Iron in PDB 9f46: Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
Protein crystallography data
The structure of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f46
was solved by
J.Duan,
A.Rutz,
E.Hofmann,
T.Happe,
G.Kurisu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.89 /
2.45
|
|
Space group
|
P 42 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
167.9,
167.9,
125.38,
90,
90,
90
|
|
R / Rfree (%)
|
23.9 /
28.9
|
Other elements in 9f46:
The structure of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii 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 Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
(pdb code 9f46). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the
Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f46:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 1 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:63.9
occ:1.00
|
FE1
|
A:SF4701
|
0.0
|
63.9
|
1.0
|
|
S3
|
A:SF4701
|
2.1
|
51.1
|
1.0
|
|
S4
|
A:SF4701
|
2.1
|
55.4
|
1.0
|
|
S2
|
A:SF4701
|
2.1
|
54.2
|
1.0
|
|
SG
|
A:CYS423
|
2.2
|
66.5
|
1.0
|
|
HB3
|
A:CYS423
|
2.7
|
75.0
|
1.0
|
|
CB
|
A:CYS423
|
2.8
|
62.4
|
1.0
|
|
FE4
|
A:SF4701
|
3.0
|
55.9
|
1.0
|
|
FE2
|
A:SF4701
|
3.0
|
63.6
|
1.0
|
|
FE3
|
A:SF4701
|
3.0
|
63.3
|
1.0
|
|
HB2
|
A:CYS423
|
3.0
|
75.0
|
1.0
|
|
HB3
|
A:ALA425
|
3.3
|
67.7
|
1.0
|
|
S1
|
A:SF4701
|
3.7
|
58.7
|
1.0
|
|
HG2
|
A:LYS426
|
3.8
|
63.2
|
1.0
|
|
HG
|
A:CYS368
|
3.9
|
74.4
|
1.0
|
|
HG2
|
A:PRO422
|
4.0
|
62.4
|
1.0
|
|
HD2
|
A:PRO369
|
4.2
|
68.1
|
1.0
|
|
CB
|
A:ALA425
|
4.3
|
56.2
|
1.0
|
|
CA
|
A:CYS423
|
4.3
|
63.3
|
1.0
|
|
HE2
|
A:LYS426
|
4.3
|
63.3
|
1.0
|
|
H
|
A:ALA425
|
4.5
|
75.2
|
1.0
|
|
HB2
|
A:ALA425
|
4.5
|
67.7
|
1.0
|
|
H
|
A:LYS426
|
4.5
|
64.2
|
1.0
|
|
HD2
|
A:PRO422
|
4.5
|
58.8
|
1.0
|
|
HD3
|
A:PRO369
|
4.7
|
68.1
|
1.0
|
|
HA
|
A:CYS571
|
4.7
|
64.2
|
1.0
|
|
HB1
|
A:ALA425
|
4.7
|
67.7
|
1.0
|
|
N
|
A:CYS423
|
4.7
|
51.7
|
1.0
|
|
CG
|
A:LYS426
|
4.7
|
52.5
|
1.0
|
|
HA3
|
A:GLY574
|
4.8
|
66.0
|
1.0
|
|
HG3
|
A:LYS426
|
4.9
|
63.2
|
1.0
|
|
HA
|
A:CYS368
|
4.9
|
75.1
|
1.0
|
|
CG
|
A:PRO422
|
4.9
|
51.8
|
1.0
|
|
HA
|
A:CYS423
|
4.9
|
76.1
|
1.0
|
|
CD
|
A:PRO369
|
4.9
|
56.6
|
1.0
|
|
SG
|
A:CYS571
|
4.9
|
51.3
|
1.0
|
|
SG
|
A:CYS567
|
4.9
|
62.7
|
1.0
|
|
H
|
A:CYS423
|
5.0
|
62.2
|
1.0
|
|
