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Iron in PDB 4y4n: Thiazole Synthase THI4 From Methanococcus Igneus

Enzymatic activity of Thiazole Synthase THI4 From Methanococcus Igneus

All present enzymatic activity of Thiazole Synthase THI4 From Methanococcus Igneus:
5.3.1.29;

Protein crystallography data

The structure of Thiazole Synthase THI4 From Methanococcus Igneus, PDB code: 4y4n was solved by X.Zhang, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 101.302, 101.302, 204.309, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 21.6

Iron Binding Sites:

The binding sites of Iron atom in the Thiazole Synthase THI4 From Methanococcus Igneus (pdb code 4y4n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Thiazole Synthase THI4 From Methanococcus Igneus, PDB code: 4y4n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4y4n

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Iron binding site 1 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:39.2
occ:1.00
 O10 A:48H302 2.0 38.1 1.0
O8 A:48H302 2.0 35.0 1.0
OD1 C:ASP161 2.1 42.8 1.0
N1 A:48H302 2.1 36.5 1.0
O A:HOH401 2.2 44.8 1.0
NE2 A:HIS176 2.2 39.1 1.0
C12 A:48H302 2.8 38.6 1.0
C8 A:48H302 2.8 36.1 1.0
C9 A:48H302 2.9 36.5 1.0
C11 A:48H302 3.0 37.4 1.0
CE1 A:HIS176 3.1 38.5 1.0
CG C:ASP161 3.2 41.5 1.0
CD2 A:HIS176 3.2 38.1 1.0
O A:HOH402 3.5 38.4 1.0
OD2 C:ASP161 3.8 42.3 1.0
O9 A:48H302 4.0 40.3 1.0
O A:HOH427 4.2 40.1 1.0
ND1 A:HIS176 4.3 40.0 1.0
C7 A:48H302 4.3 35.1 1.0
CG A:HIS176 4.3 38.9 1.0
C10 A:48H302 4.4 37.6 1.0
CB C:ASP161 4.4 41.1 1.0
NH2 A:ARG236 4.5 44.8 1.0
O7 A:48H302 4.7 37.3 1.0
CA C:ASP161 4.8 39.3 1.0
C6 A:48H302 4.9 33.7 1.0

Iron binding site 2 out of 8 in 4y4n

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Iron binding site 2 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:42.3
occ:1.00
 OD1 A:ASP161 2.1 44.8 1.0
O8 A:48H304 2.1 41.8 1.0
N1 A:48H304 2.2 43.3 1.0
O A:HOH403 2.2 38.6 1.0
O9 A:48H304 2.2 42.7 1.0
NE2 H:HIS176 2.2 42.7 1.0
C8 A:48H304 2.9 41.0 1.0
C9 A:48H304 2.9 41.9 1.0
C12 A:48H304 3.0 42.7 1.0
C11 A:48H304 3.1 45.4 1.0
CE1 H:HIS176 3.2 43.9 1.0
CG A:ASP161 3.2 43.1 1.0
CD2 H:HIS176 3.2 44.1 1.0
O A:HOH431 3.4 40.4 1.0
OD2 A:ASP161 3.8 47.5 1.0
O10 A:48H304 4.2 44.3 1.0
ND1 H:HIS176 4.3 44.5 1.0
C7 A:48H304 4.3 38.0 1.0
CG H:HIS176 4.3 43.0 1.0
C10 A:48H304 4.4 43.9 1.0
CB A:ASP161 4.4 41.5 1.0
NH2 H:ARG236 4.5 41.1 1.0
O7 A:48H304 4.8 39.3 1.0
CA A:ASP161 4.8 40.7 1.0
C6 A:48H304 4.9 36.9 1.0

