Iron in PDB 9iyl: CHCODH2 Wt
Enzymatic activity of CHCODH2 Wt
All present enzymatic activity of CHCODH2 Wt:
1.2.7.4;
Protein crystallography data
The structure of CHCODH2 Wt, PDB code: 9iyl
was solved by
S.Y.Kong,
H.J.Yoon,
S.M.Kim,
H.H.Lee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.90 /
1.28
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.94,
75.8,
71.65,
90,
111.59,
90
|
R / Rfree (%)
|
17.5 /
19.5
|
Other elements in 9iyl:
The structure of CHCODH2 Wt also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Iron atom in the CHCODH2 Wt
(pdb code 9iyl). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 11 binding sites of Iron where determined in the
CHCODH2 Wt, PDB code: 9iyl:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 1 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:10.9
occ:1.00
|
FE1
|
A:SF4701
|
0.0
|
10.9
|
1.0
|
S4
|
A:SF4701
|
2.3
|
11.2
|
1.0
|
S2
|
A:SF4701
|
2.3
|
11.3
|
1.0
|
S3
|
A:SF4701
|
2.3
|
10.5
|
1.0
|
SG
|
A:CYS70
|
2.3
|
11.2
|
1.0
|
FE2
|
A:SF4701
|
2.7
|
10.8
|
1.0
|
FE3
|
A:SF4701
|
2.7
|
11.1
|
1.0
|
FE4
|
A:SF4701
|
2.8
|
10.9
|
1.0
|
CB
|
A:CYS70
|
3.3
|
11.0
|
1.0
|
N
|
A:CYS70
|
3.9
|
11.5
|
1.0
|
S1
|
A:SF4701
|
3.9
|
10.7
|
1.0
|
NH2
|
A:ARG80
|
4.2
|
11.5
|
1.0
|
O
|
A:HOH1031
|
4.2
|
12.3
|
1.0
|
CA
|
A:CYS70
|
4.2
|
11.7
|
1.0
|
CB
|
A:ALA72
|
4.4
|
12.7
|
1.0
|
SG
|
A:CYS51
|
4.7
|
11.1
|
1.0
|
N
|
A:ILE69
|
4.7
|
11.2
|
1.0
|
CG
|
A:MET199
|
4.7
|
11.5
|
1.0
|
SG
|
A:CYS48
|
4.8
|
10.6
|
1.0
|
SG
|
A:CYS56
|
4.8
|
10.9
|
1.0
|
|
Iron binding site 2 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 2 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:10.8
occ:1.00
|
FE2
|
A:SF4701
|
0.0
|
10.8
|
1.0
|
S3
|
A:SF4701
|
2.3
|
10.5
|
1.0
|
S4
|
A:SF4701
|
2.3
|
11.2
|
1.0
|
SG
|
A:CYS48
|
2.3
|
10.6
|
1.0
|
S1
|
A:SF4701
|
2.3
|
10.7
|
1.0
|
FE3
|
A:SF4701
|
2.7
|
11.1
|
1.0
|
FE4
|
A:SF4701
|
2.7
|
10.9
|
1.0
|
FE1
|
A:SF4701
|
2.7
|
10.9
|
1.0
|
CB
|
A:CYS48
|
3.3
|
10.2
|
1.0
|
NH2
|
A:ARG80
|
3.7
|
11.5
|
1.0
|
S2
|
A:SF4701
|
3.8
|
11.3
|
1.0
|
N
|
A:HIS50
|
3.9
|
11.5
|
1.0
|
C
|
A:CYS48
|
4.2
|
11.2
|
1.0
|
O
|
A:CYS48
|