Iron binding site 2 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 2 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:63.6
occ:1.00
|
FE2
|
A:SF4701
|
0.0
|
63.6
|
1.0
|
|
S4
|
A:SF4701
|
2.1
|
55.4
|
1.0
|
|
S1
|
A:SF4701
|
2.1
|
58.7
|
1.0
|
|
S3
|
A:SF4701
|
2.1
|
51.1
|
1.0
|
|
SG
|
A:CYS567
|
2.3
|
62.7
|
1.0
|
|
HB2
|
A:CYS567
|
2.8
|
75.8
|
1.0
|
|
FE1
|
A:SF4701
|
3.0
|
63.9
|
1.0
|
|
FE3
|
A:SF4701
|
3.0
|
63.3
|
1.0
|
|
FE4
|
A:SF4701
|
3.0
|
55.9
|
1.0
|
|
CB
|
A:CYS567
|
3.1
|
63.0
|
1.0
|
|
H
|
A:CYS567
|
3.3
|
88.0
|
1.0
|
|
HA2
|
A:GLY574
|
3.4
|
66.0
|
1.0
|
|
S2
|
A:SF4701
|
3.7
|
54.2
|
1.0
|
|
HA
|
A:CYS571
|
3.7
|
64.2
|
1.0
|
|
HB3
|
A:ALA566
|
3.8
|
79.8
|
1.0
|
|
N
|
A:CYS567
|
3.8
|
73.1
|
1.0
|
|
HB3
|
A:CYS567
|
3.8
|
75.8
|
1.0
|
|
HB3
|
A:CYS423
|
3.9
|
75.0
|
1.0
|
|
HG
|
A:CYS368
|
4.0
|
74.4
|
1.0
|
|
CA
|
A:CYS567
|
4.1
|
61.9
|
1.0
|
|
HA3
|
A:GLY574
|
4.1
|
66.0
|
1.0
|
|
CA
|
A:GLY574
|
4.2
|
54.8
|
1.0
|
|
H
|
A:ALA566
|
4.4
|
86.2
|
1.0
|
|
HB2
|
A:CYS423
|
4.5
|
75.0
|
1.0
|
|
O
|
A:GLY570
|
4.5
|
65.5
|
1.0
|
|
CB
|
A:CYS423
|
4.6
|
62.4
|
1.0
|
|
HA
|
A:CYS567
|
4.6
|
74.5
|
1.0
|
|
CA
|
A:CYS571
|
4.6
|
53.3
|
1.0
|
|
CB
|
A:ALA566
|
4.7
|
66.3
|
1.0
|
|
C
|
A:ALA566
|
4.7
|
74.8
|
1.0
|
|
N
|
A:GLY574
|
4.8
|
61.4
|
1.0
|
|
H
|
A:GLY575
|
4.8
|
81.7
|
1.0
|
|
C
|
A:GLY570
|
4.8
|
57.0
|
1.0
|
|
N
|
A:ALA566
|
4.9
|
71.7
|
1.0
|
|
SG
|
A:CYS423
|
4.9
|
66.5
|
1.0
|
|
SG
|
A:CYS368
|
5.0
|
61.8
|
1.0
|
|
Iron binding site 3 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 3 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:63.3
occ:1.00
|
FE3
|
A:SF4701
|
0.0
|
63.3
|
1.0
|
|
HG
|
A:CYS368
|
1.3
|
74.4
|
1.0
|
|
S2
|
A:SF4701
|
2.1
|
54.2
|
1.0
|
|
S4
|
A:SF4701
|
2.1
|
55.4
|
1.0
|
|
S1
|
A:SF4701
|
2.1
|
58.7
|
1.0
|
|
SG
|
A:CYS368
|
2.3
|
61.8
|
1.0
|
|
HB2
|
A:CYS368
|
2.9
|
67.2
|
1.0
|
|
FE1
|
A:SF4701
|
3.0
|
63.9
|
1.0
|
|
FE2
|
A:SF4701
|
3.0
|
63.6
|
1.0
|
|
FE4
|
A:SF4701
|
3.0
|
55.9
|
1.0
|
|
CB
|
A:CYS368
|
3.1
|
55.8
|
1.0
|
|
HA
|
A:CYS368
|
3.2
|
75.1
|
1.0
|
|
H
|
A:ALA566
|
3.4
|
86.2
|
1.0
|
|
HB3
|
A:ALA566
|
3.4
|
79.8
|
1.0
|
|
HD2
|
A:PRO369
|
3.6
|
68.1
|
1.0
|
|
CA
|
A:CYS368
|
3.7
|
62.4
|
1.0
|
|
S3
|
A:SF4701
|
3.7
|
51.1
|
1.0
|
|
HB3
|
A:CYS368
|
3.9
|
67.2
|
1.0
|
|
N
|
A:ALA566
|
4.2
|
71.7
|
1.0
|
|
CB
|
A:ALA566
|
4.2
|
66.3
|
1.0
|
|
HD3
|
A:PRO369
|
4.2
|
68.1
