Sodium in PDB 7qbt: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.

Protein crystallography data

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbt was solved by C.D.Fyfe, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.71 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 156.064, 163.915, 77.805, 90, 90, 90
R / Rfree (%) 20.3 / 22.9

Other elements in 7qbt:

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Iron (Fe) 20 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. (pdb code 7qbt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7qbt

Go back to Sodium Binding Sites List in 7qbt
Sodium binding site 1 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:31.9
occ:1.00
 OG A:SER162 2.2 30.1 1.0
O A:HOH719 2.4 30.9 1.0
O A:PHE121 2.4 31.1 1.0
O A:GLY118 2.5 31.2 1.0
OD1 A:ASP156 2.6 34.2 1.0
O A:GLU158 2.7 34.5 1.0
C A:PHE121 3.4 30.6 1.0
CG A:ASP156 3.5 32.2 1.0
C A:GLU158 3.5 34.3 1.0
CB A:SER162 3.6 28.1 1.0
OD2 A:ASP156 3.6 33.3 1.0
C A:GLY118 3.6 29.8 1.0
N A:SER162 3.9 28.8 1.0
CB A:GLU158 3.9 37.3 1.0
CA A:GLU158 4.0 34.9 1.0
N A:GLU158 4.0 34.9 1.0
CA A:SER162 4.1 27.8 1.0
N A:PHE121 4.1 28.6 1.0
CA A:LYS119 4.1 28.7 1.0
CA A:PHE121 4.2 28.9 1.0
C A:LYS119 4.3 29.8 1.0
O A:LYS119 4.3 30.6 1.0
N A:LYS119 4.3 28.7 1.0
N A:SER122 4.4 32.0 1.0
CB A:PHE121 4.4 28.0 1.0
N A:PRO159 4.5 33.7 1.0
CA A:SER122 4.5 34.3 1.0
CA A:GLY118 4.7 29.6 1.0
CA A:PRO159 4.8 33.3 1.0
CB A:ALA161 4.8 30.4 1.0
C A:ALA161 4.8 29.9 1.0
N A:GLY120 4.9 29.0 1.0
CB A:ASP156 4.9 32.1 1.0
OG A:SER122 4.9 42.5 1.0

Sodium binding site 2 out of 4 in 7qbt

Go back to Sodium Binding Sites List in 7qbt
Sodium binding site 2 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:30.5
occ:1.00
 O B:HOH771 2.3 26.9 1.0
OG B:SER162 2.3 29.5 1.0
O B:GLY118 2.5 31.8 1.0
O B:PHE121 2.5 32.5 1.0
OD1 B:ASP156 2.5 32.3 1.0
O B:GLU158 2.7 32.2 1.0
CG B:ASP156 3.4 31.8 1.0
C B:GLU158 3.5 32.4 1.0
C B:PHE121 3.5 32.5 1.0
OD2 B:ASP156 3.5 30.9 1.0
CB B:SER162 3.6 27.6 1.0
C B:GLY118 3.6 31.6 1.0
CB B:GLU158 3.9 34.7 1.0
N B:GLU158 4.0 32.8 1.0
CA B:GLU158 4.0 32.6 1.0
N B:SER162 4.0 28.3 1.0
CA B:LYS119 4.1 31.1 1.0
N B:PHE121 4.1 31.1 1.0
CA B:SER162 4.1 27.6 1.0
C B:LYS119 4.2 31.5 1.0
O B:LYS119 4.2 31.9 1.0
CA B:PHE121 4.3 31.7 1.0
N B:LYS119 4.3 31.2 1.0
N B:PRO159 4.4 32.5 1.0
N B:SER122 4.4 33.2 1.0
CB B:PHE121 4.5 31.3 1.0
CA B:SER122 4.6 34.1 1.0
CA B:GLY118 4.7 31.1 1.0
CA B:PRO159 4.7 32.1 1.0
CB B:ASP156 4.8 30.2 1.0
CB B:ALA161 4.8 29.4 1.0
N B:GLY120 4.9 31.2 1.0
C B:ALA161 4.9 29.5 1.0
OG B:SER122 4.9 38.8 1.0
CD B:PRO157 5.0 30.6 1.0

