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Iron in PDB 6q2e: Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine

Enzymatic activity of Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine

All present enzymatic activity of Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine:
2.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine, PDB code: 6q2e 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) 68.90 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.082, 81.020, 130.972, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 6q2e:

The structure of Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine (pdb code 6q2e). 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 Bound to 5'- Methylthioadenosine, PDB code: 6q2e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 1 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:28.1
occ:1.00
 FE1 A:SF4402 0.0 28.1 1.0
S2 A:SF4402 2.2 28.4 1.0
S4 A:SF4402 2.3 23.5 1.0
SG A:CYS61 2.3 32.9 1.0
S3 A:SF4402 2.3 31.0 1.0
FE3 A:SF4402 2.7 27.4 1.0
FE2 A:SF4402 2.7 31.8 1.0
FE4 A:SF4402 2.8 33.4 1.0
CB A:CYS61 3.4 33.6 1.0
S1 A:SF4402 3.8 27.4 1.0
NE2 A:GLN242 4.0 23.3 1.0
CA A:GLY59 4.5 28.6 1.0
N A:CYS61 4.5 33.2 1.0
CA A:CYS61 4.6 31.8 1.0
CG A:GLN242 4.7 26.0 1.0
SG A:CYS289 4.7 27.5 1.0
N A:GLY59 4.7 28.7 1.0
SG A:CYS161 4.8 39.6 1.0
CD A:GLN242 4.8 23.9 1.0
O A:HOH585 4.8 35.6 1.0
O A:PHE58 4.9 30.2 1.0
C A:PHE58 4.9 30.8 1.0

Iron binding site 2 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 2 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:31.8
occ:1.00
 FE2 A:SF4402 0.0 31.8 1.0
S1 A:SF4402 2.2 27.4 1.0
S4 A:SF4402 2.2 23.5 1.0
SG A:CYS161 2.3 39.6 1.0
S3 A:SF4402 2.3 31.0 1.0
FE3 A:SF4402 2.6 27.4 1.0
FE1 A:SF4402 2.7 28.1 1.0
FE4 A:SF4402 2.7 33.4 1.0
CB A:CYS161 3.2 33.8 1.0
S2 A:SF4402 3.8 28.4 1.0
N A:CYS161 3.9 39.4 1.0
CA A:CYS161 4.2 33.4 1.0
C A:GLY160 4.6 42.3 1.0
SG A:CYS289 4.7 27.5 1.0
CD A:PRO290 4.7 29.5 1.0
N A:GLY160 4.8 30.4 1.0
SG A:CYS61 4.8 32.9 1.0
CA A:GLY160 4.9 31.9 1.0

Iron binding site 3 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 3 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:27.4
occ:1.00
 FE3 A:SF4402 0.0 27.4 1.0
S4 A:SF4402 2.1 23.5 1.0
S1 A:SF4402 2.3 27.4 1.0
SG A:CYS289 2.3 27.5 1.0
S2 A:SF4402 2.3 28.4 1.0
FE2 A:SF4402 2.6 31.8 1.0
FE1 A:SF4402 2.7 28.1 1.0
FE4 A:SF4402 2.8 33.4 1.0
CB A:CYS289 3.3 24.7 1.0
S3 A:SF4402 3.9 31.0 1.0
CA A:CYS289 3.9 24.0 1.0
CD A:PRO290 4.3 29.5 1.0
NE2 A:GLN242 4.3 23.3 1.0
C8 A:MTA401 4.5 23.3 1.0
C A:CYS289 4.6 28.9 1.0
N A:PRO290 4.6 24.5 1.0
SG A:CYS61 4.7 32.9 1.0
CG A:ARG291 4.7 36.2 1.0
C5' A:MTA401 4.7 46.3 1.0
SG A:CYS161 4.7 39.6 1.0
N7 A:MTA401 4.7 24.4 1.0
CD A:ARG291 4.8 38.2 1.0
N A:ARG291 4.9 30.8 1.0
CB A:CYS161 4.9 33.8 1.0
CD A:GLN242 4.9 23.9 1.0
CB A:ARG291 5.0 29.1 1.0

Iron binding site 4 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 4 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:33.4
occ:1.00
 FE4 A:SF4402 0.0 33.4 1.0
S2 A:SF4402 2.3 28.4 1.0
S1 A:SF4402 2.3 27.4 1.0
S3 A:SF4402 2.3 31.0 1.0
FE2 A:SF4402 2.7 31.8 1.0
FE1 A:SF4402 2.8 28.1 1.0
FE3 A:SF4402 2.8 27.4 1.0
S4 A:SF4402 3.9 23.5 1.0
O A:HOH789 4.3 98.3 1.0
O A:PHE58 4.3 30.2 1.0
S5' A:MTA401 4.6 59.4 1.0
N A:GLY160 4.6 30.4 1.0
O A:HOH585 4.7 35.6 1.0
SG A:CYS161 4.7 39.6 1.0
C5' A:MTA401 4.7 46.3 1.0
CD A:ARG291 4.8 38.2 1.0
SG A:CYS61 4.8 32.9 1.0
SG A:CYS289 4.9 27.5 1.0
CA A:GLY160 4.9 31.9 1.0
CA A:GLY59 4.9 28.6 1.0

