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Sodium in PDB 3iqf: Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin

Enzymatic activity of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin

All present enzymatic activity of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin:
1.5.99.9;

Protein crystallography data

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin, PDB code: 3iqf was solved by K.E.Ceh, U.Demmer, E.Warkentin, J.Moll, R.K.Thauer, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.50 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.400, 167.100, 122.500, 90.00, 113.60, 90.00
R / Rfree (%) 16 / 20

Other elements in 3iqf:

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin (pdb code 3iqf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin, PDB code: 3iqf:

Sodium binding site 1 out of 1 in 3iqf

Go back to Sodium Binding Sites List in 3iqf
Sodium binding site 1 out of 1 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na285

b:53.1
occ:1.00
O F:HOH1159 2.3 47.5 1.0
NE F:ARG276 3.7 35.2 1.0
NH1 F:ARG276 4.1 40.1 1.0
CD1 F:LEU262 4.2 25.6 1.0
CZ F:ARG276 4.3 36.1 1.0
O F:HOH1138 4.4 41.7 1.0
O F:HOH1160 4.5 46.5 1.0
CG F:ARG276 4.5 28.6 1.0
CD F:ARG276 4.5 33.4 1.0
O F:HOH782 4.8 41.1 1.0
OG F:SER274 4.8 32.6 1.0

Reference:

K.Ceh, U.Demmer, E.Warkentin, J.Moll, R.K.Thauer, S.Shima, U.Ermler. Structural Basis of the Hydride Transfer Mechanism in F(420)-Dependent Methylenetetrahydromethanopterin Dehydrogenase Biochemistry V. 48 10098 2009.
ISSN: ISSN 0006-2960
PubMed: 19761261
DOI: 10.1021/BI901104D
Page generated: Mon Oct 7 11:01:13 2024

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