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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

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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

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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

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