Iron in PDB 6tjr: Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Protein crystallography data
The structure of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans, PDB code: 6tjr
was solved by
K.Kayastha,
U.Ermler,
C.Dahl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.67 /
1.43
|
Space group
|
P 65
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.620,
145.620,
64.100,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.3 /
17.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
(pdb code 6tjr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans, PDB code: 6tjr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 1 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:14.1
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
14.1
|
1.0
|
S2
|
A:SF4401
|
2.3
|
14.1
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.7
|
1.0
|
S3
|
A:SF4401
|
2.3
|
13.5
|
1.0
|
SG
|
A:CYS180
|
2.3
|
15.3
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
14.3
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
14.6
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
15.2
|
1.0
|
CB
|
A:CYS180
|
3.2
|
12.9
|
1.0
|
N
|
A:CYS180
|
3.9
|
12.0
|
1.0
|
CA
|
A:CYS180
|
3.9
|
12.2
|
1.0
|
S1
|
A:SF4401
|
3.9
|
15.4
|
1.0
|
N
|
A:CYS181
|
4.0
|
14.4
|
1.0
|
O
|
A:HOH544
|
4.0
|
16.3
|
1.0
|
N
|
A:LYS178
|
4.1
|
13.4
|
1.0
|
C
|
A:CYS180
|
4.2
|
15.8
|
1.0
|
N
|
A:SER177
|
4.2
|
13.7
|
1.0
|
C
|
A:SER177
|
4.4
|
15.0
|
1.0
|
CB
|
A:SER177
|
4.5
|
13.7
|
1.0
|
CA
|
A:SER177
|
4.5
|
13.1
|
1.0
|
SG
|
A:CYS176
|
4.5
|
14.8
|
1.0
|
SG
|
A:CYS181
|
4.8
|
14.7
|
1.0
|
N
|
A:CYS163
|
4.8
|
16.1
|
1.0
|
SG
|
A:CYS163
|
4.9
|
16.1
|
1.0
|
N
|
A:ILE179
|
4.9
|
12.9
|
1.0
|
C
|
A:LYS178
|
4.9
|
15.3
|
1.0
|
CA
|
A:LYS178
|
5.0
|
13.2
|
1.0
|
CA
|
A:CYS163
|
5.0
|
15.2
|
1.0
|
CA
|
A:CYS181
|
5.0
|
12.5
|
1.0
|
|
Iron binding site 2 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 2 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:14.3
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
14.3
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.4
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.7
|
1.0
|
S3
|
A:SF4401
|
2.3
|
13.5
|
1.0
|
SG
|
A:CYS176
|
2.3
|
14.8
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
14.1
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
15.2
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
14.6
|
1.0
|
CB
|
A:CYS176
|
3.5
|
13.8
|
1.0
|
S2
|
A:SF4401
|
3.9
|
14.1
|
1.0
|
CD
|
A:ARG208
|
4.0
|
15.0
|
1.0
|
N
|
A:SER177
|
4.0
|
13.7
|
1.0
|
N
|
A:LYS178
|
4.0
|
13.4
|
1.0
|
CA
|
A:CYS176
|
4.1
|
13.1
|
1.0
|
CD
|
A:ARG167
|
4.1
|
17.2
|
1.0
|
NH1
|
A:ARG208
|
4.2
|
15.2
|
1.0
|
C
|
A:CYS176
|
4.3
|
15.3
|
1.0
|
CA
|
A:LYS178
|
4.6
|
13.2
|
1.0
|
CG
|
A:ARG208
|
4.6
|
14.7
|
1.0
|
NE
|
A:ARG208
|
4.7
|
15.6
|
1.0
|
SG
|
A:CYS163
|
4.7
|
16.1
|
1.0
|
SG
|
A:CYS180
|
4.8
|
15.3
|
1.0
|
CG
|
A:ARG167
|
4.8
|
17.2
|
1.0
|
C
|
A:SER177
|
4.8
|
15.0
|
1.0
|
CZ
|
A:ARG208
|
4.8
|
17.2
|
1.0
|
SG
|
A:CYS181
|
4.9
|
14.7
|
1.0
|
CA
|
A:SER177
|
4.9
|
13.1
|
1.0
|
CB
|
A:ARG208
|
4.9
|
14.5
|
1.0
|
|
Iron binding site 3 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 3 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:15.2
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
15.2
|
1.0
|
SG
|
A:CYS163
|
2.3
|
16.1
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.7
|
1.0
|
S2
|