Iron binding site 5 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 5 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:34.3
occ:1.00
 FE1 B:SF4402 0.0 34.3 1.0
S2 B:SF4402 2.3 38.8 1.0
SG B:CYS61 2.3 51.0 1.0
S4 B:SF4402 2.3 25.7 1.0
S3 B:SF4402 2.3 38.1 1.0
FE3 B:SF4402 2.6 33.0 1.0
FE4 B:SF4402 2.8 40.7 1.0
FE2 B:SF4402 2.8 34.8 1.0
CB B:CYS61 3.2 52.7 1.0
S1 B:SF4402 3.9 33.1 1.0
NE2 B:GLN242 4.0 31.0 1.0
N B:CYS61 4.4 51.0 1.0
CA B:GLY59 4.4 42.6 1.0
CA B:CYS61 4.4 56.6 1.0
SG B:CYS289 4.6 31.9 1.0
SG B:CYS161 4.6 41.5 1.0
CG B:GLN242 4.7 31.7 1.0
CD B:GLN242 4.8 29.6 1.0
O B:HOH603 4.8 38.5 1.0
N B:GLY59 4.8 43.9 1.0
CB B:CYS289 4.8 29.4 1.0
O B:PHE58 5.0 47.1 1.0
C B:GLY59 5.0 48.3 1.0

Iron binding site 6 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 6 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:34.8
occ:1.00
 FE2 B:SF4402 0.0 34.8 1.0
SG B:CYS161 2.1 41.5 1.0
S1 B:SF4402 2.2 33.1 1.0
S4 B:SF4402 2.2 25.7 1.0
S3 B:SF4402 2.3 38.1 1.0
FE3 B:SF4402 2.6 33.0 1.0
FE4 B:SF4402 2.7 40.7 1.0
FE1 B:SF4402 2.8 34.3 1.0
CB B:CYS161 3.4 29.8 1.0
N B:CYS161 3.9 40.9 1.0
S2 B:SF4402 3.9 38.8 1.0
O B:HOH603 4.1 38.5 1.0
CA B:CYS161 4.3 34.4 1.0
C B:GLY160 4.6 43.1 1.0
SG B:CYS289 4.6 31.9 1.0
CD B:PRO290 4.7 34.1 1.0
N B:GLY160 4.8 34.8 1.0
CA B:GLY160 4.9 35.5 1.0
SG B:CYS61 4.9 51.0 1.0

Iron binding site 7 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 7 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:33.0
occ:1.00
 FE3 B:SF4402 0.0 33.0 1.0
S4 B:SF4402 2.1 25.7 1.0
SG B:CYS289 2.2 31.9 1.0
S1 B:SF4402 2.3 33.1 1.0
S2 B:SF4402 2.3 38.8 1.0
FE1 B:SF4402 2.6 34.3 1.0
FE2 B:SF4402 2.6 34.8 1.0
FE4 B:SF4402 2.8 40.7 1.0
CB B:CYS289 3.2 29.4 1.0
S3 B:SF4402 3.8 38.1 1.0
CA B:CYS289 4.0 28.5 1.0
CD B:PRO290 4.3 34.1 1.0
SG B:CYS161 4.5 41.5 1.0
NE2 B:GLN242 4.5 31.0 1.0
C B:CYS289 4.5 31.5 1.0
N B:PRO290 4.6 28.6 1.0
C8 B:MTA401 4.6 31.3 1.0
CG B:ARG291 4.6 34.1 1.0
CD B:ARG291 4.7 37.9 1.0
SG B:CYS61 4.7 51.0 1.0
N B:ARG291 4.8 28.8 1.0
CB B:ARG291 4.8 32.9 1.0
N7 B:MTA401 4.9 27.4 1.0

Iron binding site 8 out of 8 in 6q2e

Go back to Iron Binding Sites List in 6q2e
Iron binding site 8 out of 8 in the Crystal Structure of Methanobrevibacter Smithii DPH2 Bound to 5'- Methylthioadenosine


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 Bound to 5'- Methylthioadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:40.7
occ:1.00
 FE4 B:SF4402 0.0 40.7 1.0
S3 B:SF4402 2.3 38.1 1.0
S2 B:SF4402 2.3 38.8 1.0
S1 B:SF4402 2.3 33.1 1.0
FE2 B:SF4402 2.7 34.8 1.0
FE1 B:SF4402 2.8 34.3 1.0
FE3 B:SF4402 2.8 33.0 1.0
S4 B:SF4402 3.8 25.7 1.0
O B:PHE58 4.4 47.1 1.0
CD B:ARG291 4.6 37.9 1.0
SG B:CYS161 4.6 41.5 1.0
N B:GLY160 4.7 34.8 1.0
S5' B:MTA401 4.7 66.2 1.0
SG B:CYS289 4.7 31.9 1.0
SG B:CYS61 4.8 51.0 1.0
CA B:GLY59 4.8 42.6 1.0
C5' B:MTA401 4.9 65.4 1.0
CA B:GLY160 4.9 35.5 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: Sun Dec 13 16:50:06 2020

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