Iron in PDB 4upv: Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
Enzymatic activity of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
All present enzymatic activity of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant:
1.12.2.1;
Protein crystallography data
The structure of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4upv
was solved by
A.Volbeda,
L.Martin,
E.Barbier,
O.Gutierrez-Sanz,
A.L.Delacey,
P.P.Liebgott,
S.Dementin,
M.Rousset,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.52
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.690,
100.850,
116.700,
90.00,
105.96,
90.00
|
R / Rfree (%)
|
12.001 /
15.39
|
Other elements in 4upv:
The structure of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant 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 Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
(pdb code 4upv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant, PDB code: 4upv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 1 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1265
b:8.0
occ:1.00
|
FE1
|
A:SF41265
|
0.0
|
8.0
|
1.0
|
S4
|
A:SF41265
|
2.3
|
8.6
|
1.0
|
SG
|
A:CYS212
|
2.3
|
9.4
|
1.0
|
S3
|
A:SF41265
|
2.3
|
7.4
|
1.0
|
S2
|
A:SF41265
|
2.3
|
7.7
|
1.0
|
FE3
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
FE2
|
A:SF41265
|
2.7
|
7.4
|
1.0
|
FE4
|
A:SF41265
|
2.7
|
7.5
|
1.0
|
CB
|
A:CYS212
|
3.4
|
8.5
|
1.0
|
N
|
A:LEU213
|
3.8
|
6.4
|
1.0
|
CA
|
A:CYS212
|
3.9
|
8.1
|
1.0
|
S1
|
A:SF41265
|
3.9
|
7.5
|
1.0
|
N
|
A:TYR214
|
4.3
|
8.2
|
1.0
|
CB
|
A:PHE193
|
4.3
|
9.3
|
1.0
|
C
|
A:CYS212
|
4.3
|
7.2
|
1.0
|
CD2
|
A:PHE193
|
4.4
|
10.8
|
1.0
|
ND1
|
A:HIS184
|
4.4
|
8.2
|
1.0
|
CB
|
A:ARG189
|
4.6
|
7.2
|
1.0
|
O
|
A:ARG189
|
4.6
|
8.5
|
1.0
|
CE1
|
A:HIS184
|
4.7
|
10.5
|
1.0
|
CB
|
A:TYR214
|
4.8
|
9.8
|
1.0
|
CG
|
A:PHE193
|
4.8
|
10.2
|
1.0
|
CA
|
A:LEU213
|
4.8
|
6.9
|
1.0
|
SG
|
A:CYS218
|
4.8
|
7.2
|
1.0
|
SG
|
A:CYS187
|
4.8
|
7.6
|
1.0
|
C
|
A:LEU213
|
4.9
|
7.1
|
1.0
|
CA
|
A:TYR214
|
4.9
|
8.6
|
1.0
|
C
|
A:ARG189
|
4.9
|
7.7
|
1.0
|
|
Iron binding site 2 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 2 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1265
b:7.4
occ:1.00
|
FE2
|
A:SF41265
|
0.0
|
7.4
|
1.0
|
S3
|
A:SF41265
|
2.3
|
7.4
|
1.0
|
SG
|
A:CYS187
|
2.3
|
7.6
|
1.0
|
S4
|
A:SF41265
|
2.3
|
8.6
|