|
1.0
|
|
HB2
|
A:ALA566
|
4.3
|
79.8
|
1.0
|
|
CD
|
A:PRO369
|
4.3
|
56.6
|
1.0
|
|
H
|
A:SER370
|
4.3
|
73.0
|
1.0
|
|
H
|
A:CYS567
|
4.3
|
88.0
|
1.0
|
|
HB3
|
A:ALA425
|
4.5
|
67.7
|
1.0
|
|
HB2
|
A:SER370
|
4.5
|
69.9
|
1.0
|
|
C
|
A:CYS368
|
4.5
|
62.5
|
1.0
|
|
HA
|
A:MET565
|
4.5
|
74.0
|
1.0
|
|
N
|
A:PRO369
|
4.7
|
61.4
|
1.0
|
|
OG
|
A:SER370
|
4.7
|
56.8
|
1.0
|
|
CA
|
A:ALA566
|
4.8
|
65.2
|
1.0
|
|
N
|
A:CYS368
|
4.8
|
45.1
|
1.0
|
|
SD
|
A:MET565
|
4.8
|
65.1
|
1.0
|
|
HB1
|
A:ALA566
|
4.9
|
79.8
|
1.0
|
|
N
|
A:CYS567
|
5.0
|
73.1
|
1.0
|
|
SG
|
A:CYS567
|
5.0
|
62.7
|
1.0
|
|
SG
|
A:CYS571
|
5.0
|
51.3
|
1.0
|
|
HB3
|
A:MET565
|
5.0
|
72.5
|
1.0
|
|
Iron binding site 4 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 4 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:55.9
occ:1.00
|
FE4
|
A:SF4701
|
0.0
|
55.9
|
1.0
|
|
S3
|
A:SF4701
|
2.1
|
51.1
|
1.0
|
|
S1
|
A:SF4701
|
2.1
|
58.7
|
1.0
|
|
S2
|
A:SF4701
|
2.1
|
54.2
|
1.0
|
|
SG
|
A:CYS571
|
2.3
|
51.3
|
1.0
|
|
HA
|
A:CYS571
|
2.6
|
64.2
|
1.0
|
|
FE1
|
A:SF4701
|
3.0
|
63.9
|
1.0
|
|
FE2
|
A:SF4701
|
3.0
|
63.6
|
1.0
|
|
FE3
|
A:SF4701
|
3.0
|
63.3
|
1.0
|
|
CB
|
A:CYS571
|
3.2
|
52.0
|
1.0
|
|
CA
|
A:CYS571
|
3.2
|
53.3
|
1.0
|
|
HB3
|
A:CYS571
|
3.4
|
62.7
|
1.0
|
|
S4
|
A:SF4701
|
3.7
|
55.4
|
1.0
|
|
N
|
A:CYS571
|
3.7
|
56.0
|
1.0
|
|
H
|
A:CYS571
|
4.0
|
67.4
|
1.0
|
|
HG2
|
A:PRO422
|
4.0
|
62.4
|
1.0
|
|
HB2
|
A:CYS571
|
4.0
|
62.7
|
1.0
|
|
HG
|
A:CYS368
|
4.2
|
74.4
|
1.0
|
|
C
|
A:GLY570
|
4.4
|
57.0
|
1.0
|
|
HB2
|
A:CYS368
|
4.4
|
67.2
|
1.0
|
|
C
|
A:CYS571
|
4.6
|
51.9
|
1.0
|
|
HB2
|
A:CYS567
|
4.6
|
75.8
|
1.0
|
|
SD
|
A:MET565
|
4.6
|
65.1
|
1.0
|
|
O
|
A:GLY570
|
4.7
|
65.5
|
1.0
|
|
HA
|
A:CYS368
|
4.7
|
75.1
|
1.0
|
|
HB3
|
A:CYS423
|
4.8
|
75.0
|
1.0
|
|
CG
|
A:PRO422
|
4.8
|
51.8
|
1.0
|
|
HG3
|
A:PRO422
|
4.8
|
62.4
|
1.0
|
|
O
|
A:CYS571
|
4.8
|
58.3
|
1.0
|
|
HA2
|
A:GLY570
|
4.9
|
69.9
|
1.0
|
|
SG
|
A:CYS423
|
4.9
|
66.5
|
1.0
|
|
Iron binding site 5 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 5 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:82.9
occ:1.00
|
FE1
|
A:SF4702
|
0.0
|
82.9
|
1.0
|
|
S4
|
A:SF4702
|
2.1
|
78.0
|
1.0
|
|
S2
|
A:SF4702
|
2.1
|
77.3
|
1.0
|
|
S3
|
A:SF4702
|
2.1
|
97.5
|
1.0
|
|
SG
|
A:CYS228
|
2.3
|
81.7
|
1.0
|
|
HB3
|
A:CYS228
|
2.6
|
103.6
|
1.0
|
|
H
|
A:CYS228