Iron binding site 3 out of 8 in 4y4n

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Iron binding site 3 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:39.7
occ:1.00
 O8 B:48H302 2.0 36.4 1.0
OD1 D:ASP161 2.1 40.0 1.0
N1 B:48H302 2.1 39.7 1.0
O D:HOH405 2.2 37.6 1.0
O10 B:48H302 2.2 39.9 1.0
NE2 B:HIS176 2.2 41.7 1.0
C8 B:48H302 2.8 38.4 1.0
C9 B:48H302 2.8 41.5 1.0
C12 B:48H302 3.0 41.7 1.0
C11 B:48H302 3.1 40.1 1.0
CE1 B:HIS176 3.2 44.1 1.0
CD2 B:HIS176 3.2 41.4 1.0
CG D:ASP161 3.2 37.6 1.0
O D:HOH406 3.3 37.4 1.0
OD2 D:ASP161 3.8 37.5 1.0
O9 B:48H302 4.2 46.1 1.0
C7 B:48H302 4.2 38.2 1.0
ND1 B:HIS176 4.3 44.2 1.0
O B:HOH421 4.3 33.7 1.0
C10 B:48H302 4.3 41.6 1.0
CG B:HIS176 4.3 41.9 1.0
CB D:ASP161 4.4 35.5 1.0
NH2 B:ARG236 4.5 34.7 1.0
O7 B:48H302 4.7 38.9 1.0
CA D:ASP161 4.8 36.3 1.0
C6 B:48H302 4.9 35.7 1.0

Iron binding site 4 out of 8 in 4y4n

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Iron binding site 4 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:39.5
occ:1.00
 O10 B:48H304 2.0 40.1 1.0
O8 B:48H304 2.1 36.5 1.0
O B:HOH426 2.1 43.2 1.0
N1 B:48H304 2.1 38.5 1.0
OD1 B:ASP161 2.1 41.9 1.0
NE2 G:HIS176 2.2 39.1 1.0
C12 B:48H304 2.8 40.4 1.0
C8 B:48H304 2.8 36.9 1.0
C9 B:48H304 2.9 37.5 1.0
C11 B:48H304 3.0 39.6 1.0
CE1 G:HIS176 3.1 39.1 1.0
CD2 G:HIS176 3.3 38.2 1.0
CG B:ASP161 3.3 41.8 1.0
O B:HOH427 3.5 35.6 1.0
OD2 B:ASP161 3.8 42.4 1.0
O9 B:48H304 4.0 44.5 1.0
C7 B:48H304 4.3 36.0 1.0
ND1 G:HIS176 4.3 40.7 1.0
C10 B:48H304 4.3 38.7 1.0
CG G:HIS176 4.4 38.7 1.0
CB B:ASP161 4.4 42.0 1.0
NH2 G:ARG236 4.5 43.5 1.0
O7 B:48H304 4.7 37.0 1.0
CA B:ASP161 4.8 39.5 1.0
C6 B:48H304 4.9 33.9 1.0

Iron binding site 5 out of 8 in 4y4n

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Iron binding site 5 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:40.3
occ:1.00
 O8 C:48H302 2.1 35.0 1.0
OD1 F:ASP161 2.1 40.4 1.0
O10 C:48H302 2.1 41.8 1.0
N1 C:48H302 2.1 40.5 1.0
O F:HOH405 2.2 32.5 1.0
NE2 C:HIS176 2.2 40.4 1.0
C8 C:48H302 2.8 37.9 1.0
C9 C:48H302 2.9 40.6 1.0
C12 C:48H302 3.0 42.2 1.0
C11 C:48H302 3.1 41.4 1.0
CE1 C:HIS176 3.1 41.3 1.0
CD2 C:HIS176 3.2 41.2 1.0
CG F:ASP161 3.2 38.9 1.0
O F:HOH406 3.4 37.8 1.0
OD2 F:ASP161 3.8 40.1 1.0
O9 C:48H302 4.2 45.4 1.0
C7 C:48H302 4.2 38.5 1.0
ND1 C:HIS176 4.2 41.6 1.0
CG C:HIS176 4.3 41.1 1.0
C10 C:48H302 4.3 41.9 1.0
CB F:ASP161 4.4 36.6 1.0
NH2 C:ARG236 4.5 33.8 1.0
O7 C:48H302 4.7 39.9 1.0
CA F:ASP161 4.8 36.9 1.0
C6 C:48H302 4.9 35.6 1.0

