7
|
6.4
|
1.0
|
|
SG
|
S:CYS216
|
4.7
|
6.4
|
1.0
|
|
HA
|
S:TYR218
|
4.7
|
7.3
|
0.3
|
|
SG
|
S:CYS191
|
4.8
|
6.2
|
1.0
|
|
HB2
|
S:TYR218
|
4.8
|
5.4
|
0.3
|
|
HA
|
S:TYR218
|
4.8
|
5.4
|
0.7
|
|
HA
|
S:HIS188
|
4.8
|
4.5
|
0.8
|
|
HB2
|
S:HIS188
|
4.8
|
5.0
|
0.7
|
|
H
|
S:TYR218
|
4.8
|
5.3
|
0.3
|
|
H
|
S:TYR218
|
4.8
|
11.7
|
0.7
|
|
N
|
S:TYR218
|
4.8
|
6.1
|
0.3
|
|
N
|
S:LEU217
|
4.9
|
6.0
|
1.0
|
|
N
|
S:TYR218
|
4.9
|
6.2
|
0.7
|
|
CB
|
S:LEU217
|
4.9
|
6.0
|
1.0
|
|
C
|
S:CYS222
|
4.9
|
5.4
|
1.0
|
|
HB2
|
S:TYR218
|
4.9
|
5.9
|
0.7
|
|
HB3
|
S:CYS249
|
4.9
|
6.0
|
1.0
|
|
HG23
|
S:VAL243
|
4.9
|
6.7
|
1.0
|
|
HA
|
S:CYS222
|
4.9
|
7.8
|
1.0
|
|
HD2
|
S:PRO225
|
4.9
|
6.7
|
1.0
|
|
HD1
|
S:TYR218
|
5.0
|
6.6
|
0.7
|
|
Iron binding site 7 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 7 out
of 12 in the Ultra 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 Ultra 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:Fe1002
b:6.0
occ:1.00
|
FE3
|
S:SF41002
|
0.0
|
6.0
|
1.0
|
|
S1
|
S:SF41002
|
2.3
|
6.0
|
1.0
|
|
S2
|
S:SF41002
|
2.3
|
6.6
|
1.0
|
|
SG
|
S:CYS191
|
2.3
|
6.2
|
1.0
|
|
S4
|
S:SF41002
|
2.3
|
6.1
|
1.0
|
|
FE1
|
S:SF41002
|
2.6
|
6.3
|
1.0
|
|
FE2
|
S:SF41002
|
2.7
|
5.7
|
1.0
|
|
FE4
|
S:SF41002
|
2.7
|
6.2
|
1.0
|
|
HB2
|
S:ARG193
|
3.0
|
6.8
|
1.0
|
|
HB3
|
S:CYS191
|
3.1
|
7.5
|
0.7
|
|
CB
|
S:CYS191
|
3.1
|
7.0
|
1.0
|
|
HB2
|
S:CYS191
|
3.2
|
5.9
|
1.0
|
|
HG11
|
S:VAL243
|
3.4
|
10.4
|
1.0
|
|
HG21
|
S:VAL243
|
3.8
|
5.5
|
1.0
|
|
S3
|
S:SF41002
|
3.9
|
6.2
|
1.0
|
|
H
|
S:ARG193
|
4.0
|
7.5
|
1.0
|
|
CB
|
S:ARG193
|
4.0
|
7.2
|
1.0
|
|
HA
|
S:HIS188
|
4.1
|
4.5
|
0.8
|
|
HD2
|
S:ARG193
|
4.2
|
7.0
|
0.9
|
|
HH2
|
S:TRP241
|
4.3
|
7.1
|
1.0
|
|
CG1
|
S:VAL243
|
4.3
|
6.8
|
1.0
|
|
HG3
|
S:ARG193
|
4.4
|
6.8
|
0.9
|
|
ND1
|
S:HIS188
|
4.4
|
7.0
|
1.0
|
|
HB3
|
S:ARG193
|
4.5
|
5.6
|
0.9
|
|
HG13
|
S:VAL243
|
4.5
|
8.7
|
1.0
|
|
CA
|
S:CYS191
|
4.6
|
6.8
|
1.0
|
|
CG2
|
S:VAL243
|
4.6
|
6.5
|
1.0
|
|
CA
|
S:ARG193
|
4.6
|
7.5
|
1.0
|
|
N
|
S:ARG193
|
4.6
|
7.3
|
1.0
|
|
CG
|
S:ARG193
|
4.6
|
7.2
|