A:SF4401
|
2.3
|
14.1
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.4
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
14.3
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
14.6
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
14.1
|
1.0
|
CB
|
A:CYS163
|
3.4
|
15.5
|
1.0
|
CA
|
A:CYS163
|
3.5
|
15.2
|
1.0
|
N
|
A:CYS163
|
3.6
|
16.1
|
1.0
|
O
|
A:HOH648
|
3.9
|
17.4
|
1.0
|
S3
|
A:SF4401
|
3.9
|
13.5
|
1.0
|
CD
|
A:ARG167
|
4.0
|
17.2
|
1.0
|
CB
|
A:LEU162
|
4.6
|
14.6
|
1.0
|
C
|
A:LEU162
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH544
|
4.6
|
16.3
|
1.0
|
CG
|
A:ARG167
|
4.6
|
17.2
|
1.0
|
SG
|
A:CYS181
|
4.7
|
14.7
|
1.0
|
NH1
|
A:ARG167
|
4.8
|
19.7
|
1.0
|
SG
|
A:CYS180
|
4.8
|
15.3
|
1.0
|
SG
|
A:CYS176
|
4.9
|
14.8
|
1.0
|
CB
|
A:SER166
|
5.0
|
17.7
|
1.0
|
|
Iron binding site 4 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 4 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:14.6
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
14.6
|
1.0
|
S3
|
A:SF4401
|
2.3
|
13.5
|
1.0
|
SG
|
A:CYS181
|
2.3
|
14.7
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.4
|
1.0
|
S2
|
A:SF4401
|
2.3
|
14.1
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
14.1
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
15.2
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
14.3
|
1.0
|
CB
|
A:CYS181
|
3.3
|
12.8
|
1.0
|
N
|
A:CYS181
|
3.6
|
14.4
|
1.0
|
CA
|
A:CYS181
|
3.8
|
12.5
|
1.0
|
S4
|
A:SF4401
|
3.9
|
15.7
|
1.0
|
CB
|
A:ARG208
|
4.3
|
14.5
|
1.0
|
O
|
A:ASP206
|
4.4
|
17.6
|
1.0
|
CG
|
A:ARG208
|
4.4
|
14.7
|
1.0
|
O
|
A:HOH648
|
4.4
|
17.4
|
1.0
|
C
|
A:CYS180
|
4.5
|
15.8
|
1.0
|
SG
|
A:CYS163
|
4.6
|
16.1
|
1.0
|
CD
|
A:ARG208
|
4.6
|
15.0
|
1.0
|
CD1
|
A:LEU162
|
4.7
|
16.1
|
1.0
|
N
|
A:ARG208
|
4.7
|
14.0
|
1.0
|
SG
|
A:CYS180
|
4.8
|
15.3
|
1.0
|
SG
|
A:CYS176
|
4.9
|
14.8
|
1.0
|
CB
|
A:CYS180
|
5.0
|
12.9
|
1.0
|
|
Iron binding site 5 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 5 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.1
occ:1.00
|
FE1
|
B:SF4401
|
0.0
|
16.1
|
1.0
|
S3
|
B:SF4401
|
2.3
|
14.7
|
1.0
|
SG
|
B:CYS181
|
2.3
|
17.5
|
1.0
|
S2
|
B:SF4401
|
2.3
|
16.1
|
1.0
|
S4
|
B:SF4401
|
2.3
|
16.8
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
16.9
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
16.2
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
15.7
|
1.0
|
CB
|
B:CYS181
|
3.3
|
15.4
|
1.0
|
N
|
B:CYS181
|
3.6
|
15.5
|
1.0
|
CA
|
B:CYS181
|
3.8
|
16.1
|
1.0
|
S1
|
B:SF4401
|
3.9
|
16.5
|
1.0
|
CB
|
B:ARG208
|
4.3
|
14.0
|
1.0
|
CG
|
B:ARG208
|
4.3
|
15.8
|
1.0
|
O
|
B:ASP206
|
4.4
|
19.5
|
1.0
|
O
|
B:HOH575
|
4.4
|
20.9
|
1.0
|
C
|
B:CYS180
|
4.5
|
19.1
|
1.0
|
CD
|
B:ARG208
|
4.6
|
15.8
|
1.0
|
SG
|
B:CYS163
|
4.6
|
18.8
|
1.0
|
CD1
|
B:LEU162
|
4.7
|
20.9
|
1.0
|
N
|
B:ARG208
|
4.7
|
15.2
|
1.0
|
SG
|
B:CYS180
|
4.8
|
17.2
|
1.0
|
SG
|
B:CYS176
|
4.8
|
15.7
|
1.0
|
CB
|
B:CYS180
|
5.0
|
16.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 6 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.2
occ:1.00
|
FE2
|
B:SF4401
|
0.0
|
16.2
|
1.0
|
S4
|
B:SF4401
|
2.3
|
16.8
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
SG
|
B:CYS180
|
2.3
|
17.2
|
1.0
|
S3
|
B:SF4401
|
2.3
|
14.7
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
15.7
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
16.1
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