1.0
|
S1
|
A:SF41265
|
2.3
|
7.5
|
1.0
|
FE3
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
FE1
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
FE4
|
A:SF41265
|
2.7
|
7.5
|
1.0
|
CB
|
A:CYS187
|
3.1
|
7.5
|
1.0
|
S2
|
A:SF41265
|
3.9
|
7.7
|
1.0
|
CB
|
A:ARG189
|
4.0
|
7.2
|
1.0
|
CG1
|
A:VAL239
|
4.3
|
8.1
|
1.0
|
ND1
|
A:HIS184
|
4.5
|
8.2
|
1.0
|
CA
|
A:CYS187
|
4.5
|
7.8
|
1.0
|
C
|
A:ARG189
|
4.6
|
7.7
|
1.0
|
CG2
|
A:VAL239
|
4.6
|
7.4
|
1.0
|
CA
|
A:ARG189
|
4.6
|
7.8
|
1.0
|
N
|
A:ARG189
|
4.7
|
7.3
|
1.0
|
N
|
A:LEU190
|
4.7
|
7.8
|
1.0
|
SG
|
A:CYS218
|
4.8
|
7.2
|
1.0
|
CG
|
A:ARG189
|
4.9
|
7.3
|
1.0
|
CH2
|
A:TRP237
|
4.9
|
6.4
|
1.0
|
SG
|
A:CYS212
|
4.9
|
9.4
|
1.0
|
CB
|
A:VAL239
|
5.0
|
6.2
|
1.0
|
O
|
A:ARG189
|
5.0
|
8.5
|
1.0
|
C
|
A:CYS187
|
5.0
|
7.3
|
1.0
|
|
Iron binding site 3 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 3 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1265
b:8.0
occ:1.00
|
FE3
|
A:SF41265
|
0.0
|
8.0
|
1.0
|
ND1
|
A:HIS184
|
2.1
|
8.2
|
1.0
|
S2
|
A:SF41265
|
2.3
|
7.7
|
1.0
|
S1
|
A:SF41265
|
2.3
|
7.5
|
1.0
|
S4
|
A:SF41265
|
2.3
|
8.6
|
1.0
|
FE1
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
FE2
|
A:SF41265
|
2.7
|
7.4
|
1.0
|
FE4
|
A:SF41265
|
2.7
|
7.5
|
1.0
|
CE1
|
A:HIS184
|
2.9
|
10.5
|
1.0
|
CG
|
A:HIS184
|
3.2
|
8.2
|
1.0
|
CB
|
A:HIS184
|
3.6
|
7.7
|
1.0
|
S3
|
A:SF41265
|
3.9
|
7.4
|
1.0
|
CA
|
A:HIS184
|
4.0
|
7.3
|
1.0
|
NE2
|
A:HIS184
|
4.1
|
12.0
|
1.0
|
CG
|
A:PRO221
|
4.2
|
7.8
|
1.0
|
CD
|
A:PRO221
|
4.2
|
7.3
|
1.0
|
CD2
|
A:HIS184
|
4.2
|
10.7
|
1.0
|
CB
|
A:CYS187
|
4.5
|
7.5
|
1.0
|
O
|
A:HIS184
|
4.5
|
8.2
|
1.0
|
SG
|
A:CYS212
|
4.6
|
9.4
|
1.0
|
SG
|
A:CYS187
|
4.6
|
7.6
|
1.0
|
CD2
|
A:PHE193
|
4.7
|
10.8
|
1.0
|
C
|
A:HIS184
|
4.8
|
7.3
|
1.0
|
SG
|
A:CYS218
|
4.8
|
7.2
|
1.0
|
N
|
A:PRO221
|
4.8
|
7.7
|
1.0
|
CA
|
A:GLY220
|
4.9
|
7.6
|
1.0
|
CB
|
A:PHE193
|
4.9
|
9.3
|
1.0
|
CG
|
A:PHE193
|
4.9
|
10.2
|
1.0
|
|
Iron binding site 4 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 4 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1265
b:7.5
occ:1.00
|
FE4
|
A:SF41265
|
0.0
|
7.5
|
1.0
|
S1
|
A:SF41265
|
2.3
|
7.5
|
1.0
|
S2
|
A:SF41265
|
2.3
|
7.7
|
1.0
|
SG
|
A:CYS218
|
2.3
|
7.2
|
1.0
|
S3
|
A:SF41265
|
2.3
|
7.4
|
1.0
|
FE2
|
A:SF41265
|
2.7
|
7.4
|
1.0
|
FE3
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
