Sodium in PDB 3k13: Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron

The structure of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron, PDB code: 3k13 was solved by M.E.Cuff, H.Li, G.Cobb, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.652, 79.992, 127.068, 90.00, 90.12, 90.00
R / Rfree (%)	16 / 18.8

The structure of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron (pdb code 3k13). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron, PDB code: 3k13:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ A:Na647 b:48.5 occ:1.00 O A:LEU404 2.3 27.9 1.0 O A:HOH757 2.4 40.7 1.0 O A:ASP401 2.4 31.3 1.0 O A:HOH282 2.5 31.8 1.0 C A:ASP401 3.4 31.0 1.0 C A:LEU404 3.5 28.2 1.0 CA A:GLY402 4.0 32.3 1.0 N A:GLY402 4.1 31.9 1.0 N A:LEU404 4.1 30.5 1.0 N A:ASP401 4.2 28.5 1.0 O A:HOH719 4.2 49.3 1.0 N A:ALA406 4.2 24.2 1.0 C A:GLY402 4.3 32.7 1.0 CA A:LEU404 4.3 28.9 1.0 O A:GLY402 4.3 32.6 1.0 CA A:ASP401 4.4 29.9 1.0 N A:ASP405 4.5 26.4 1.0 CB A:ALA406 4.5 24.4 1.0 O A:HOH257 4.7 30.5 1.0 CA A:ASP405 4.7 25.2 1.0 CB A:LEU404 4.7 28.1 1.0 CA A:ALA406 4.9 24.3 1.0 N A:LEU403 5.0 33.9 1.0 C A:ASP405 5.0 25.0 1.0

Sodium binding site 2 out of 5 in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Na644 b:62.9 occ:1.00 OE2 B:THH643 2.5 54.5 1.0 OG B:SER365 3.0 32.4 1.0 CD B:THH643 3.2 49.6 1.0 OE1 B:THH643 3.6 48.7 1.0 CB B:SER365 3.7 32.7 1.0 CA B:SER365 4.0 32.5 1.0 CB B:LYS367 4.1 31.8 1.0 N B:ARG366 4.1 33.1 1.0 N B:LYS367 4.1 31.9 1.0 NH2 B:ARG359 4.2 49.0 1.0 CG B:THH643 4.3 44.6 1.0 C B:SER365 4.3 33.1 1.0 CA B:LYS367 4.7 31.7 1.0 CA B:ARG366 5.0 34.4 1.0

Sodium binding site 3 out of 5 in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Na647 b:50.7 occ:1.00 O B:HOH649 2.4 42.3 1.0 O B:LEU404 2.4 27.2 1.0 O B:ASP401 2.5 32.8 1.0 O B:HOH58 2.5 32.7 1.0 C B:ASP401 3.4 31.9 1.0 C B:LEU404 3.6 28.2 1.0 CA B:GLY402 4.1 32.6 1.0 N B:ASP401 4.1 29.6 1.0 N B:GLY402 4.1 32.6 1.0 N B:ALA406 4.2 25.1 1.0 N B:LEU404 4.2 30.6 1.0 O B:HOH726 4.2 46.6 1.0 C B:GLY402 4.3 32.6 1.0 O B:GLY402 4.4 32.7 1.0 CA B:LEU404 4.4 29.4 1.0 CB B:ALA406 4.4 25.4 1.0 CA B:ASP401 4.4 30.9 1.0 O B:HOH155 4.5 35.2 1.0 N B:ASP405 4.6 27.2 1.0 CA B:ASP405 4.8 26.2 1.0 CB B:LEU404 4.8 28.6 1.0 CA B:ALA406 4.9 25.0 1.0 N B:LEU403 4.9 33.5 1.0

Sodium binding site 4 out of 5 in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ C:Na644 b:59.4 occ:1.00 OE2 C:THH643 2.5 56.6 1.0 OG C:SER365 2.8 30.7 1.0 CD C:THH643 3.3 50.2 1.0 CB C:SER365 3.6 30.8 1.0 OE1 C:THH643 3.8 49.4 1.0 CA C:SER365 3.9 30.7 1.0 NH2 C:ARG359 3.9 48.2 1.0 N C:ARG366 4.0 32.5 1.0 N C:LYS367 4.1 31.6 1.0 CB C:LYS367 4.1 31.7 1.0 C C:SER365 4.2 31.9 1.0 CG C:THH643 4.3 46.3 1.0 CA C:LYS367 4.7 31.4 1.0 O C:HOH732 4.9 54.1 1.0 O C:HOH243 5.0 38.1 1.0

Sodium binding site 5 out of 5 in the Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Pterin-Binding Domain Metr of 5- Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ C:Na646 b:51.0 occ:1.00 O C:HOH762 2.3 42.0 1.0 O C:LEU404 2.3 28.3 1.0 O C:HOH761 2.5 31.6 1.0 O C:ASP401 2.5 32.0 1.0 C C:ASP401 3.5 31.8 1.0 C C:LEU404 3.5 28.3 1.0 CA C:GLY402 4.0 32.6 1.0 N C:GLY402 4.1 32.0 1.0 N C:LEU404 4.2 30.8 1.0 O C:HOH764 4.2 48.2 1.0 N C:ASP401 4.2 29.4 1.0 C C:GLY402 4.2 32.6 1.0 O C:GLY402 4.2 32.4 1.0 N C:ALA406 4.2 24.7 1.0 CA C:LEU404 4.3 29.4 1.0 O C:HOH763 4.4 39.1 1.0 CA C:ASP401 4.5 30.5 1.0 N C:ASP405 4.6 27.0 1.0 CB C:ALA406 4.6 24.9 1.0 O C:HOH246 4.6 37.0 1.0 CA C:ASP405 4.8 26.1 1.0 CB C:LEU404 4.8 28.2 1.0 N C:LEU403 5.0 33.9 1.0 CA C:ALA406 5.0 25.4 1.0

M.E.Cuff, H.Li, G.Cobb, A.Joachimiak. Structure of the Pterin-Binding Domain Metr of 5-Methyltetrahydrofolate-Homocysteine Methyltransferase From Bacteroides Thetaiotaomicron To Be Published.