1.0
|
|
HG22
|
S:VAL243
|
4.7
|
7.5
|
1.0
|
|
H
|
S:LEU217
|
4.7
|
10.7
|
1.0
|
|
C
|
S:ARG193
|
4.7
|
7.7
|
1.0
|
|
N
|
S:LEU194
|
4.8
|
7.9
|
1.0
|
|
H
|
S:LEU194
|
4.8
|
4.4
|
0.9
|
|
SG
|
S:CYS222
|
4.8
|
5.5
|
1.0
|
|
HA
|
S:CYS216
|
4.8
|
5.8
|
0.9
|
|
CD
|
S:ARG193
|
4.9
|
6.9
|
1.0
|
|
HA
|
S:LEU194
|
4.9
|
6.2
|
1.0
|
|
HG12
|
S:VAL243
|
4.9
|
6.3
|
1.0
|
|
HA
|
S:CYS191
|
4.9
|
5.7
|
1.0
|
|
SG
|
S:CYS216
|
5.0
|
6.4
|
1.0
|
|
CB
|
S:VAL243
|
5.0
|
6.0
|
1.0
|
|
Iron binding site 8 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 8 out
of 12 in the Ultra 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 Ultra 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:Fe1002
b:6.2
occ:1.00
|
FE4
|
S:SF41002
|
0.0
|
6.2
|
1.0
|
|
S2
|
S:SF41002
|
2.3
|
6.6
|
1.0
|
|
SG
|
S:CYS216
|
2.3
|
6.4
|
1.0
|
|
S1
|
S:SF41002
|
2.3
|
6.0
|
1.0
|
|
S3
|
S:SF41002
|
2.3
|
6.2
|
1.0
|
|
FE1
|
S:SF41002
|
2.7
|
6.3
|
1.0
|
|
FE3
|
S:SF41002
|
2.7
|
6.0
|
1.0
|
|
FE2
|
S:SF41002
|
2.8
|
5.7
|
1.0
|
|
H
|
S:LEU217
|
3.1
|
10.7
|
1.0
|
|
CB
|
S:CYS216
|
3.4
|
7.0
|
1.0
|
|
HA
|
S:CYS216
|
3.4
|
5.8
|
0.9
|
|
HB2
|
S:PHE197
|
3.4
|
9.8
|
1.0
|
|
HB2
|
S:CYS216
|
3.4
|
9.0
|
1.0
|
|
H
|
S:TYR218
|
3.7
|
5.3
|
0.3
|
|
H
|
S:TYR218
|
3.7
|
11.7
|
0.7
|
|
HB2
|
S:ARG193
|
3.7
|
6.8
|
1.0
|
|
HD2
|
S:PHE197
|
3.7
|
9.6
|
1.0
|
|
N
|
S:LEU217
|
3.8
|
6.0
|
1.0
|
|
HB2
|
S:TYR218
|
3.8
|
5.9
|
0.7
|
|
HB2
|
S:TYR218
|
3.8
|
5.4
|
0.3
|
|
CA
|
S:CYS216
|
3.9
|
6.8
|
1.0
|
|
S4
|
S:SF41002
|
4.0
|
6.1
|
1.0
|
|
N
|
S:TYR218
|
4.2
|
6.1
|
0.3
|
|
N
|
S:TYR218
|
4.2
|
6.2
|
0.7
|
|
HB3
|
S:CYS216
|
4.2
|
5.4
|
1.0
|
|
HE1
|
S:HIS188
|
4.2
|
7.9
|
0.7
|
|
C
|
S:CYS216
|
4.3
|
6.3
|
1.0
|
|
CB
|
S:PHE197
|
4.4
|
9.6
|
1.0
|
|
HB3
|
S:ARG193
|
4.4
|
5.6
|
0.9
|
|
ND1
|
S:HIS188
|
4.4
|
7.0
|
1.0
|
|
CD2
|
S:PHE197
|
4.4
|
10.4
|
1.0
|
|
CB
|
S:ARG193
|
4.5
|
7.2
|
1.0
|
|
HB3
|
S:CYS222
|
4.5
|
6.5
|
1.0
|
|
HB2
|
S:LEU217
|
4.6
|
4.7
|
1.0
|
|
CB
|
S:TYR218
|
4.6
|
6.0
|
0.3
|
|
CB
|
S:TYR218
|
4.7
|
6.5
|
0.7
|
|
CE1
|
S:HIS188
|
4.7
|
8.0
|
1.0
|
|
HD2
|
S:ARG193