FE1
|
A:SF41265
|
2.7
|
8.0
|
1.0
|
CB
|
A:CYS218
|
3.2
|
7.4
|
1.0
|
S4
|
A:SF41265
|
3.9
|
8.6
|
1.0
|
CG2
|
A:VAL239
|
4.4
|
7.4
|
1.0
|
N
|
A:GLY220
|
4.5
|
7.1
|
1.0
|
CA
|
A:GLY220
|
4.5
|
7.6
|
1.0
|
CA
|
A:CYS218
|
4.6
|
6.8
|
1.0
|
CD
|
A:PRO221
|
4.6
|
7.3
|
1.0
|
SG
|
A:CYS212
|
4.7
|
9.4
|
1.0
|
ND1
|
A:HIS184
|
4.7
|
8.2
|
1.0
|
SG
|
A:CYS187
|
4.8
|
7.6
|
1.0
|
C
|
A:CYS218
|
4.8
|
6.2
|
1.0
|
N
|
A:LEU213
|
4.9
|
6.4
|
1.0
|
N
|
A:TYR214
|
4.9
|
8.2
|
1.0
|
CB
|
A:LEU213
|
5.0
|
6.8
|
1.0
|
|
Iron binding site 5 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 5 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_05.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1266
b:6.6
occ:1.00
|
FE1
|
A:F3S1266
|
0.0
|
6.6
|
1.0
|
S1
|
A:F3S1266
|
2.2
|
7.0
|
1.0
|
S2
|
A:F3S1266
|
2.3
|
7.1
|
1.0
|
S3
|
A:F3S1266
|
2.3
|
6.9
|
1.0
|
SG
|
A:CYS248
|
2.3
|
7.0
|
1.0
|
FE4
|
A:F3S1266
|
2.7
|
7.0
|
1.0
|
FE3
|
A:F3S1266
|
2.7
|
6.9
|
1.0
|
CB
|
A:CYS248
|
3.5
|
7.0
|
1.0
|
O
|
Q:HOH2717
|
3.7
|
6.9
|
1.0
|
N
|
A:CYS248
|
3.8
|
6.0
|
1.0
|
S4
|
A:F3S1266
|
3.8
|
7.7
|
1.0
|
CA
|
A:CYS248
|
4.1
|
6.0
|
1.0
|
O
|
A:HOH2417
|
4.1
|
6.8
|
1.0
|
ND2
|
A:ASN225
|
4.4
|
8.1
|
1.0
|
C
|
A:CYS248
|
4.6
|
6.6
|
1.0
|
N
|
A:SER249
|
4.7
|
6.0
|
1.0
|
SG
|
A:CYS245
|
4.7
|
7.0
|
1.0
|
SG
|
A:CYS227
|
4.7
|
6.7
|
1.0
|
O
|
A:HOH2404
|
4.8
|
6.8
|
1.0
|
CE
|
Q:LYS225
|
4.9
|
5.7
|
1.0
|
C
|
A:GLY247
|
5.0
|
6.1
|
1.0
|
|
Iron binding site 6 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 6 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_06.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1266
b:6.9
occ:1.00
|
FE3
|
A:F3S1266
|
0.0
|
6.9
|
1.0
|
S4
|
A:F3S1266
|
2.2
|
7.7
|
1.0
|
S1
|
A:F3S1266
|
2.3
|
7.0
|
1.0
|
S3
|
A:F3S1266
|
2.3
|
6.9
|
1.0
|
SG
|
A:CYS227
|
2.3
|
6.7
|
1.0
|
FE1
|
A:F3S1266
|
2.7
|
6.6
|
1.0
|
FE4
|
A:F3S1266
|
2.7
|
7.0
|
1.0
|
CB
|
A:CYS227
|
3.3
|
6.6
|
1.0
|
ND2
|
A:ASN225
|
3.9
|
8.1
|
1.0
|
S2
|
A:F3S1266
|
4.0
|
7.1
|
1.0
|
CE2
|
A:PHE232
|
4.3
|
6.4
|
1.0
|
O
|
A:HOH2417
|
4.4
|
6.8
|
1.0
|
CZ
|
A:PHE232
|
4.5
|
6.9
|
1.0
|
CG
|
A:ASN225
|
4.5
|
6.8
|
1.0
|
CB
|
A:ASN225
|
4.6
|
7.1
|
1.0
|
CG2
|
A:VAL183
|
4.7
|
8.5
|
1.0
|
CA
|
A:CYS227
|
4.7
|
6.4
|
1.0
|
SG
|
A:CYS245
|
4.7
|
7.0
|
1.0
|
SG
|
A:CYS248
|
4.8
|
7.0
|
1.0
|
CD
|
A:PRO238