|
2.9
|
108.1
|
1.0
|
|
CB
|
A:CYS228
|
3.0
|
86.1
|
1.0
|
|
FE4
|
A:SF4702
|
3.0
|
102.5
|
1.0
|
|
FE2
|
A:SF4702
|
3.0
|
95.7
|
1.0
|
|
FE3
|
A:SF4702
|
3.0
|
90.4
|
1.0
|
|
HD11
|
A:ILE267
|
3.3
|
87.6
|
1.0
|
|
N
|
A:CYS228
|
3.7
|
89.9
|
1.0
|
|
HD13
|
A:ILE218
|
3.7
|
90.0
|
1.0
|
|
HB2
|
A:CYS228
|
3.7
|
103.6
|
1.0
|
|
S1
|
A:SF4702
|
3.7
|
94.3
|
1.0
|
|
HB2
|
A:HIS245
|
3.8
|
110.0
|
1.0
|
|
CA
|
A:CYS228
|
3.9
|
78.0
|
1.0
|
|
H
|
A:GLY226
|
4.2
|
125.6
|
1.0
|
|
CD1
|
A:ILE267
|
4.3
|
72.8
|
1.0
|
|
H
|
A:LYS229
|
4.3
|
106.6
|
1.0
|
|
HD1
|
A:HIS245
|
4.4
|
118.4
|
1.0
|
|
H
|
A:ALA227
|
4.4
|
113.8
|
1.0
|
|
HG23
|
A:ILE218
|
4.5
|
96.2
|
1.0
|
|
CB
|
A:HIS245
|
4.6
|
91.5
|
1.0
|
|
CD1
|
A:ILE218
|
4.6
|
74.8
|
1.0
|
|
ND1
|
A:HIS245
|
4.6
|
98.4
|
1.0
|
|
HA
|
A:CYS228
|
4.6
|
93.8
|
1.0
|
|
HD13
|
A:ILE267
|
4.6
|
87.6
|
1.0
|
|
N
|
A:ALA227
|
4.6
|
94.7
|
1.0
|
|
HA2
|
A:GLY226
|
4.7
|
116.0
|
1.0
|
|
HB3
|
A:HIS245
|
4.7
|
110.0
|
1.0
|
|
HB3
|
A:ALA227
|
4.7
|
102.6
|
1.0
|
|
HB2
|
A:CYS262
|
4.7
|
118.8
|
1.0
|
|
HG12
|
A:ILE267
|
4.7
|
92.7
|
1.0
|
|
CG
|
A:HIS245
|
4.7
|
94.3
|
1.0
|
|
HG21
|
A:ILE218
|
4.7
|
96.2
|
1.0
|
|
HG21
|
A:ILE237
|
4.7
|
108.3
|
1.0
|
|
HG13
|
A:ILE267
|
4.8
|
92.7
|
1.0
|
|
HD12
|
A:ILE218
|
4.8
|
90.0
|
1.0
|
|
HA
|
A:CYS262
|
4.8
|
119.9
|
1.0
|
|
N
|
A:GLY226
|
4.8
|
104.5
|
1.0
|
|
HD12
|
A:ILE267
|
4.9
|
87.6
|
1.0
|
|
HD11
|
A:ILE218
|
4.9
|
90.0
|
1.0
|
|
C
|
A:ALA227
|
4.9
|
95.6
|
1.0
|
|
CG1
|
A:ILE267
|
4.9
|
77.1
|
1.0
|
|
N
|
A:LYS229
|
4.9
|
88.6
|
1.0
|
|
SG
|
A:CYS225
|
4.9
|
115.3
|
1.0
|
|
C
|
A:CYS228
|
4.9
|
84.3
|
1.0
|
|
SG
|
A:CYS222
|
5.0
|
93.8
|
1.0
|
|
C
|
A:GLY226
|
5.0
|
97.5
|
1.0
|
|
Iron binding site 6 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 6 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:95.7
occ:1.00
|
FE2
|
A:SF4702
|
0.0
|
95.7
|
1.0
|
|
S1
|
A:SF4702
|
2.1
|
94.3
|
1.0
|
|
S3
|
A:SF4702
|
2.1
|
97.5
|
1.0
|
|
S4
|
A:SF4702
|
2.1
|
78.0
|
1.0
|
|
SG
|
A:CYS225
|
2.3
|
115.3
|
1.0
|
|
H
|
A:CYS225
|
2.7
|
138.7
|
1.0
|
|
FE3
|
A:SF4702
|
3.0
|
90.4
|
1.0
|
|
FE4
|
A:SF4702
|
3.0
|
102.5
|
1.0
|
|
FE1
|
A:SF4702
|
3.0
|
82.9
|
1.0
|
|
H
|
A:GLY226
|
3.1
|
125.6
|
1.0
|
|
H
|
A:ALA227
|
3.4
|
113.8
|
1.0
|
|
N
|
A:CYS225
|
3.4
|
115.4
|
1.0
|
|
CB
|
A:CYS225
|
3.4
|
111.7
|
1.0
|
|
HD2
|
A:PRO263
|
3.4
|
116.8
|
