Iron in PDB 6q2d: Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
Enzymatic activity of Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
All present enzymatic activity of Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2:
2.5.1.108;
Protein crystallography data
The structure of Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2, PDB code: 6q2d
was solved by
M.K.Fenwick,
M.Dong,
H.Lin,
S.E.Ealick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.36 /
3.45
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.899,
322.979,
172.432,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.4 /
26.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
(pdb code 6q2d). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2, PDB code: 6q2d:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 1 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:0.6
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
0.6
|
1.0
|
S2
|
A:SF4401
|
2.2
|
0.1
|
1.0
|
S4
|
A:SF4401
|
2.3
|
0.0
|
1.0
|
S3
|
A:SF4401
|
2.3
|
0.5
|
1.0
|
SG
|
A:CYS61
|
2.5
|
0.8
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
0.5
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
0.1
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
0.4
|
1.0
|
CB
|
A:CYS61
|
3.5
|
0.1
|
1.0
|
S1
|
A:SF4401
|
3.8
|
0.3
|
1.0
|
N
|
A:CYS61
|
4.0
|
0.4
|
1.0
|
CA
|
A:GLY59
|
4.1
|
0.6
|
1.0
|
SG
|
A:CYS161
|
4.1
|
1.0
|
1.0
|
N
|
A:ALA60
|
4.2
|
0.8
|
1.0
|
CA
|
A:CYS61
|
4.4
|
0.1
|
1.0
|
C
|
A:GLY59
|
4.4
|
0.1
|
1.0
|
NE2
|
A:GLN242
|
4.7
|
0.3
|
1.0
|
N
|
A:GLY59
|
4.7
|
0.4
|
1.0
|
SG
|
A:CYS289
|
5.0
|
0.4
|
1.0
|
|
Iron binding site 2 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 2 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:0.1
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
0.1
|
1.0
|
SG
|
A:CYS161
|
1.6
|
1.0
|
1.0
|
S1
|
A:SF4401
|
2.2
|
0.3
|
1.0
|
S4
|
A:SF4401
|
2.2
|
0.0
|
1.0
|
S3
|
A:SF4401
|
2.3
|
0.5
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
0.5
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
0.4
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
0.6
|
1.0
|
CB
|
A:CYS161
|
3.2
|
0.2
|
1.0
|
N
|
A:CYS161
|
3.7
|
0.8
|
1.0
|
SG
|
A:CYS289
|
3.8
|
0.4
|
1.0
|
S2
|
A:SF4401
|
3.9
|
0.1
|
1.0
|
CA
|
A:CYS161
|
4.0
|
0.4
|
1.0
|
N
|
A:GLY160
|
4.6
|
0.2
|
1.0
|
C
|
A:GLY160
|
4.7
|
0.3
|
1.0
|
C
|
A:CYS161
|
4.7
|
0.4
|
1.0
|
CD1
|
A:ILE327
|
4.7
|
0.1
|
1.0
|
CB
|
A:LEU159
|
4.7
|
0.7
|
1.0
|
SG
|
A:CYS61
|
4.8
|
0.8
|
1.0
|
CB
|
A:CYS289
|
4.8
|
0.9
|
1.0
|
CA
|
A:GLY160
|
4.9
|
0.6
|
1.0
|
|
Iron binding site 3 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 3 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:0.5
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
0.5
|
1.0
|
S4
|
A:SF4401
|
2.1
|
0.0
|
1.0
|
S1
|
A:SF4401
|
2.3
|
0.3
|
1.0
|
S2
|
A:SF4401
|
2.3
|
0.1
|
1.0
|
SG
|
A:CYS289
|
2.5
|
0.4
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
0.1
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
0.6
|
1.0
|
FE4
|
A:SF4401
|
2.8
|
0.4
|
1.0
|
CB
|
A:CYS289
|
3.2
|
0.9
|
1.0
|
NE2
|
A:GLN242
|
3.7
|
0.3
|
1.0
|
SG
|
A:CYS61
|
3.7
|
0.8
|
1.0
|
SG
|
A:CYS161
|
3.8
|
1.0
|
1.0
|
S3
|
A:SF4401
|
3.9
|
0.5
|
1.0
|
CA
|
A:CYS289
|
4.5
|
0.6
|
1.0
|
CD
|
A:GLN242
|
4.6
|
0.1
|
1.0
|
CB
|
A:CYS161
|
4.9
|
0.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 4 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:0.4
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
0.4
|
1.0
|
S2
|
A:SF4401
|
2.3
|
0.1
|
1.0
|
S3
|
A:SF4401
|
2.3
|
0.5
|
1.0
|
S1
|
A:SF4401
|
2.3
|
0.3
|
1.0
|
FE2
|
A:SF4401
|
2.7
|
0.1
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
0.6
|
1.0
|
FE3
|
A:SF4401
|
2.8
|
0.5
|
1.0
|
S4
|
A:SF4401
|
3.9
|
0.0
|
1.0
|
SG
|
A:CYS161
|
4.3
|
1.0
|
1.0
|
N
|
A:GLY160
|
4.5
|
0.2
|
1.0
|
O
|
A:PHE58