|
4.9
|
6.4
|
1.0
|
|
Iron binding site 7 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 7 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_07.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1266
b:7.0
occ:1.00
|
FE4
|
A:F3S1266
|
0.0
|
7.0
|
1.0
|
S4
|
A:F3S1266
|
2.2
|
7.7
|
1.0
|
S2
|
A:F3S1266
|
2.3
|
7.1
|
1.0
|
SG
|
A:CYS245
|
2.3
|
7.0
|
1.0
|
S3
|
A:F3S1266
|
2.3
|
6.9
|
1.0
|
FE1
|
A:F3S1266
|
2.7
|
6.6
|
1.0
|
FE3
|
A:F3S1266
|
2.7
|
6.9
|
1.0
|
CB
|
A:CYS245
|
3.2
|
6.4
|
1.0
|
CA
|
A:CYS245
|
3.6
|
5.8
|
1.0
|
S1
|
A:F3S1266
|
3.9
|
7.0
|
1.0
|
N
|
A:LEU246
|
4.0
|
6.1
|
1.0
|
N
|
A:GLY247
|
4.2
|
5.9
|
1.0
|
C
|
A:CYS245
|
4.3
|
5.7
|
1.0
|
N
|
A:CYS248
|
4.5
|
6.0
|
1.0
|
NE2
|
Q:GLN230
|
4.7
|
6.0
|
1.0
|
CG2
|
A:THR223
|
4.7
|
7.2
|
1.0
|
SG
|
A:CYS248
|
4.8
|
7.0
|
1.0
|
CG2
|
A:VAL183
|
4.8
|
8.5
|
1.0
|
SG
|
A:CYS227
|
4.8
|
6.7
|
1.0
|
CA
|
A:GLY247
|
4.8
|
6.8
|
1.0
|
N
|
A:CYS245
|
5.0
|
6.3
|
1.0
|
|
Iron binding site 8 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 8 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_08.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1267
b:6.5
occ:1.00
|
FE1
|
A:SF41267
|
0.0
|
6.5
|
1.0
|
SG
|
A:CYS147
|
2.3
|
6.7
|
1.0
|
S3
|
A:SF41267
|
2.3
|
6.6
|
1.0
|
S4
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
S2
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
FE3
|
A:SF41267
|
2.6
|
6.9
|
1.0
|
FE4
|
A:SF41267
|
2.7
|
6.5
|
1.0
|
FE2
|
A:SF41267
|
2.8
|
6.8
|
1.0
|
CB
|
A:CYS147
|
3.4
|
6.0
|
1.0
|
CA
|
A:CYS147
|
3.4
|
6.0
|
1.0
|
O
|
A:HOH2415
|
3.8
|
7.2
|
1.0
|
C
|
A:CYS147
|
3.9
|
5.3
|
1.0
|
S1
|
A:SF41267
|
3.9
|
6.7
|
1.0
|
CG
|
Q:ARG70
|
4.2
|
6.2
|
1.0
|
O
|
A:CYS147
|
4.3
|
6.3
|
1.0
|
SG
|
A:CYS114
|
4.4
|
7.1
|
1.0
|
N
|
A:PRO148
|
4.4
|
5.3
|
1.0
|
SG
|
A:CYS17
|
4.6
|
6.5
|
1.0
|
CD2
|
Q:HIS228
|
4.6
|
5.8
|
1.0
|
O
|
A:GLY146
|
4.6
|
6.1
|
1.0
|
CA
|
A:PRO148
|
4.7
|
5.2
|
1.0
|
NE2
|
Q:HIS228
|
4.7
|
6.1
|
1.0
|
NE
|
Q:ARG70
|
4.7
|
5.4
|
1.0
|
N
|
A:CYS147
|
4.7
|
5.5
|
1.0
|
SG
|
A:CYS20
|
4.8
|
7.3
|
1.0
|
|
Iron binding site 9 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 9 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_09.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1267
b:6.8
occ:1.00
|
FE2
|
A:SF41267
|
0.0
|
6.8
|
1.0
|
S4
|
A:SF41267
|
2.2
|
6.7
|
1.0
|
SG
|