1.0
|
|
HB3
|
A:CYS225
|
3.5
|
134.2
|
1.0
|
|
N
|
A:GLY226
|
3.6
|
104.5
|
1.0
|
|
S2
|
A:SF4702
|
3.7
|
77.3
|
1.0
|
|
CA
|
A:CYS225
|
3.8
|
110.6
|
1.0
|
|
HG12
|
A:ILE223
|
3.8
|
108.8
|
1.0
|
|
HD3
|
A:PRO263
|
3.9
|
116.8
|
1.0
|
|
HB3
|
A:ALA227
|
4.0
|
102.6
|
1.0
|
|
H
|
A:CYS228
|
4.0
|
108.1
|
1.0
|
|
C
|
A:CYS225
|
4.0
|
110.2
|
1.0
|
|
CD
|
A:PRO263
|
4.1
|
97.1
|
1.0
|
|
N
|
A:ALA227
|
4.1
|
94.7
|
1.0
|
|
H
|
A:GLY224
|
4.2
|
119.0
|
1.0
|
|
HB2
|
A:CYS225
|
4.2
|
134.2
|
1.0
|
|
H
|
A:ILE223
|
4.3
|
109.4
|
1.0
|
|
HA
|
A:CYS262
|
4.3
|
119.9
|
1.0
|
|
HG2
|
A:PRO263
|
4.4
|
111.0
|
1.0
|
|
C
|
A:GLY224
|
4.5
|
104.9
|
1.0
|
|
N
|
A:GLY224
|
4.6
|
98.9
|
1.0
|
|
CA
|
A:GLY226
|
4.6
|
96.5
|
1.0
|
|
CG1
|
A:ILE223
|
4.6
|
90.5
|
1.0
|
|
CG
|
A:PRO263
|
4.7
|
92.3
|
1.0
|
|
HA2
|
A:GLY224
|
4.7
|
121.5
|
1.0
|
|
CB
|
A:ALA227
|
4.7
|
85.3
|
1.0
|
|
HG13
|
A:ILE223
|
4.7
|
108.8
|
1.0
|
|
HG3
|
A:PRO263
|
4.7
|
111.0
|
1.0
|
|
HD1
|
A:HIS245
|
4.7
|
118.4
|
1.0
|
|
HA
|
A:CYS225
|
4.7
|
132.9
|
1.0
|
|
HB2
|
A:ALA227
|
4.7
|
102.6
|
1.0
|
|
HG22
|
A:VAL264
|
4.7
|
114.4
|
1.0
|
|
HA2
|
A:GLY226
|
4.8
|
116.0
|
1.0
|
|
CA
|
A:GLY224
|
4.8
|
101.0
|
1.0
|
|
C
|
A:GLY226
|
4.8
|
97.5
|
1.0
|
|
N
|
A:CYS228
|
4.8
|
89.9
|
1.0
|
|
SG
|
A:CYS262
|
4.8
|
80.1
|
1.0
|
|
HD11
|
A:ILE223
|
4.9
|
118.7
|
1.0
|
|
CA
|
A:ALA227
|
5.0
|
96.0
|
1.0
|
|
SG
|
A:CYS228
|
5.0
|
81.7
|
1.0
|
|
HB3
|
A:CYS228
|
5.0
|
103.6
|
1.0
|
|
Iron binding site 7 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 7 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:90.4
occ:1.00
|
FE3
|
A:SF4702
|
0.0
|
90.4
|
1.0
|
|
S4
|
A:SF4702
|
2.1
|
78.0
|
1.0
|
|
S2
|
A:SF4702
|
2.1
|
77.3
|
1.0
|
|
S1
|
A:SF4702
|
2.1
|
94.3
|
1.0
|
|
SG
|
A:CYS262
|
2.2
|
80.1
|
1.0
|
|
HB3
|
A:ALA266
|
2.9
|
106.2
|
1.0
|
|
FE2
|
A:SF4702
|
3.0
|
95.7
|
1.0
|
|
FE1
|
A:SF4702
|
3.0
|
82.9
|
1.0
|
|
FE4
|
A:SF4702
|
3.0
|
102.5
|
1.0
|
|
HB2
|
A:CYS262
|
3.1
|
118.8
|
1.0
|
|
CB
|
A:CYS262
|
3.2
|
98.8
|
1.0
|
|
HD2
|
A:PRO263
|
3.2
|
116.8
|
1.0
|
|
HA
|
A:CYS262
|
3.3
|
119.9
|
1.0
|
|
HG23
|
A:VAL264
|
3.4
|
114.4
|
1.0
|
|
HG13
|
A:ILE267
|
3.5
|
92.7
|
1.0
|
|
HG22
|
A:VAL264
|
3.7
|
114.4
|
1.0
|
|
S3
|
A:SF4702
|
3.7
|
97.5
|
1.0
|
|
HD11
|
A:ILE267
|
3.7
|
87.6
|
1.0
|
|
CA
|
A:CYS262
|
3.8
|
99.8
|
1.0
|
|
CB
|
A:ALA266
|
3.8
|
88.3
|
1.0
|
|
