Sodium in PDB 7qbv: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.

Protein crystallography data

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv 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) 49.40 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 155.498, 163, 77.328, 90, 90, 90
R / Rfree (%) 21.4 / 23.5

Other elements in 7qbv:

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. (pdb code 7qbv). 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-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7qbv

Go back to Sodium Binding Sites List in 7qbv
Sodium binding site 1 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:42.0
occ:1.00
 OD1 A:ASP156 2.5 46.6 1.0
O A:PHE121 2.7 45.2 1.0
O A:GLU158 2.9 45.0 1.0
O A:GLY118 3.1 45.8 1.0
OG A:SER162 3.1 43.7 1.0
N A:GLU158 3.3 44.5 1.0
CB A:GLU158 3.4 48.7 1.0
C A:GLU158 3.4 44.8 1.0
C A:PHE121 3.5 45.2 1.0
O A:LYS119 3.5 45.5 1.0
CA A:GLU158 3.6 45.2 1.0
CG A:ASP156 3.7 46.1 1.0
C A:LYS119 3.8 45.4 1.0
CA A:LYS119 3.9 45.4 1.0
CD A:PRO157 4.1 42.6 1.0
CG A:PRO157 4.1 44.3 1.0
C A:GLY118 4.1 45.6 1.0
OD2 A:ASP156 4.2 47.4 1.0
CA A:SER122 4.2 45.9 1.0
N A:SER122 4.2 45.4 1.0
N A:PHE121 4.2 44.5 1.0
OG A:SER122 4.3 50.6 1.0
CG A:GLU158 4.4 57.4 1.0
N A:PRO157 4.4 43.1 1.0
CA A:PHE121 4.4 44.6 1.0
C A:PRO157 4.5 44.2 1.0
N A:PRO159 4.5 44.2 1.0
N A:LYS119 4.5 45.1 1.0
CB A:SER162 4.5 42.0 1.0
N A:GLY120 4.7 45.1 1.0
N A:SER162 4.8 41.2 1.0
C A:ASP156 4.8 43.3 1.0
CA A:PRO157 4.9 43.4 1.0
CB A:SER122 4.9 47.5 1.0
CB A:ASP156 4.9 43.6 1.0
CB A:PHE121 4.9 44.0 1.0
C A:GLY120 4.9 44.9 1.0

Sodium binding site 2 out of 4 in 7qbv

Go back to Sodium Binding Sites List in 7qbv
Sodium binding site 2 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:39.7
occ:1.00
 OD1 B:ASP156 2.5 52.7 1.0
O B:PHE121 2.6 42.6 1.0
O B:GLY118 2.9 40.3 1.0
O B:GLU158 3.0 50.0 1.0
OG B:SER162 3.1 46.8 1.0
N B:GLU158 3.4 50.1 1.0
O B:LYS119 3.5 40.8 1.0
C B:PHE121 3.5 42.5 1.0
C B:GLU158 3.6 49.8 1.0
CB B:GLU158 3.6 53.9 1.0
CG B:ASP156 3.7 52.2 1.0
C B:LYS119 3.7 40.6 1.0
CA B:GLU158 3.7 50.5 1.0
CA B:LYS119 3.8 40.1 1.0
C B:GLY118 4.0 40.1 1.0
CD B:PRO157 4.1 49.1 1.0
N B:PHE121 4.1 40.9 1.0
OD2 B:ASP156 4.1 53.5 1.0
CG B:PRO157 4.1 50.7 1.0
N B:SER122 4.2 43.1 1.0
CA B:SER122 4.2 44.0 1.0
OG B:SER122 4.3 48.9 1.0
CA B:PHE121 4.3 41.4 1.0
N B:LYS119 4.4 39.8 1.0
N B:PRO157 4.5 49.8 1.0
CB B:SER162 4.5 45.0 1.0
CG B:GLU158 4.5 61.5 1.0
N B:GLY120 4.5 40.4 1.0
C B:PRO157 4.6 50.4 1.0
N B:PRO159 4.7 48.9 1.0
CB B:PHE121 4.8 40.9 1.0
C B:GLY120 4.8 40.9 1.0
N B:SER162 4.8 44.4 1.0
C B:ASP156 4.9 49.8 1.0
CB B:ASP156 4.9 49.7 1.0
CB B:SER122 4.9 45.8 1.0
CA B:PRO157 5.0 49.9 1.0