Iron binding site 6 out of 8 in 4y4n

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Iron binding site 6 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:41.6
occ:1.00
 O8 D:48H302 2.0 37.8 1.0
OD1 E:ASP161 2.1 42.2 1.0
O E:HOH401 2.1 43.6 1.0
N1 D:48H302 2.1 39.5 1.0
O10 D:48H302 2.1 37.9 1.0
NE2 D:HIS176 2.3 44.7 1.0
C8 D:48H302 2.8 38.6 1.0
C9 D:48H302 2.9 39.9 1.0
C12 D:48H302 2.9 42.0 1.0
C11 D:48H302 3.0 40.2 1.0
CE1 D:HIS176 3.2 42.6 1.0
CG E:ASP161 3.2 40.7 1.0
O E:HOH410 3.2 45.2 1.0
CD2 D:HIS176 3.3 42.0 1.0
OD2 E:ASP161 3.8 43.1 1.0
O9 D:48H302 4.1 40.9 1.0
C7 D:48H302 4.2 37.5 1.0
C10 D:48H302 4.3 41.0 1.0
ND1 D:HIS176 4.3 43.7 1.0
CB E:ASP161 4.4 37.7 1.0
CG D:HIS176 4.4 42.5 1.0
NH2 D:ARG236 4.5 37.5 1.0
O7 D:48H302 4.7 37.6 1.0
CA E:ASP161 4.8 37.3 1.0
C6 D:48H302 4.9 35.7 1.0

Iron binding site 7 out of 8 in 4y4n

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Iron binding site 7 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:42.4
occ:1.00
 OD1 G:ASP161 2.1 46.0 1.0
O8 E:48H302 2.1 44.1 1.0
O9 E:48H302 2.2 46.5 1.0
N1 E:48H302 2.2 46.5 1.0
O G:HOH402 2.2 38.3 1.0
NE2 E:HIS176 2.2 43.0 1.0
C8 E:48H302 2.9 43.0 1.0
C9 E:48H302 2.9 44.5 1.0
C12 E:48H302 3.0 46.3 1.0
C11 E:48H302 3.1 48.0 1.0
CE1 E:HIS176 3.2 43.4 1.0
CD2 E:HIS176 3.2 42.7 1.0
CG G:ASP161 3.2 42.9 1.0
O G:HOH403 3.4 40.8 1.0
OD2 G:ASP161 3.8 47.5 1.0
O10 E:48H302 4.2 47.3 1.0
O E:HOH419 4.2 38.5 1.0
ND1 E:HIS176 4.3 43.0 1.0
C7 E:48H302 4.3 39.8 1.0
CG E:HIS176 4.3 42.3 1.0
CB G:ASP161 4.4 41.6 1.0
C10 E:48H302 4.4 46.4 1.0
NH2 E:ARG236 4.5 39.2 1.0
CA G:ASP161 4.8 40.8 1.0
O7 E:48H302 4.8 40.3 1.0
C6 E:48H302 5.0 37.6 1.0

Iron binding site 8 out of 8 in 4y4n

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Iron binding site 8 out of 8 in the Thiazole Synthase THI4 From Methanococcus Igneus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Thiazole Synthase THI4 From Methanococcus Igneus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe301

b:41.6
occ:1.00
 O8 F:48H302 2.0 38.4 1.0
OD1 H:ASP161 2.1 44.1 1.0
N1 F:48H302 2.1 40.0 1.0
O10 F:48H302 2.1 37.0 1.0
O H:HOH301 2.1 45.8 1.0
NE2 F:HIS176 2.3 45.1 1.0
C8 F:48H302 2.8 40.0 1.0
C9 F:48H302 2.8 41.2 1.0
C12 F:48H302 2.9 40.8 1.0
C11 F:48H302 3.0 40.5 1.0
CE1 F:HIS176 3.2 42.9 1.0
CG H:ASP161 3.2 41.4 1.0
CD2 F:HIS176 3.3 43.5 1.0
O F:HOH407 3.4 47.4 1.0
OD2 H:ASP161 3.8 42.0 1.0
O9 F:48H302 4.1 40.0 1.0
C7 F:48H302 4.2 37.7 1.0
C10 F:48H302 4.3 41.9 1.0
ND1 F:HIS176 4.3 44.4 1.0
CG F:HIS176 4.4 44.1 1.0
CB H:ASP161 4.4 38.7 1.0
NH2 F:ARG236 4.6 38.9 1.0
O7 F:48H302 4.7 38.7 1.0
CA H:ASP161 4.8 37.7 1.0
C6 F:48H302 4.9 36.1 1.0

Reference:

X.Zhang, B.E.Eser, P.K.Chanani, T.P.Begley, S.E.Ealick. Structural Basis For Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases. Biochemistry V. 55 1826 2016.
ISSN: ISSN 0006-2960
PubMed: 26919468
DOI: 10.1021/ACS.BIOCHEM.6B00030
Page generated: Mon Aug 5 16:05:25 2024

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