4.2
|
11.7
|
1.0
|
CA
|
A:CYS48
|
4.3
|
10.4
|
1.0
|
CB
|
A:HIS50
|
4.4
|
11.4
|
1.0
|
N
|
A:CYS51
|
4.5
|
10.7
|
1.0
|
CA
|
A:HIS50
|
4.5
|
11.5
|
1.0
|
N
|
A:ARG49
|
4.6
|
11.8
|
1.0
|
CB
|
A:CYS56
|
4.7
|
12.7
|
1.0
|
SG
|
A:CYS56
|
4.7
|
10.9
|
1.0
|
C
|
A:HIS50
|
4.8
|
10.5
|
1.0
|
CZ
|
A:ARG80
|
4.8
|
11.4
|
1.0
|
SG
|
A:CYS70
|
4.9
|
11.2
|
1.0
|
SG
|
A:CYS51
|
4.9
|
11.1
|
1.0
|
C
|
A:ARG49
|
4.9
|
12.6
|
1.0
|
|
Iron binding site 3 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 3 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:11.1
occ:1.00
|
FE3
|
A:SF4701
|
0.0
|
11.1
|
1.0
|
S2
|
A:SF4701
|
2.2
|
11.3
|
1.0
|
S1
|
A:SF4701
|
2.3
|
10.7
|
1.0
|
S4
|
A:SF4701
|
2.3
|
11.2
|
1.0
|
SG
|
A:CYS56
|
2.3
|
10.9
|
1.0
|
FE2
|
A:SF4701
|
2.7
|
10.8
|
1.0
|
FE4
|
A:SF4701
|
2.7
|
10.9
|
1.0
|
FE1
|
A:SF4701
|
2.7
|
10.9
|
1.0
|
CB
|
A:CYS56
|
3.2
|
12.7
|
1.0
|
S3
|
A:SF4701
|
3.9
|
10.5
|
1.0
|
N
|
A:ILE69
|
4.0
|
11.2
|
1.0
|
CA
|
A:CYS56
|
4.4
|
11.9
|
1.0
|
N
|
A:CYS56
|
4.4
|
11.9
|
1.0
|
CB
|
A:ILE69
|
4.4
|
12.2
|
1.0
|
CA
|
A:GLY54
|
4.5
|
12.8
|
1.0
|
N
|
A:GLY54
|
4.6
|
12.7
|
1.0
|
O
|
A:CYS48
|
4.6
|
11.7
|
1.0
|
SG
|
A:CYS51
|
4.7
|
11.1
|
1.0
|
SG
|
A:CYS48
|
4.7
|
10.6
|
1.0
|
N
|
A:CYS70
|
4.7
|
11.5
|
1.0
|
CA
|
A:GLY68
|
4.7
|
12.0
|
1.0
|
CB
|
A:CYS48
|
4.8
|
10.2
|
1.0
|
CA
|
A:ILE69
|
4.8
|
12.4
|
1.0
|
SG
|
A:CYS70
|
4.8
|
11.2
|
1.0
|
C
|
A:GLY68
|
4.8
|
10.9
|
1.0
|
CG1
|
A:ILE69
|
4.9
|
11.5
|
1.0
|
|
Iron binding site 4 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 4 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe701
b:10.9
occ:1.00
|
FE4
|
A:SF4701
|
0.0
|
10.9
|
1.0
|
SG
|
A:CYS51
|
2.3
|
11.1
|
1.0
|
S1
|
A:SF4701
|
2.3
|
10.7
|
1.0
|
S2
|
A:SF4701
|
2.3
|
11.3
|
1.0
|
S3
|
A:SF4701
|
2.3
|
10.5
|
1.0
|
FE2
|
A:SF4701
|
2.7
|
10.8
|
1.0
|
FE3
|
A:SF4701
|
2.7
|
11.1
|
1.0
|
FE1
|
A:SF4701
|
2.8
|
10.9
|
1.0
|
CB
|
A:CYS51
|
3.3
|
10.9
|
1.0
|
N
|
A:CYS51
|
3.5
|
10.7
|
1.0
|
CA
|
A:CYS51
|
3.9
|
10.7
|
1.0
|
S4
|
A:SF4701
|
3.9
|
11.2
|
1.0
|
O
|
A:CYS51
|
4.2
|
12.2
|
1.0
|
C
|
A:CYS51
|
4.3
|
11.8
|
1.0
|
C
|
A:HIS50
|
4.4
|
10.5
|
1.0
|
CG
|
A:MET199
|
4.4
|
11.5
|
1.0
|
N
|
A:GLY54
|
4.5
|
12.7
|
1.0
|
CB
|
A:GLN53
|
4.6
|
12.3
|
1.0
|
CB
|
A:MET199
|
4.7
|
11.2
|
1.0
|
N
|
A:HIS50
|
4.8
|
11.5
|
1.0
|
NE2
|
A:GLN53
|
4.8
|
14.2
|
1.0
|
SG
|
A:CYS48
|
4.8
|
10.6
|
1.0
|
N
|
A:GLN53
|
4.8
|
11.9
|
1.0
|
SG
|
A:CYS70
|
4.8
|
11.2
|
1.0
|
SG
|
A:CYS56
|
4.9
|
10.9
|
1.0
|
CA
|
A:HIS50
|
5.0
|
11.5
|
1.0
|
|
Iron binding site 5 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 5 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:12.6
occ:1.00
|
FE1
|
A:FES702
|
0.0
|
12.6
|
1.0
|
S1
|
A:FES702
|
2.3
|
12.7
|
1.0
|
S2
|
A:FES702
|
2.3
|
12.8
|
1.0
|
SG
|
A:CYS47
|
2.3
|
12.2
|
1.0
|
FE2
|
A:FES702
|
2.7
|
12.3
|
1.0
|
CB
|
A:CYS47
|
3.2
|
11.5
|
1.0
|
O
|
A:HOH1170
|
3.6
|
18.7
|
1.0
|
CA
|
A:CYS47
|
4.6
|
10.9
|
1.0
|
SG
|
A:CYS39
|
4.8
|
13.4
|
1.0
|
CD
|
A:ARG49
|
4.9
|
17.6
|
1.0
|
CB
|
A:PHE41
|
5.0
|
13.9
|
1.0
|
N
|
A:GLY42
|
5.0
|
13.4
|
1.0
|
CB
|
A:PRO55
|
5.0
|
14.4
|
1.0
|
|
Iron binding site 6 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 6 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe702
b:12.3
occ:1.00
|
FE2
|
A:FES702
|
0.0
|
12.3
|
1.0
|
S2
|
A:FES702
|
2.3
|
12.8
|
1.0
|
S1
|
A:FES702
|
2.3
|
12.7
|
1.0
|
SG
|
A:CYS39
|
2.3
|
13.4
|
1.0
|
FE1
|
A:FES702
|
2.7
|
12.6
|
1.0
|
CB
|
A:CYS39
|
3.2
|
14.1
|
1.0
|
N
|
A:GLY42
|
4.2
|
13.4
|
1.0
|
CB
|
A:PHE41
|
4.4
|
13.9
|
1.0
|
CA
|
A:CYS39
|
4.6
|
13.6
|
1.0
|
CA
|
A:GLY42
|
4.8
|
14.4
|
1.0
|
SG
|
A:CYS47
|
4.8
|
12.2
|
1.0
|
CD2
|
A:PHE41
|
4.9
|
16.2
|
1.0
|
|
Iron binding site 7 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 7 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:29.8
occ:0.49
|
FE1
|
A:XCC703
|
0.0
|
29.8
|
0.5
|
FE
|
A:FE704
|
1.4
|
22.1
|
0.5
|
S3
|
A:XCC703
|
2.3
|
26.2
|
0.5
|
S4
|
A:XCC703
|
2.3
|
27.2
|
0.5
|
SG
|
A:CYS476
|
2.3
|
23.6
|
1.0
|
S2
|
A:XCC703
|
2.3
|
25.3
|
0.5
|
FE4
|
A:XCC703
|
2.6
|
30.2
|
0.5
|
FE3
|
A:XCC703
|
2.9
|
25.8
|
0.5
|
CB
|
A:CYS476
|
3.3
|
21.0
|
1.0
|
FE2
|
A:XCC703
|
3.4
|
24.9
|
0.5
|
SG
|
A:CYS294
|
3.7
|
20.9
|
0.4
|
O
|
A:HOH982
|
3.9
|
28.1
|
1.0
|
N
|
A:CYS476
|
4.1
|
14.6
|
1.0
|
O
|
A:HOH1201
|
4.1
|
23.8
|
0.6
|
S1
|
A:XCC703
|
4.2
|
29.9
|
0.5
|
SG
|
A:CYS294
|
4.2
|
21.7
|
0.6
|
NI
|
A:XCC703
|
4.3
|
27.2
|
0.5
|
CA
|
A:CYS476
|
4.3
|
15.6
|
1.0
|
CA
|
A:CYS446
|
4.5
|
17.2
|
1.0
|
CB
|
A:SER312
|
4.5
|
17.6
|
1.0
|
SG
|
A:CYS333
|
4.6
|
21.3
|
1.0
|
OG
|
A:SER312
|
4.7
|
18.6
|
1.0
|
O
|
A:GLY445
|
4.7
|
17.7
|
1.0
|
NE2
|
A:HIS261
|
4.7
|
26.2
|
1.0
|
CB
|
A:CYS294
|
4.7
|
16.3
|
0.6
|
SG
|
A:CYS295
|
4.8
|
22.3
|
1.0
|
CB
|
A:CYS333
|
4.8
|
17.7
|
1.0
|
CB
|
A:CYS446
|
4.8
|
13.9
|
1.0
|
SG
|
A:CYS526
|
4.9
|
18.2
|
0.5
|
CA
|
A:SER312
|
5.0
|
16.2
|
1.0
|
CB
|
A:CYS294
|
5.0
|
16.6
|
0.4
|
CE1
|
A:HIS261
|
5.0
|
22.3
|
1.0
|
|
Iron binding site 8 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 8 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:24.9
occ:0.49
|
FE2
|
A:XCC703
|
0.0
|
24.9
|
0.5
|
NE2
|
A:HIS261
|
1.7
|
26.2
|
1.0
|
S3
|
A:XCC703
|
2.2
|
26.2
|
0.5
|
O
|
A:HOH801
|
2.7
|
28.0
|
0.5
|
CD2
|
A:HIS261
|
2.7
|
19.2
|
1.0
|
SG
|
A:CYS295
|
2.7
|
22.3
|
1.0
|
CE1
|
A:HIS261
|
2.7
|
22.3
|
1.0
|
NI
|
A:XCC703
|
3.1
|
27.2
|
0.5
|
FE4
|
A:XCC703
|
3.1
|
30.2
|
0.5
|
SG
|
A:CYS526
|
3.3
|
18.2
|
0.5
|
CB
|
A:CYS295
|
3.3
|
15.6
|
1.0
|
FE1
|
A:XCC703
|
3.4
|
29.8
|
0.5
|
S4
|
A:XCC703
|
3.5
|
27.2
|
0.5
|
S1
|
A:XCC703
|
3.6
|
29.9
|
0.5
|
NZ
|
A:LYS563
|
3.8
|
19.5
|
1.0
|
CG
|
A:HIS261
|
3.8
|
16.4
|
1.0
|
ND1
|
A:HIS261
|
3.8
|
21.0
|
1.0
|
CB
|
A:CYS526
|
3.9
|
16.5
|
0.5
|
SG
|
A:CYS294
|
3.9
|
20.9
|
0.4
|
FE
|
A:FE704
|
3.9
|
22.1
|
0.5
|
CB
|
A:CYS526
|
4.0
|
16.4
|
0.5
|
SG
|
A:CYS526
|
4.1
|
31.7
|
0.5
|
FE3
|
A:XCC703
|
4.3
|
25.8
|
0.5
|
N
|
A:CYS295
|
4.3
|
15.7
|
1.0
|
SG
|
A:CYS333
|
4.4
|
21.3
|
1.0
|
CA
|
A:CYS295
|
4.4
|
14.6
|
1.0
|
O
|
A:HOH982
|
4.4
|
28.1
|
1.0
|
O
|
A:HOH1201
|
4.6
|
23.8
|
0.6
|
O
|
A:HOH1047
|
4.8
|
18.3
|
1.0
|
S2
|
A:XCC703
|
5.0
|
25.3
|
0.5
|
N
|
A:CYS526
|
5.0
|
14.8
|
1.0
|
|
Iron binding site 9 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 9 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:25.8
occ:0.49
|
FE3
|
A:XCC703
|
0.0
|
25.8
|
0.5
|
O
|
A:HOH1201
|
1.8
|
23.8
|
0.6
|
S1
|
A:XCC703
|
2.2
|
29.9
|
0.5
|
FE4
|
A:XCC703
|
2.3
|
30.2
|
0.5
|
S4
|
A:XCC703
|
2.3
|
27.2
|
0.5
|
S2
|
A:XCC703
|
2.4
|
25.3
|
0.5
|
SG
|
A:CYS446
|
2.6
|
20.6
|
1.0
|
FE1
|
A:XCC703
|
2.9
|
29.8
|
0.5
|
CB
|
A:CYS446
|
3.1
|
13.9
|
1.0
|
NI
|
A:XCC703
|
3.2
|
27.2
|
0.5
|
CA
|
A:CYS446
|
3.5
|
17.2
|
1.0
|
N
|
A:CYS446
|
3.8
|
18.2
|
1.0
|
FE
|
A:FE704
|
3.9
|
22.1
|
0.5
|
SG
|
A:CYS333
|
4.0
|
21.3
|
1.0
|
S3
|
A:XCC703
|
4.0
|
26.2
|
0.5
|
C
|
A:GLY445
|
4.2
|
16.9
|
1.0
|
FE2
|
A:XCC703
|
4.3
|
24.9
|
0.5
|
CB
|
A:HIS561
|
4.4
|
13.4
|
1.0
|
O
|
A:GLY445
|
4.6
|
17.7
|
1.0
|
CE
|
A:MET560
|
4.6
|
19.3
|
1.0
|
CA
|
A:GLY445
|
4.7
|
16.1
|
1.0
|
SG
|
A:CYS526
|
4.8
|
18.2
|
0.5
|
O
|
A:HOH801
|
4.9
|
28.0
|
0.5
|
SG
|
A:CYS476
|
4.9
|
23.6
|
1.0
|
C
|
A:CYS446
|
5.0
|
16.2
|
1.0
|
|
Iron binding site 10 out
of 11 in 9iyl
Go back to
Iron Binding Sites List in 9iyl
Iron binding site 10 out
of 11 in the CHCODH2 Wt
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of CHCODH2 Wt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe703
b:30.2
occ:0.49
|
FE4
|
A:XCC703
|
0.0
|
30.2
|
0.5
|
SG
|
A:CYS333
|
2.1
|
21.3
|
1.0
|
FE3
|
A:XCC703
|
2.3
|
25.8
|
0.5
|
S3
|
A:XCC703
|
2.3
|
26.2
|
0.5
|
S2
|
A:XCC703
|
2.4
|
25.3
|
0.5
|
S1
|
A:XCC703
|
2.4
|
29.9
|
0.5
|
FE1
|
A:XCC703
|
2.6
|
29.8
|
0.5
|
FE
|
A:FE704
|
3.0
|
22.1
|
0.5
|
CB
|
A:CYS333
|
3.0
|
17.7
|
1.0
|
FE2
|
A:XCC703
|
3.1
|
24.9
|
0.5
|
S4
|
A:XCC703
|
3.3
|
27.2
|
0.5
|
O
|
A:HOH1201
|
3.5
|
23.8
|
0.6
|
NE2
|
A:HIS261
|
3.7
|
26.2
|
1.0
|
CE1
|
A:HIS261
|
3.7
|
22.3
|
1.0
|
NI
|
A:XCC703
|
3.7
|
27.2
|
0.5
|
SG
|
A:CYS294
|
4.0
|
20.9
|
0.4
|
NZ
|
A:LYS563
|
4.0
|
19.5
|
1.0
|
O
|
A:HOH801
|
4.2
|
28.0
|
0.5
|
CA
|
A:CYS333
|
4.4
|
15.8
|
1.0
|
SG
|
A:CYS446
|
4.7
|
20.6
|
1.0
|
O
|
A:HOH933
|
4.7
|
21.9
|
1.0
|
CE
|
A:LYS563
|
4.8
|
16.8
|
1.0
|
CE
|
A:MET560
|
4.8
|
19.3
|
1.0
|
SG
|
A:CYS476
|
4.9
|
23.6
|
1.0
|
CB
|
A:HIS561
|
4.9
|
13.4
|
1.0
|
ND1
|
A:HIS261
|
5.0
|
21.0
|
1.0
|
|
Reference:
S.Y.Kong,
H.J.Yoon,
S.M.Kim,
H.H.Lee.
Air-Viable, Rapid Co Dehydrogenase with A Selectively Sealed Tunnel To Be Published.
Page generated: Sat Aug 23 03:20:13 2025
|