A:CYS20
|
2.3
|
7.3
|
1.0
|
S3
|
A:SF41267
|
2.3
|
6.6
|
1.0
|
S1
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
FE4
|
A:SF41267
|
2.7
|
6.5
|
1.0
|
FE3
|
A:SF41267
|
2.8
|
6.9
|
1.0
|
FE1
|
A:SF41267
|
2.8
|
6.5
|
1.0
|
CB
|
A:CYS20
|
3.5
|
6.7
|
1.0
|
N
|
A:CYS20
|
3.7
|
6.0
|
1.0
|
O
|
A:HOH2414
|
3.9
|
6.6
|
1.0
|
S2
|
A:SF41267
|
3.9
|
6.7
|
1.0
|
CA
|
A:CYS20
|
4.1
|
6.8
|
1.0
|
CB
|
A:PRO148
|
4.4
|
5.4
|
1.0
|
CA
|
A:PRO148
|
4.4
|
5.2
|
1.0
|
CA
|
A:GLY112
|
4.4
|
6.1
|
1.0
|
C
|
A:GLY19
|
4.4
|
6.1
|
1.0
|
SG
|
A:CYS17
|
4.7
|
6.5
|
1.0
|
O
|
A:GLY146
|
4.7
|
6.1
|
1.0
|
CA
|
A:CYS147
|
4.8
|
6.0
|
1.0
|
CA
|
A:GLY19
|
4.8
|
6.8
|
1.0
|
N
|
A:PRO148
|
4.9
|
5.3
|
1.0
|
N
|
A:GLY19
|
4.9
|
5.8
|
1.0
|
SG
|
A:CYS114
|
4.9
|
7.1
|
1.0
|
SG
|
A:CYS147
|
4.9
|
6.7
|
1.0
|
|
Iron binding site 10 out
of 24 in 4upv
Go back to
Iron Binding Sites List in 4upv
Iron binding site 10 out
of 24 in the Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant
![](/pictures/FE/pdb/up/4upv-FE-sphere_10.jpg) Mono view
![](/pictures/FE/pdb/up/4upv-FE-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Low X-Ray Dose Structure of A Ni-A Ni-Sox Mixture of the D. Fructosovorans Nife-Hydrogenase L122A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1267
b:6.9
occ:1.00
|
FE3
|
A:SF41267
|
0.0
|
6.9
|
1.0
|
SG
|
A:CYS114
|
2.3
|
7.1
|
1.0
|
S2
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
S1
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
S4
|
A:SF41267
|
2.3
|
6.7
|
1.0
|
FE1
|
A:SF41267
|
2.6
|
6.5
|
1.0
|
FE4
|
A:SF41267
|
2.7
|
6.5
|
1.0
|
FE2
|
A:SF41267
|
2.8
|
6.8
|
1.0
|
CB
|
A:CYS114
|
3.3
|
6.9
|
1.0
|
S3
|
A:SF41267
|
3.9
|
6.6
|
1.0
|
O
|
A:HOH2414
|
3.9
|
6.6
|
1.0
|
O
|
A:HOH2415
|
3.9
|
7.2
|
1.0
|
N
|
A:CYS114
|
4.1
|
6.3
|
1.0
|
O
|
A:HOH2405
|
4.2
|
7.4
|
1.0
|
CA
|
A:CYS114
|
4.3
|
6.3
|
1.0
|
SG
|
A:CYS147
|
4.5
|
6.7
|
1.0
|
SG
|
A:CYS20
|
4.7
|
7.3
|
1.0
|
N
|
A:CYS17
|
4.8
|
6.0
|
1.0
|
SG
|
A:CYS17
|
4.8
|
6.5
|
1.0
|
CA
|
A:GLU16
|
4.9
|
6.3
|
1.0
|
|
Reference:
A.Volbeda,
L.Martin,
E.Barbier,
O.Gutierrez-Sanz,
A.L.De Lacey,
P.Liebgott,
S.Dementin,
M.Rousset,
J.C.Fontecilla-Camps.
Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures For the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25315838
DOI: 10.1007/S00775-014-1203-9
Page generated: Mon Aug 5 13:34:12 2024
|