CG2
|
A:VAL264
|
3.9
|
95.2
|
1.0
|
|
HB2
|
A:ALA266
|
4.1
|
106.2
|
1.0
|
|
HB3
|
A:CYS262
|
4.1
|
118.8
|
1.0
|
|
H
|
A:VAL264
|
4.1
|
116.8
|
1.0
|
|
CD
|
A:PRO263
|
4.1
|
97.1
|
1.0
|
|
HG12
|
A:ILE267
|
4.2
|
92.7
|
1.0
|
|
HB1
|
A:ALA266
|
4.2
|
106.2
|
1.0
|
|
CG1
|
A:ILE267
|
4.2
|
77.1
|
1.0
|
|
HG21
|
A:VAL264
|
4.2
|
114.4
|
1.0
|
|
H
|
A:ALA266
|
4.3
|
101.6
|
1.0
|
|
HA
|
A:CYS222
|
4.3
|
105.6
|
1.0
|
|
HD3
|
A:PRO263
|
4.3
|
116.8
|
1.0
|
|
HB3
|
A:CYS228
|
4.4
|
103.6
|
1.0
|
|
CD1
|
A:ILE267
|
4.4
|
72.8
|
1.0
|
|
HG23
|
A:ILE218
|
4.5
|
96.2
|
1.0
|
|
C
|
A:CYS262
|
4.6
|
97.1
|
1.0
|
|
N
|
A:PRO263
|
4.7
|
98.9
|
1.0
|
|
H
|
A:ILE267
|
4.7
|
101.6
|
1.0
|
|
HB2
|
A:CYS222
|
4.7
|
114.2
|
1.0
|
|
H
|
A:ILE223
|
4.8
|
109.4
|
1.0
|
|
HD12
|
A:ILE267
|
4.8
|
87.6
|
1.0
|
|
SG
|
A:CYS225
|
4.8
|
115.3
|
1.0
|
|
CA
|
A:ALA266
|
4.9
|
90.5
|
1.0
|
|
N
|
A:ALA266
|
4.9
|
84.5
|
1.0
|
|
H
|
A:CYS228
|
4.9
|
108.1
|
1.0
|
|
N
|
A:CYS262
|
4.9
|
96.3
|
1.0
|
|
N
|
A:VAL264
|
5.0
|
97.2
|
1.0
|
|
Iron binding site 8 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 8 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:102.5
occ:1.00
|
FE4
|
A:SF4702
|
0.0
|
102.5
|
1.0
|
|
S1
|
A:SF4702
|
2.1
|
94.3
|
1.0
|
|
S3
|
A:SF4702
|
2.1
|
97.5
|
1.0
|
|
S2
|
A:SF4702
|
2.1
|
77.3
|
1.0
|
|
SG
|
A:CYS222
|
2.3
|
93.8
|
1.0
|
|
H
|
A:GLY224
|
3.0
|
119.0
|
1.0
|
|
FE1
|
A:SF4702
|
3.0
|
82.9
|
1.0
|
|
FE2
|
A:SF4702
|
3.0
|
95.7
|
1.0
|
|
FE3
|
A:SF4702
|
3.0
|
90.4
|
1.0
|
|
HB2
|
A:CYS222
|
3.1
|
114.2
|
1.0
|
|
CB
|
A:CYS222
|
3.2
|
95.0
|
1.0
|
|
HA
|
A:CYS222
|
3.2
|
105.6
|
1.0
|
|
H
|
A:ILE223
|
3.3
|
109.4
|
1.0
|
|
HD1
|
A:HIS245
|
3.5
|
118.4
|
1.0
|
|
CA
|
A:CYS222
|
3.6
|
87.8
|
1.0
|
|
S4
|
A:SF4702
|
3.7
|
78.0
|
1.0
|
|
HB2
|
A:HIS245
|
3.7
|
110.0
|
1.0
|
|
HG21
|
A:ILE218
|
3.8
|
96.2
|
1.0
|
|
N
|
A:GLY224
|
3.8
|
98.9
|
1.0
|
|
N
|
A:ILE223
|
3.8
|
91.0
|
1.0
|
|
H
|
A:CYS225
|
3.9
|
138.7
|
1.0
|
|
HG23
|
A:ILE218
|
3.9
|
96.2
|
1.0
|
|
HA2
|
A:GLY224
|
3.9
|
121.5
|
1.0
|
|
HB3
|
A:ALA266
|
4.0
|
106.2
|
1.0
|
|
HB3
|
A:CYS222
|
4.0
|
114.2
|
1.0
|
|
H
|
A:HIS245
|
4.1
|
109.3
|
1.0
|
|
C
|
A:CYS222
|
4.1
|
92.7
|
1.0
|
|
CG2
|
A:ILE218
|
4.2
|
80.0
|
1.0
|
|
HB1
|
A:ALA266
|
4.2
|
106.2
|
1.0
|
|
ND1
|
A:HIS245
|
4.2
|
98.4
|
1.0
|
|
HG22
|
A:ILE218
|
4.3
|
96.2
|
1.0
|
|
CA
|
A:GLY224
|
4.4