|
4.7
|
7.0
|
0.9
|
|
CA
|
S:LEU217
|
4.8
|
6.0
|
1.0
|
|
HB3
|
S:PHE197
|
4.8
|
7.5
|
0.8
|
|
C
|
S:LEU217
|
4.8
|
5.8
|
1.0
|
|
HB3
|
S:TYR218
|
4.8
|
3.6
|
0.3
|
|
CG
|
S:PHE197
|
4.8
|
9.9
|
1.0
|
|
O
|
S:ARG193
|
4.9
|
8.5
|
1.0
|
|
HA
|
S:TYR218
|
4.9
|
7.3
|
0.3
|
|
CA
|
S:TYR218
|
4.9
|
6.0
|
0.3
|
|
SG
|
S:CYS222
|
4.9
|
5.5
|
1.0
|
|
HA
|
S:LEU194
|
4.9
|
6.2
|
1.0
|
|
CA
|
S:TYR218
|
4.9
|
6.1
|
0.7
|
|
SG
|
S:CYS191
|
4.9
|
6.2
|
1.0
|
|
HA
|
S:TYR218
|
4.9
|
5.4
|
0.7
|
|
H
|
S:PHE197
|
5.0
|
9.3
|
0.9
|
|
Iron binding site 9 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 9 out
of 12 in the Ultra 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 Ultra 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:Fe1003
b:4.9
occ:1.00
|
FE1
|
S:F3S1003
|
0.0
|
4.9
|
1.0
|
|
S1
|
S:F3S1003
|
2.2
|
5.8
|
1.0
|
|
S2
|
S:F3S1003
|
2.3
|
5.1
|
1.0
|
|
S3
|
S:F3S1003
|
2.3
|
5.0
|
1.0
|
|
SG
|
S:CYS249
|
2.3
|
5.0
|
1.0
|
|
FE4
|
S:F3S1003
|
2.7
|
4.7
|
1.0
|
|
FE3
|
S:F3S1003
|
2.7
|
5.3
|
1.0
|
|
HA
|
S:CYS249
|
3.2
|
6.7
|
1.0
|
|
CB
|
S:CYS249
|
3.3
|
5.4
|
1.0
|
|
HB2
|
S:CYS249
|
3.3
|
7.3
|
1.0
|
|
H
|
S:GLY251
|
3.4
|
7.1
|
1.0
|
|
H
|
S:ILE250
|
3.5
|
3.6
|
0.8
|
|
HG23
|
S:THR227
|
3.6
|
4.7
|
0.9
|
|
H
|
S:CYS252
|
3.7
|
4.6
|
1.0
|
|
CA
|
S:CYS249
|
3.7
|
5.3
|
1.0
|
|
HG21
|
S:VAL187
|
3.7
|
7.9
|
1.0
|
|
S4
|
S:F3S1003
|
3.9
|
5.3
|
1.0
|
|
HE22
|
L:GLN237
|
4.1
|
3.8
|
0.9
|
|
N
|
S:ILE250
|
4.1
|
5.0
|
1.0
|
|
HG2
|
S:PRO242
|
4.1
|
5.3
|
1.0
|
|
HB3
|
S:CYS249
|
4.1
|
6.0
|
1.0
|
|
HG11
|
S:VAL187
|
4.2
|
6.1
|
0.8
|
|
N
|
S:GLY251
|
4.2
|
5.1
|
1.0
|
|
C
|
S:CYS249
|
4.3
|
5.2
|
1.0
|
|
N
|
S:CYS252
|
4.5
|
5.1
|
1.0
|
|
HA2
|
S:GLY251
|
4.5
|
6.2
|
1.0
|
|
CG2
|
S:THR227
|
4.6
|
6.2
|
1.0
|
|
CG2
|
S:VAL187
|
4.7
|
6.5
|
1.0
|
|
HB2
|
S:PRO242
|
4.7
|
7.2
|
1.0
|
|
CA
|
S:GLY251
|
4.8
|
5.3
|
1.0
|
|
SG
|
S:CYS231
|
4.8
|
5.4
|
1.0
|
|
HG21
|
S:THR227
|
4.8
|
4.8
|
1.0
|
|
HD22
|
S:ASN229
|
4.8
|
5.7
|
0.9
|
|
SG
|
S:CYS252
|
4.8
|
5.0
|
1.0
|
|
NE2
|
L:GLN237
|
4.8
|
5.5
|
1.0
|
|
HZ3
|
S:TRP241
|
4.9
|
5.4
|
