Iron in PDB 6scy: U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster

Protein crystallography data

The structure of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster, PDB code: 6scy was solved by O.Bimai, P.Legrand, B.Golinelli-Pimaneau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.85 / 2.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.980, 84.480, 145.440, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 28.7

Other elements in 6scy:

The structure of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster (pdb code 6scy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster, PDB code: 6scy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6scy

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Iron binding site 1 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.3
occ:0.80
FE1 A:SF4403 0.0 0.3 0.8
S3 A:SF4403 2.3 0.6 0.8
S2 A:SF4403 2.3 0.5 0.8
S4 A:SF4403 2.3 0.5 0.8
SG A:CYS142 2.3 0.8 1.0
FE4 A:SF4403 2.7 0.5 0.8
FE2 A:SF4403 2.8 0.1 0.8
FE3 A:SF4403 2.8 0.1 0.7
CB A:CYS142 3.2 0.8 1.0
CA A:CYS142 3.3 0.1 1.0
CB A:SER236 3.5 0.4 1.0
O A:CYS142 3.5 0.9 1.0
OG A:SER236 3.7 0.2 1.0
C A:CYS142 3.9 0.5 1.0
S1 A:SF4403 3.9 0.8 0.8
N A:CYS142 4.5 0.0 1.0
CB A:CYS145 4.5 0.6 1.0
SG A:CYS233 4.6 0.7 1.0
SG A:CYS145 4.7 0.2 1.0
O3 A:SO4405 4.8 1.0 0.7
CA A:SER236 5.0 1.0 1.0

Iron binding site 2 out of 8 in 6scy

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Iron binding site 2 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.1
occ:0.80
FE2 A:SF4403 0.0 0.1 0.8
SG A:CYS145 2.2 0.2 1.0
S4 A:SF4403 2.3 0.5 0.8
S1 A:SF4403 2.3 0.8 0.8
S3 A:SF4403 2.3 0.6 0.8
FE3 A:SF4403 2.7 0.1 0.7
FE1 A:SF4403 2.8 0.3 0.8
FE4 A:SF4403 2.8 0.5 0.8
CB A:CYS145 2.8 0.6 1.0
NH1 A:ARG149 3.7 82.1 0.5
S2 A:SF4403 3.9 0.5 0.8
CA A:CYS145 4.2 0.8 1.0
O3 A:SO4405 4.2 1.0 0.7
OE2 A:GLU88 4.2 0.0 1.0
O A:CYS142 4.4 0.9 1.0
C A:CYS145 4.4 0.6 1.0
NH2 A:ARG94 4.5 0.6 1.0
N A:GLY146 4.5 0.8 1.0
CD A:GLU88 4.6 0.3 1.0
CD1 A:ILE90 4.6 0.8 1.0
CG A:GLU88 4.8 0.3 1.0
CZ A:ARG149 4.9 94.3 0.5
CA A:CYS142 4.9 0.1 1.0
O A:CYS145 4.9 0.7 1.0
SG A:CYS233 5.0 0.7 1.0
SG A:CYS142 5.0 0.8 1.0

Iron binding site 3 out of 8 in 6scy

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Iron binding site 3 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.1
occ:0.70
FE3 A:SF4403 0.0 0.1 0.7
O3 A:SO4405 2.2 1.0 0.7
S1 A:SF4403 2.3 0.8 0.8
S4 A:SF4403 2.3 0.5 0.8
S2 A:SF4403 2.3 0.5 0.8
FE2 A:SF4403 2.7 0.1 0.8
FE4 A:SF4403 2.7 0.5 0.8
FE1 A:SF4403 2.8 0.3 0.8
S A:SO4405 3.3 0.9 0.7
O1 A:SO4405 3.5 0.9 0.7
O4 A:SO4405 3.7 0.9 0.7
S3 A:SF4403 3.9 0.6 0.8
NH1 A:ARG149 4.1 82.1 0.5
NH2 A:ARG149 4.3 78.0 0.5
SG A:CYS142 4.5 0.8 1.0
O2 A:SO4405 4.5 0.7 0.7
CZ A:ARG149 4.6 94.3 0.5
SG A:CYS145 4.6 0.2 1.0
SG A:CYS233 4.8 0.7 1.0
OE2 A:GLU88 4.8 0.0 1.0
O A:HOH556 4.9 66.1 1.0

Iron binding site 4 out of 8 in 6scy

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Iron binding site 4 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:0.5
occ:0.80
FE4 A:SF4403 0.0 0.5 0.8
S2 A:SF4403 2.3 0.5 0.8
S1 A:SF4403 2.3 0.8 0.8
S3 A:SF4403 2.3 0.6 0.8
SG A:CYS233 2.3 0.7 1.0
FE3 A:SF4403 2.7 0.1 0.7
FE1 A:SF4403 2.7 0.3 0.8
FE2 A:SF4403 2.8 0.1 0.8
NH2 A:ARG94 3.3 0.6 1.0
CB A:CYS233 3.4 0.9 1.0
CB A:SER236 3.8 0.4 1.0
S4 A:SF4403 3.9 0.5 0.8
OG A:SER236 4.3 0.2 1.0
CZ A:ARG94 4.3 0.8 1.0
NH1 A:ARG94 4.5 0.4 1.0
CA A:CYS233 4.7 0.4 1.0
SG A:CYS145 4.7 0.2 1.0
O3 A:SO4405 4.7 1.0 0.7
N A:SER236 4.8 0.4 1.0
CA A:SER236 4.8 1.0 1.0
SG A:CYS142 4.9 0.8 1.0
O1 A:SO4405 5.0 0.9 0.7