|
101.0
|
1.0
|
|
HG12
|
A:ILE223
|
4.4
|
108.8
|
1.0
|
|
CB
|
A:ALA266
|
4.5
|
88.3
|
1.0
|
|
H
|
A:GLY226
|
4.5
|
125.6
|
1.0
|
|
HD13
|
A:ILE218
|
4.5
|
90.0
|
1.0
|
|
N
|
A:CYS225
|
4.6
|
115.4
|
1.0
|
|
HB2
|
A:ALA266
|
4.6
|
106.2
|
1.0
|
|
CB
|
A:HIS245
|
4.6
|
91.5
|
1.0
|
|
C
|
A:ILE223
|
4.7
|
93.2
|
1.0
|
|
CG
|
A:HIS245
|
4.8
|
94.3
|
1.0
|
|
CA
|
A:ILE223
|
4.8
|
91.0
|
1.0
|
|
N
|
A:HIS245
|
4.9
|
90.9
|
1.0
|
|
SG
|
A:CYS228
|
4.9
|
81.7
|
1.0
|
|
HA
|
A:LYS244
|
4.9
|
116.0
|
1.0
|
|
N
|
A:CYS222
|
5.0
|
84.9
|
1.0
|
|
C
|
A:GLY224
|
5.0
|
104.9
|
1.0
|
|
Iron binding site 9 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 9 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:64.6
occ:1.00
|
FE1
|
A:SF4703
|
0.0
|
64.6
|
1.0
|
|
S2
|
A:SF4703
|
2.1
|
63.9
|
1.0
|
|
S3
|
A:SF4703
|
2.1
|
69.3
|
1.0
|
|
S4
|
A:SF4703
|
2.1
|
63.7
|
1.0
|
|
SG
|
A:CYS255
|
2.3
|
70.9
|
1.0
|
|
H
|
A:CYS255
|
2.9
|
74.9
|
1.0
|
|
H
|
A:GLY256
|
3.0
|
84.9
|
1.0
|
|
FE2
|
A:SF4703
|
3.0
|
73.5
|
1.0
|
|
FE4
|
A:SF4703
|
3.0
|
74.9
|
1.0
|
|
FE3
|
A:SF4703
|
3.0
|
66.6
|
1.0
|
|
H
|
A:ALA257
|
3.3
|
85.5
|
1.0
|
|
CB
|
A:CYS255
|
3.4
|
85.0
|
1.0
|
|
N
|
A:CYS255
|
3.4
|
62.2
|
1.0
|
|
HD2
|
A:PRO233
|
3.5
|
91.8
|
1.0
|
|
HB3
|
A:CYS255
|
3.5
|
102.3
|
1.0
|
|
N
|
A:GLY256
|
3.6
|
70.6
|
1.0
|
|
S1
|
A:SF4703
|
3.7
|
70.2
|
1.0
|
|
CA
|
A:CYS255
|
3.8
|
74.8
|
1.0
|
|
HB3
|
A:ALA257
|
3.9
|
84.2
|
1.0
|
|
OG1
|
A:THR253
|
3.9
|
66.6
|
1.0
|
|
H
|
A:CYS258
|
4.0
|
95.5
|
1.0
|
|
C
|
A:CYS255
|
4.0
|
68.1
|
1.0
|
|
N
|
A:ALA257
|
4.0
|
71.1
|
1.0
|
|
H
|
A:HIS254
|
4.1
|
77.9
|
1.0
|
|
HD3
|
A:PRO233
|
4.2
|
91.8
|
1.0
|
|
HG1
|
A:THR253
|
4.2
|
80.2
|
1.0
|
|
CD
|
A:PRO233
|
4.2
|
76.3
|
1.0
|
|
HB2
|
A:CYS255
|
4.2
|
102.3
|
1.0
|
|
H
|
A:THR253
|
4.3
|
91.1
|
1.0
|
|
C
|
A:HIS254
|
4.4
|
62.6
|
1.0
|
|
N
|
A:HIS254
|
4.4
|
64.8
|
1.0
|
|
HA
|
A:CYS232
|
4.4
|
90.3
|
1.0
|
|
HA
|
A:HIS254
|
4.5
|
85.5
|
1.0
|
|
CA
|
A:GLY256
|
4.5
|
65.7
|
1.0
|
|
HA2
|
A:GLY256
|
4.6
|
79.0
|
1.0
|
|
CB
|
A:ALA257
|
4.6
|
69.9
|
1.0
|
|
CA
|
A:HIS254
|
4.7
|
71.0
|
1.0
|
|
HB2
|
A:ALA257
|
4.7
|
84.2
|
1.0
|
|
HA
|
A:CYS255
|
4.7
|
90.0
|
1.0
|
|
HG2
|
A:PRO233
|
4.7
|
97.4
|
1.0
|
|
C
|
A:GLY256
|
4.8
|
67.3
|
1.0
|
|
HG3
|
A:PRO233
|
4.8
|
97.4
|
1.0
|
|
N
|
A:CYS258
|
4.8
|
79.4
|
1.0
|
|
CG
|
A:PRO233
|
4.8
|
81.0
|
1.0
|
|
SG