Sodium binding site 3 out of 4 in 7qbt

Go back to Sodium Binding Sites List in 7qbt
Sodium binding site 3 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:38.8
occ:1.00
 O C:HOH690 2.2 35.6 1.0
OG C:SER162 2.3 34.8 1.0
O C:PHE121 2.3 39.2 1.0
O C:GLY118 2.5 37.8 1.0
O C:GLU158 2.6 38.3 1.0
OD1 C:ASP156 2.7 40.2 1.0
C C:PHE121 3.4 39.4 1.0
C C:GLU158 3.5 39.0 1.0
CG C:ASP156 3.5 39.1 1.0
CB C:SER162 3.6 34.5 1.0
OD2 C:ASP156 3.7 39.6 1.0
C C:GLY118 3.7 37.2 1.0
CB C:GLU158 3.9 44.1 1.0
N C:SER162 3.9 34.0 1.0
CA C:GLU158 4.0 41.1 1.0
N C:GLU158 4.0 41.5 1.0
CA C:SER162 4.1 34.7 1.0
N C:PHE121 4.1 38.2 1.0
CA C:PHE121 4.2 38.6 1.0
CA C:LYS119 4.2 37.0 1.0
C C:LYS119 4.3 37.5 1.0
N C:SER122 4.3 40.1 1.0
O C:LYS119 4.3 38.0 1.0
CB C:PHE121 4.4 38.7 1.0
N C:LYS119 4.4 36.8 1.0
N C:PRO159 4.5 38.3 1.0
CA C:SER122 4.5 42.0 1.0
CB C:ALA161 4.7 35.4 1.0
CA C:GLY118 4.7 36.4 1.0
CA C:PRO159 4.8 37.5 1.0
C C:ALA161 4.8 34.9 1.0
OG C:SER122 4.9 50.8 1.0
N C:GLY120 4.9 37.4 1.0
CB C:ASP156 5.0 38.3 1.0

Sodium binding site 4 out of 4 in 7qbt

Go back to Sodium Binding Sites List in 7qbt
Sodium binding site 4 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na505

b:30.2
occ:1.00
 O D:HOH770 2.2 30.2 1.0
OG D:SER162 2.2 28.2 1.0
O D:PHE121 2.4 31.4 1.0
O D:GLY118 2.4 31.9 1.0
OD1 D:ASP156 2.7 31.0 1.0
O D:GLU158 2.7 30.5 1.0
C D:PHE121 3.4 32.1 1.0
C D:GLU158 3.5 31.1 1.0
CG D:ASP156 3.5 29.6 1.0
CB D:SER162 3.6 27.9 1.0
C D:GLY118 3.6 31.1 1.0
OD2 D:ASP156 3.7 30.7 1.0
N D:SER162 3.9 28.4 1.0
CB D:GLU158 3.9 35.3 1.0
N D:PHE121 4.0 30.6 1.0
CA D:GLU158 4.1 32.0 1.0
CA D:SER162 4.1 28.1 1.0
N D:GLU158 4.1 32.4 1.0
CA D:PHE121 4.1 31.2 1.0
CA D:LYS119 4.1 29.9 1.0
C D:LYS119 4.3 30.3 1.0
O D:LYS119 4.3 30.1 1.0
CB D:PHE121 4.3 31.2 1.0
N D:LYS119 4.3 29.6 1.0
N D:SER122 4.4 32.9 1.0
N D:PRO159 4.5 30.9 1.0
CA D:SER122 4.5 34.7 1.0
CA D:GLY118 4.6 31.1 1.0
CB D:ALA161 4.8 30.3 1.0
CA D:PRO159 4.8 31.5 1.0
C D:ALA161 4.8 29.4 1.0
N D:GLY120 4.8 29.7 1.0
OG D:SER122 5.0 44.5 1.0
CB D:ASP156 5.0 28.7 1.0

Reference:

C.D.Fyfe, N.Bernardo-Garcia, L.Fradale, S.Grimaldi, A.Guillot, C.Brewee, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau. Crystallographic Snapshots of A B 12 -Dependent Radical Sam Methyltransferase. Nature V. 602 336 2022.
ISSN: ESSN 1476-4687
PubMed: 35110733
DOI: 10.1038/S41586-021-04355-9
Page generated: Wed Oct 9 08:20:29 2024

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