16.9
|
1.0
|
CB
|
B:CYS180
|
3.2
|
16.2
|
1.0
|
N
|
B:CYS180
|
3.9
|
14.5
|
1.0
|
S2
|
B:SF4401
|
3.9
|
16.1
|
1.0
|
CA
|
B:CYS180
|
3.9
|
15.2
|
1.0
|
N
|
B:CYS181
|
4.0
|
15.5
|
1.0
|
O
|
B:HOH533
|
4.0
|
18.0
|
1.0
|
N
|
B:LYS178
|
4.2
|
14.9
|
1.0
|
N
|
B:SER177
|
4.2
|
15.2
|
1.0
|
C
|
B:CYS180
|
4.2
|
19.1
|
1.0
|
C
|
B:SER177
|
4.4
|
17.2
|
1.0
|
CB
|
B:SER177
|
4.4
|
14.7
|
1.0
|
CA
|
B:SER177
|
4.5
|
14.4
|
1.0
|
SG
|
B:CYS176
|
4.5
|
15.7
|
1.0
|
N
|
B:CYS163
|
4.8
|
17.7
|
1.0
|
SG
|
B:CYS181
|
4.8
|
17.5
|
1.0
|
SG
|
B:CYS163
|
4.9
|
18.8
|
1.0
|
CA
|
B:CYS163
|
4.9
|
18.2
|
1.0
|
N
|
B:ILE179
|
4.9
|
14.7
|
1.0
|
C
|
B:LYS178
|
5.0
|
16.3
|
1.0
|
CA
|
B:LYS178
|
5.0
|
14.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 7 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:16.9
occ:1.00
|
FE3
|
B:SF4401
|
0.0
|
16.9
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
SG
|
B:CYS163
|
2.3
|
18.8
|
1.0
|
S2
|
B:SF4401
|
2.3
|
16.1
|
1.0
|
S4
|
B:SF4401
|
2.3
|
16.8
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
15.7
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
16.1
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
16.2
|
1.0
|
CB
|
B:CYS163
|
3.4
|
17.6
|
1.0
|
CA
|
B:CYS163
|
3.5
|
18.2
|
1.0
|
N
|
B:CYS163
|
3.6
|
17.7
|
1.0
|
O
|
B:HOH575
|
3.9
|
20.9
|
1.0
|
S3
|
B:SF4401
|
3.9
|
14.7
|
1.0
|
CD
|
B:ARG167
|
4.0
|
19.2
|
1.0
|
C
|
B:LEU162
|
4.6
|
21.0
|
1.0
|
CB
|
B:LEU162
|
4.6
|
17.4
|
1.0
|
CG
|
B:ARG167
|
4.7
|
18.2
|
1.0
|
O
|
B:HOH533
|
4.7
|
18.0
|
1.0
|
SG
|
B:CYS181
|
4.7
|
17.5
|
1.0
|
NH1
|
B:ARG167
|
4.8
|
19.2
|
1.0
|
SG
|
B:CYS180
|
4.8
|
17.2
|
1.0
|
SG
|
B:CYS176
|
4.9
|
15.7
|
1.0
|
C
|
B:CYS163
|
5.0
|
21.7
|
1.0
|
|
Iron binding site 8 out
of 8 in 6tjr
Go back to
Iron Binding Sites List in 6tjr
Iron binding site 8 out
of 8 in the Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Structure of Hdra-Like Subunit From Hyphomicrobium Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:15.7
occ:1.00
|
FE4
|
B:SF4401
|
0.0
|
15.7
|
1.0
|
S2
|
B:SF4401
|
2.3
|
16.1
|
1.0
|
S1
|
B:SF4401
|
2.3
|
16.5
|
1.0
|
S3
|
B:SF4401
|
2.3
|
14.7
|
1.0
|
SG
|
B:CYS176
|
2.3
|
15.7
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
16.2
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
16.9
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
16.1
|
1.0
|
CB
|
B:CYS176
|
3.5
|
15.2
|
1.0
|
S4
|
B:SF4401
|
3.9
|
16.8
|
1.0
|
N
|
B:SER177
|
3.9
|
15.2
|
1.0
|
CD
|
B:ARG208
|
4.0
|
15.8
|
1.0
|
N
|
B:LYS178
|
4.0
|
14.9
|
1.0
|
CA
|
B:CYS176
|
4.0
|
15.6
|
1.0
|
CD
|
B:ARG167
|
4.2
|
19.2
|
1.0
|
NH1
|
B:ARG208
|
4.2
|
16.2
|
1.0
|
C
|
B:CYS176
|
4.3
|
17.3
|
1.0
|
CA
|
B:LYS178
|
4.6
|
14.7
|
1.0
|
CG
|
B:ARG208
|
4.6
|
15.8
|
1.0
|
NE
|
B:ARG208
|
4.7
|
14.2
|
1.0
|
SG
|
B:CYS163
|
4.7
|
18.8
|
1.0
|
SG
|
B:CYS180
|
4.7
|
17.2
|
1.0
|
C
|
B:SER177
|
4.8
|
17.2
|
1.0
|
CG
|
B:ARG167
|
4.8
|
18.2
|
1.0
|
CZ
|
B:ARG208
|
4.8
|
17.0
|
1.0
|
CA
|
B:SER177
|
4.9
|
14.4
|
1.0
|
SG
|
B:CYS181
|
4.9
|
17.5
|
1.0
|
CB
|
B:ARG208
|
4.9
|
14.0
|
1.0
|
|
Reference:
C.Ernst,
K.Kayastha,
T.Koch,
S.S.Venceslau,
I.A.C.Pereira,
U.Demmer,
U.Ermler,
C.Dahl.
Structural and Spectroscopic Characterization of A Hdra-Like Subunit From Hyphomicrobium Denitrificans. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32750208
DOI: 10.1111/FEBS.15505
Page generated: Wed Aug 7 10:52:47 2024
|