|
A:CYS232
|
4.8
|
71.2
|
1.0
|
|
HG22
|
A:VAL234
|
4.9
|
94.1
|
1.0
|
|
CA
|
A:ALA257
|
4.9
|
78.3
|
1.0
|
|
N
|
A:THR253
|
4.9
|
75.8
|
1.0
|
|
SG
|
A:CYS252
|
5.0
|
74.7
|
1.0
|
|
SG
|
A:CYS258
|
5.0
|
72.4
|
1.0
|
|
Iron binding site 10 out
of 24 in 9f46
Go back to
Iron Binding Sites List in 9f46
Iron binding site 10 out
of 24 in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:73.5
occ:1.00
|
FE2
|
A:SF4703
|
0.0
|
73.5
|
1.0
|
|
S1
|
A:SF4703
|
2.1
|
70.2
|
1.0
|
|
S3
|
A:SF4703
|
2.1
|
69.3
|
1.0
|
|
S4
|
A:SF4703
|
2.1
|
63.7
|
1.0
|
|
SG
|
A:CYS232
|
2.3
|
71.2
|
1.0
|
|
FE3
|
A:SF4703
|
3.0
|
66.6
|
1.0
|
|
FE1
|
A:SF4703
|
3.0
|
64.6
|
1.0
|
|
FE4
|
A:SF4703
|
3.0
|
74.9
|
1.0
|
|
HB2
|
A:CYS232
|
3.1
|
86.4
|
1.0
|
|
CB
|
A:CYS232
|
3.2
|
71.8
|
1.0
|
|
HB3
|
A:CYS236
|
3.2
|
92.5
|
1.0
|
|
HA
|
A:CYS232
|
3.3
|
90.3
|
1.0
|
|
HD2
|
A:PRO233
|
3.3
|
91.8
|
1.0
|
|
HB2
|
A:CYS236
|
3.5
|
92.5
|
1.0
|
|
HG13
|
A:ILE237
|
3.7
|
98.7
|
1.0
|
|
S2
|
A:SF4703
|
3.7
|
63.9
|
1.0
|
|
HD11
|
A:ILE237
|
3.8
|
87.9
|
1.0
|
|
CB
|
A:CYS236
|
3.8
|
76.9
|
1.0
|
|
CA
|
A:CYS232
|
3.8
|
75.1
|
1.0
|
|
HG22
|
A:VAL234
|
3.9
|
94.1
|
1.0
|
|
HG23
|
A:VAL234
|
4.0
|
94.1
|
1.0
|
|
HB3
|
A:CYS232
|
4.1
|
86.4
|
1.0
|
|
H
|
A:CYS236
|
4.1
|
108.3
|
1.0
|
|
CD
|
A:PRO233
|
4.2
|
76.3
|
1.0
|
|
HB3
|
A:CYS258
|
4.3
|
86.4
|
1.0
|
|
CG2
|
A:VAL234
|
4.3
|
78.2
|
1.0
|
|
CG1
|
A:ILE237
|
4.4
|
82.1
|
1.0
|
|
HG12
|
A:ILE237
|
4.4
|
98.7
|
1.0
|
|
H
|
A:VAL234
|
4.4
|
96.9
|
1.0
|
|
CD1
|
A:ILE237
|
4.5
|
73.1
|
1.0
|
|
HD3
|
A:PRO233
|
4.5
|
91.8
|
1.0
|
|
HG21
|
A:VAL234
|
4.6
|
94.1
|
1.0
|
|
C
|
A:CYS232
|
4.7
|
78.9
|
1.0
|
|
HA
|
A:CYS252
|
4.7
|
102.6
|
1.0
|
|
HG
|
A:CYS236
|
4.7
|
134.2
|
1.0
|
|
N
|
A:PRO233
|
4.8
|
72.9
|
1.0
|
|
N
|
A:CYS236
|
4.8
|
90.0
|
1.0
|
|
H
|
A:CYS258
|
4.8
|
95.5
|
1.0
|
|
H
|
A:THR253
|
4.8
|
91.1
|
1.0
|
|
CA
|
A:CYS236
|
4.8
|
82.2
|
1.0
|
|
SG
|
A:CYS255
|
4.8
|
70.9
|
1.0
|
|
N
|
A:CYS232
|
4.9
|
83.3
|
1.0
|
|
SG
|
A:CYS236
|
5.0
|
111.7
|
1.0
|
|
HB3
|
A:ALA257
|
5.0
|
84.2
|
1.0
|
|
Reference:
J.Duan,
A.Rutz,
A.Kawamoto,
S.Naskar,
K.Edenharter,
S.Leimkuehler,
E.Hofmann,
T.Happe,
G.Kurisu.
A Zinc Binding Four-Helix Domain Stabilizes the Dimeric Structure of O2-Stable [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii To Be Published.
Page generated: Sat Feb 8 19:40:33 2025
|
