Sodium in PDB 1y5y: Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1

The structure of Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1, PDB code: 1y5y was solved by P.Acharya, M.Goenrich, C.H.Hagemeier, U.Demmer, J.A.Vorholt, R.K.Thauer, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.659, 120.659, 205.947, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.9

The structure of Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1 (pdb code 1y5y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1, PDB code: 1y5y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1


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 Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:27.6 occ:1.00 O C:HOH540 2.9 47.9 1.0 OE1 C:GLN2143 3.0 51.0 1.0 O C:HOH539 3.1 43.7 1.0 CA C:ILE2103 3.8 27.7 1.0 CD C:GLN2143 3.9 48.0 1.0 CG1 C:ILE2103 3.9 26.4 1.0 CG C:GLN2143 4.0 39.1 1.0 ND2 C:ASN2147 4.0 34.4 1.0 CB C:ILE2103 4.2 32.2 1.0 CG2 C:ILE2103 4.2 28.8 1.0 O C:GLY2102 4.2 30.7 1.0 O C:HOH387 4.5 48.6 1.0 NZ C:LYS2003 4.6 59.3 1.0 N C:ILE2103 4.6 28.1 1.0 O C:ILE2103 4.8 32.0 1.0 C C:GLY2102 4.8 30.1 1.0 C C:ILE2103 4.8 32.1 1.0

Sodium binding site 2 out of 2 in the Structure of the Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1


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 Tetrahydromethanopterin Dependent Formaldehyde- Activating Enzyme (Fae) From Methylobacterium Extorquens AM1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na203 b:28.0 occ:1.00 OE1 E:GLN4143 2.7 38.3 0.5 OE1 E:GLN4143 3.0 40.8 0.5 CD E:GLN4143 3.4 41.4 0.5 NE2 E:GLN4143 3.4 40.6 0.5 CA E:ILE4103 3.8 25.5 1.0 CG1 E:ILE4103 3.8 29.2 1.0 CD E:GLN4143 3.9 43.4 0.5 ND2 E:ASN4147 4.0 31.4 1.0 CG E:GLN4143 4.1 38.0 0.5 NZ E:LYS4003 4.2 60.5 1.0 CB E:ILE4103 4.2 29.8 1.0 O E:GLY4102 4.2 28.4 1.0 CG2 E:ILE4103 4.4 31.6 1.0 N E:ILE4103 4.6 28.6 1.0 C E:GLY4102 4.7 31.9 1.0 O E:ILE4103 4.8 31.0 1.0 CG E:GLN4143 4.9 37.0 0.5 C E:ILE4103 4.9 29.1 1.0

P.Acharya, M.Goenrich, C.H.Hagemeier, U.Demmer, J.A.Vorholt, R.K.Thauer, U.Ermler. How An Enzyme Binds the C1-Carrier Tetrahydromethanopterin: Structure of the Tetrahydromethanopterin Dependent Formaldehyde-Activating Enzyme (Fae) From Methylobacterium Extorquens AM1 J.Biol.Chem. V. 280 13712 2005.
ISSN: ISSN 0021-9258
PubMed: 15632161
DOI: 10.1074/JBC.M412320200