|
4.5
|
1.0
|
1.0
|
NH1
|
A:ARG291
|
4.6
|
0.7
|
1.0
|
SG
|
A:CYS289
|
4.6
|
0.4
|
1.0
|
CA
|
A:GLY59
|
4.8
|
0.6
|
1.0
|
CB
|
A:LEU159
|
4.9
|
0.7
|
1.0
|
SG
|
A:CYS61
|
5.0
|
0.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 5 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:1.0
occ:1.00
|
FE1
|
B:SF4401
|
0.0
|
1.0
|
1.0
|
S2
|
B:SF4401
|
2.2
|
0.3
|
1.0
|
S4
|
B:SF4401
|
2.3
|
0.9
|
1.0
|
S3
|
B:SF4401
|
2.3
|
0.7
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
0.5
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
0.9
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
0.6
|
1.0
|
SG
|
B:CYS61
|
2.8
|
0.1
|
1.0
|
CB
|
B:CYS61
|
3.4
|
0.8
|
1.0
|
S1
|
B:SF4401
|
3.8
|
0.5
|
1.0
|
N
|
B:CYS61
|
4.5
|
0.2
|
1.0
|
CA
|
B:CYS61
|
4.6
|
0.4
|
1.0
|
SG
|
B:CYS161
|
4.7
|
0.1
|
1.0
|
CA
|
B:GLY59
|
4.7
|
0.6
|
1.0
|
|
Iron binding site 6 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 6 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:0.9
occ:1.00
|
FE2
|
B:SF4401
|
0.0
|
0.9
|
1.0
|
S1
|
B:SF4401
|
2.2
|
0.5
|
1.0
|
SG
|
B:CYS161
|
2.2
|
0.1
|
1.0
|
S4
|
B:SF4401
|
2.3
|
0.9
|
1.0
|
S3
|
B:SF4401
|
2.3
|
0.7
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
0.5
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
0.6
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
1.0
|
1.0
|
CB
|
B:CYS161
|
3.6
|
0.3
|
1.0
|
N
|
B:CYS161
|
3.7
|
0.5
|
1.0
|
S2
|
B:SF4401
|
3.9
|
0.3
|
1.0
|
CA
|
B:CYS161
|
4.3
|
0.4
|
1.0
|
CD1
|
B:ILE327
|
4.5
|
0.2
|
1.0
|
C
|
B:GLY160
|
4.5
|
0.4
|
1.0
|
SG
|
B:CYS289
|
4.7
|
0.7
|
1.0
|
N
|
B:GLY160
|
4.8
|
0.9
|
1.0
|
CA
|
B:GLY160
|
4.8
|
0.3
|
1.0
|
CD2
|
B:LEU159
|
4.9
|
0.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 7 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:0.5
occ:1.00
|
FE3
|
B:SF4401
|
0.0
|
0.5
|
1.0
|
S4
|
B:SF4401
|
2.1
|
0.9
|
1.0
|
S1
|
B:SF4401
|
2.3
|
0.5
|
1.0
|
S2
|
B:SF4401
|
2.3
|
0.3
|
1.0
|
SG
|
B:CYS289
|
2.4
|
0.7
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
1.0
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
0.9
|
1.0
|
FE4
|
B:SF4401
|
2.8
|
0.6
|
1.0
|
CB
|
B:CYS289
|
3.2
|
0.1
|
1.0
|
S3
|
B:SF4401
|
3.9
|
0.7
|
1.0
|
SG
|
B:CYS161
|
4.1
|
0.1
|
1.0
|
CA
|
B:CYS289
|
4.1
|
1.0
|
1.0
|
CG
|
B:ARG291
|
4.4
|
0.6
|
1.0
|
CD
|
B:ARG291
|
4.4
|
0.9
|
1.0
|
CD1
|
B:ILE327
|
4.8
|
0.2
|
1.0
|
CB
|
B:ARG291
|
4.8
|
0.4
|
1.0
|
CD
|
B:PRO290
|
4.8
|
0.8
|
1.0
|
C
|
B:CYS289
|
4.8
|
0.8
|
1.0
|
SG
|
B:CYS61
|
4.9
|
0.1
|
1.0
|
N
|
B:ARG291
|
5.0
|
0.5
|
1.0
|
|
Iron binding site 8 out
of 8 in 6q2d
Go back to
Iron Binding Sites List in 6q2d
Iron binding site 8 out
of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2
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 Methanobrevibacter Smithii DPH2 in Complex with Methanobrevibacter Smithii Elongation Factor 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:0.6
occ:1.00
|
FE4
|
B:SF4401
|
0.0
|
0.6
|
1.0
|
S2
|
B:SF4401
|
2.3
|
0.3
|
1.0
|
S3
|
B:SF4401
|
2.3
|
0.7
|
1.0
|
S1
|
B:SF4401
|
2.3
|
0.5
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
0.9
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
1.0
|
1.0
|
FE3
|
B:SF4401
|
2.8
|
0.5
|
1.0
|
S4
|
B:SF4401
|
3.9
|
0.9
|
1.0
|
CD
|
B:ARG291
|
4.1
|
0.9
|
1.0
|
N
|
B:GLY160
|
4.5
|
0.9
|
1.0
|
NH1
|
B:ARG291
|
4.6
|
0.9
|
1.0
|
CA
|
B:GLY160
|
4.6
|
0.3
|
1.0
|
SG
|
B:CYS161
|
4.8
|
0.1
|
1.0
|
SG
|
B:CYS289
|
4.8
|
0.7
|
1.0
|
CG
|
B:ARG291
|
4.9
|
0.6
|
1.0
|
N
|
B:CYS161
|
5.0
|
0.5
|
1.0
|
|
Reference:
M.K.Fenwick,
M.Dong,
H.Lin,
S.E.Ealick.
The Crystal Structure of DPH2 in Complex with Elongation Factor 2 Reveals the Structural Basis For the First Step of Diphthamide Biosynthesis. Biochemistry V. 58 4343 2019.
ISSN: ISSN 0006-2960
PubMed: 31566354
DOI: 10.1021/ACS.BIOCHEM.9B00718
Page generated: Wed Aug 7 06:49:31 2024
|