1.0
|
|
H2
|
L:HOH825
|
5.0
|
11.1
|
1.0
|
|
HG22
|
S:VAL187
|
5.0
|
5.4
|
1.0
|
|
N
|
S:CYS249
|
5.0
|
5.3
|
1.0
|
|
HD2
|
S:PRO242
|
5.0
|
7.1
|
1.0
|
|
Iron binding site 10 out
of 12 in 4u9h
Go back to
Iron Binding Sites List in 4u9h
Iron binding site 10 out
of 12 in the Ultra 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 Ultra 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:Fe1003
b:5.3
occ:1.00
|
FE3
|
S:F3S1003
|
0.0
|
5.3
|
1.0
|
|
S1
|
S:F3S1003
|
2.2
|
5.8
|
1.0
|
|
S4
|
S:F3S1003
|
2.3
|
5.3
|
1.0
|
|
S3
|
S:F3S1003
|
2.3
|
5.0
|
1.0
|
|
SG
|
S:CYS231
|
2.3
|
5.4
|
1.0
|
|
FE4
|
S:F3S1003
|
2.7
|
4.7
|
1.0
|
|
FE1
|
S:F3S1003
|
2.7
|
4.9
|
1.0
|
|
CB
|
S:CYS231
|
3.3
|
5.8
|
1.0
|
|
HD22
|
S:ASN229
|
3.4
|
5.7
|
0.9
|
|
HB3
|
S:CYS231
|
3.4
|
6.3
|
1.0
|
|
HB2
|
S:CYS231
|
3.5
|
8.3
|
1.0
|
|
HE2
|
S:PHE236
|
3.7
|
7.5
|
1.0
|
|
H2
|
S:HOH1176
|
3.8
|
10.2
|
1.0
|
|
ND2
|
S:ASN229
|
3.9
|
5.6
|
1.0
|
|
HG21
|
S:VAL187
|
3.9
|
7.9
|
1.0
|
|
S2
|
S:F3S1003
|
4.0
|
5.1
|
1.0
|
|
HB3
|
S:ASN229
|
4.0
|
7.4
|
1.0
|
|
HZ
|
S:PHE236
|
4.0
|
7.3
|
0.9
|
|
HD2
|
S:PRO242
|
4.0
|
7.1
|
1.0
|
|
HG2
|
S:PRO242
|
4.0
|
5.3
|
1.0
|
|
HD21
|
S:ASN229
|
4.2
|
6.2
|
0.8
|
|
HE3
|
S:TRP241
|
4.3
|
6.2
|
1.0
|
|
HG22
|
S:VAL187
|
4.3
|
5.4
|
1.0
|
|
CE2
|
S:PHE236
|
4.4
|
6.5
|
1.0
|
|
O
|
S:HOH1176
|
4.4
|
6.7
|
1.0
|
|
CZ
|
S:PHE236
|
4.6
|
6.2
|
1.0
|
|
CG
|
S:ASN229
|
4.6
|
5.3
|
1.0
|
|
H1
|
S:HOH1167
|
4.6
|
11.7
|
0.9
|
|
CG2
|
S:VAL187
|
4.6
|
6.5
|
1.0
|
|
CB
|
S:ASN229
|
4.6
|
5.6
|
1.0
|
|
H
|
S:CYS231
|
4.6
|
8.4
|
1.0
|
|
HB2
|
S:ASN229
|
4.7
|
7.7
|
1.0
|
|
HE2
|
L:LYS232
|
4.7
|
4.7
|
1.0
|
|
CA
|
S:CYS231
|
4.7
|
5.5
|
1.0
|
|
CD
|
S:PRO242
|
4.8
|
5.6
|
1.0
|
|
SG
|
S:CYS252
|
4.8
|
5.0
|
1.0
|
|
H1
|
S:HOH1171
|
4.8
|
11.3
|
1.0
|
|
HG11
|
S:VAL187
|
4.8
|
6.1
|
0.8
|
|
SG
|
S:CYS249
|
4.8
|
5.0
|
1.0
|
|
CG
|
S:PRO242
|
4.8
|
5.6
|
1.0
|
|
HA
|
S:CYS231
|
5.0
|
4.2
|
1.0
|
|
HG23
|
S:THR227
|
5.0
|
4.7
|
0.9
|
|
HD3
|
S:PRO242
|
5.0
|
5.8
|
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: Tue Aug 5 15:18:31 2025
|