Iron binding site 5 out of 8 in 6scy

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Iron binding site 5 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.2
occ:0.80
FE1 B:SF4403 0.0 0.2 0.8
S3 B:SF4403 2.3 0.8 0.8
S2 B:SF4403 2.3 0.9 0.8
S4 B:SF4403 2.3 0.7 0.8
SG B:CYS142 2.3 0.5 1.0
FE2 B:SF4403 2.8 0.3 0.8
FE4 B:SF4403 2.8 0.3 0.8
FE3 B:SF4403 2.8 0.9 0.7
CB B:CYS142 3.2 0.5 1.0
CA B:CYS142 3.3 0.1 1.0
CB B:SER236 3.5 0.0 1.0
O B:CYS142 3.6 0.8 1.0
OG B:SER236 3.7 0.5 1.0
C B:CYS142 3.9 0.4 1.0
S1 B:SF4403 3.9 0.3 0.8
N B:CYS142 4.5 0.0 1.0
CB B:CYS145 4.5 1.0 1.0
SG B:CYS233 4.7 0.6 1.0
SG B:CYS145 4.7 0.8 1.0
O2 B:SO4407 4.8 0.4 0.7
CA B:SER236 5.0 0.2 1.0

Iron binding site 6 out of 8 in 6scy

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Iron binding site 6 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.3
occ:0.80
FE2 B:SF4403 0.0 0.3 0.8
SG B:CYS145 2.2 0.8 1.0
S4 B:SF4403 2.3 0.7 0.8
S1 B:SF4403 2.3 0.3 0.8
S3 B:SF4403 2.3 0.8 0.8
FE4 B:SF4403 2.7 0.3 0.8
FE3 B:SF4403 2.8 0.9 0.7
FE1 B:SF4403 2.8 0.2 0.8
CB B:CYS145 2.8 1.0 1.0
NH1 B:ARG149 3.6 0.5 1.0
S2 B:SF4403 3.9 0.9 0.8
CA B:CYS145 4.2 0.8 1.0
O B:CYS142 4.4 0.8 1.0
C B:CYS145 4.4 0.3 1.0
OE1 B:GLU88 4.5 0.7 1.0
N B:GLY146 4.5 0.4 1.0
CZ B:ARG149 4.7 0.7 1.0
CG B:GLU88 4.8 0.3 1.0
CD B:GLU88 4.8 0.9 1.0
O2 B:SO4407 4.9 0.4 0.7
NH2 B:ARG149 4.9 0.3 1.0
CA B:CYS142 4.9 0.1 1.0
SG B:CYS233 4.9 0.6 1.0
SG B:CYS142 4.9 0.5 1.0
O B:CYS145 5.0 0.7 1.0

Iron binding site 7 out of 8 in 6scy

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Iron binding site 7 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.9
occ:0.70
FE3 B:SF4403 0.0 0.9 0.7
O2 B:SO4407 2.3 0.4 0.7
S1 B:SF4403 2.3 0.3 0.8
S2 B:SF4403 2.3 0.9 0.8
S4 B:SF4403 2.3 0.7 0.8
FE2 B:SF4403 2.8 0.3 0.8
FE4 B:SF4403 2.8 0.3 0.8
FE1 B:SF4403 2.8 0.2 0.8
S B:SO4407 3.7 0.3 0.7
S3 B:SF4403 3.9 0.8 0.8
NH1 B:ARG149 4.3 0.5 1.0
O1 B:SO4407 4.3 0.2 0.7
NH2 B:ARG149 4.4 0.3 1.0
O4 B:SO4407 4.4 0.5 0.7
SG B:CYS142 4.5 0.5 1.0
O3 B:SO4407 4.5 0.2 0.7
CZ B:ARG149 4.6 0.7 1.0
SG B:CYS145 4.7 0.8 1.0
SG B:CYS233 4.8 0.6 1.0
O B:HOH523 4.8 72.6 1.0
NH1 B:ARG94 4.9 0.8 1.0
NH2 B:ARG94 5.0 0.2 1.0

Iron binding site 8 out of 8 in 6scy

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Iron binding site 8 out of 8 in the U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of U34-Trna Thiolase Ncsa From Methanococcus Maripaludis with Its [4FE- 4S] Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:0.3
occ:0.80
FE4 B:SF4403 0.0 0.3 0.8
S3 B:SF4403 2.3 0.8 0.8
S1 B:SF4403 2.3 0.3 0.8
SG B:CYS233 2.3 0.6 1.0
S2 B:SF4403 2.3 0.9 0.8
FE2 B:SF4403 2.7 0.3 0.8
FE3 B:SF4403 2.8 0.9 0.7
FE1 B:SF4403 2.8 0.2 0.8
CB B:CYS233 3.4 0.6 1.0
NH1 B:ARG94 3.5 0.8 1.0
CB B:SER236 3.8 0.0 1.0
S4 B:SF4403 3.9 0.7 0.8
O2 B:SO4407 4.2 0.4 0.7
OG B:SER236 4.3 0.5 1.0
CZ B:ARG94 4.4 0.7 1.0
NH2 B:ARG94 4.6 0.2 1.0
SG B:CYS145 4.7 0.8 1.0
CA B:CYS233 4.7 0.3 1.0
N B:SER236 4.8 0.1 1.0
CA B:SER236 4.8 0.2 1.0
SG B:CYS142 4.9 0.5 1.0

Reference:

O.Bimai, P.Legrand, N.He, N.Touati, L.Binet, M.Fontecave, B.Golinelli-Pimpaneau. The Thiolation of Uridine 34 in Trna, Which Controls Protein Translation, Depends on A [4FE-4S] Cluster in the Archeum Methanococcus Maripaludis. To Be Published.
Page generated: Sun Dec 13 17:05:38 2020

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