Sodium binding site 3 out of 4 in 7qbv

Go back to Sodium Binding Sites List in 7qbv
Sodium binding site 3 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:42.7
occ:1.00
 OD1 C:ASP156 2.5 51.8 1.0
O C:PHE121 2.5 47.2 1.0
O C:GLY118 2.6 46.5 1.0
OG C:SER162 2.7 47.9 1.0
O C:GLU158 2.9 49.9 1.0
C C:PHE121 3.5 47.3 1.0
CG C:ASP156 3.6 51.8 1.0
C C:GLU158 3.6 49.9 1.0
O C:LYS119 3.7 47.0 1.0
N C:GLU158 3.7 50.3 1.0
C C:GLY118 3.7 46.5 1.0
CA C:LYS119 3.8 46.5 1.0
C C:LYS119 3.8 46.9 1.0
CB C:GLU158 3.8 53.6 1.0
CA C:GLU158 3.9 50.5 1.0
OD2 C:ASP156 3.9 53.2 1.0
N C:PHE121 4.1 46.6 1.0
CB C:SER162 4.1 46.3 1.0
N C:LYS119 4.2 46.3 1.0
CA C:PHE121 4.3 46.9 1.0
N C:SER122 4.3 47.7 1.0
CA C:SER122 4.4 48.3 1.0
CD C:PRO157 4.4 49.3 1.0
N C:SER162 4.5 45.8 1.0
CG C:PRO157 4.5 50.9 1.0
N C:GLY120 4.6 46.9 1.0
CB C:PHE121 4.6 46.5 1.0
N C:PRO159 4.6 49.2 1.0
OG C:SER122 4.6 52.6 1.0
N C:PRO157 4.7 50.0 1.0
CA C:SER162 4.7 45.4 1.0
CG C:GLU158 4.8 59.9 1.0
C C:GLY120 4.9 46.9 1.0
CB C:ASP156 4.9 50.0 1.0
C C:PRO157 4.9 50.5 1.0
CA C:GLY118 5.0 46.5 1.0

Sodium binding site 4 out of 4 in 7qbv

Go back to Sodium Binding Sites List in 7qbv
Sodium binding site 4 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na505

b:36.7
occ:1.00
 O D:PHE121 2.4 54.7 1.0
OD1 D:ASP156 2.6 60.3 1.0
OG D:SER162 2.6 52.0 1.0
O D:GLY118 2.7 52.2 1.0
O D:GLU158 2.7 55.8 1.0
C D:PHE121 3.4 54.5 1.0
C D:GLU158 3.5 55.9 1.0
CG D:ASP156 3.7 60.0 1.0
CB D:GLU158 3.7 60.1 1.0
N D:GLU158 3.7 56.5 1.0
CA D:GLU158 3.8 56.8 1.0
C D:GLY118 3.8 51.8 1.0
O D:LYS119 3.8 52.6 1.0
CA D:LYS119 4.0 51.7 1.0
C D:LYS119 4.0 52.4 1.0
OD2 D:ASP156 4.0 61.4 1.0
CB D:SER162 4.0 50.7 1.0
N D:PHE121 4.1 53.3 1.0
N D:SER122 4.2 55.2 1.0
CA D:PHE121 4.2 53.6 1.0
CA D:SER122 4.3 56.4 1.0
N D:SER162 4.3 51.4 1.0
N D:LYS119 4.4 51.5 1.0
CB D:PHE121 4.5 52.9 1.0
CD D:PRO157 4.6 56.3 1.0
N D:PRO159 4.6 55.0 1.0
CA D:SER162 4.6 50.5 1.0
OG D:SER122 4.6 61.6 1.0
CG D:PRO157 4.7 57.9 1.0
N D:GLY120 4.7 52.4 1.0
CG D:GLU158 4.7 67.3 1.0
CB D:ALA161 4.8 53.0 1.0
N D:PRO157 4.8 56.8 1.0
C D:GLY120 4.9 53.6 1.0
C D:PRO157 4.9 56.9 1.0
CB D:ASP156 5.0 57.5 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 08:20:34 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy