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Sodium in PDB 3iqe: Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420

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

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

Protein crystallography data

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420, PDB code: 3iqe 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) 92.45 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.148, 165.539, 93.552, 90.00, 99.14, 90.00
R / Rfree (%) 19 / 22.8

Other elements in 3iqe:

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

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420 (pdb code 3iqe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420, PDB code: 3iqe:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3iqe

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


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 Methylene-Tetrahydromethanopterin and Coenzyme F420 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na287

b:42.6
occ:1.00
OD2 C:ASP215 2.3 29.7 1.0
O C:HOH607 2.5 29.3 1.0
CG C:ASP215 3.1 24.9 1.0
CB C:ASP215 3.4 19.5 1.0
OD1 F:ASN212 3.8 29.4 1.0
O F:HOH300 4.1 35.0 1.0
OD1 C:ASN212 4.1 29.6 1.0
CA C:ASN212 4.2 17.9 1.0
OD1 C:ASP215 4.2 25.9 1.0
CB C:ASN212 4.2 19.0 1.0
O C:ASN212 4.3 16.6 1.0
CG C:ASN212 4.4 23.3 1.0
OE1 F:GLU208 4.4 27.0 1.0
CG F:ASN212 4.5 23.0 1.0
ND2 F:ASN212 4.6 23.9 1.0
C C:ASN212 4.7 17.1 1.0
CA C:ASP215 4.8 18.7 1.0

Sodium binding site 2 out of 3 in 3iqe

Go back to Sodium Binding Sites List in 3iqe
Sodium binding site 2 out of 3 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na287

b:39.1
occ:1.00
OD1 D:ASP29 2.3 22.8 1.0
N D:ARG27 2.8 18.6 1.0
OD1 D:ASP25 2.9 22.0 1.0
N D:GLU26 3.3 18.8 1.0
C D:ASP25 3.4 20.4 1.0
CG D:ASP29 3.4 20.7 1.0
CA D:ARG27 3.5 18.5 1.0
N D:ASP29 3.5 20.5 1.0
N D:ALA28 3.5 19.4 1.0
CB D:ARG27 3.5 18.6 1.0
C D:ARG27 3.6 19.3 1.0
CA D:ASP25 3.8 21.3 1.0
O D:ASP25 3.8 21.2 1.0
C D:GLU26 3.9 18.0 1.0
NH1 D:ARG27 3.9 24.1 1.0
CD D:GLU26 3.9 21.5 1.0
CG D:ASP25 4.0 22.9 1.0
OE2 D:GLU26 4.0 21.6 1.0
CA D:GLU26 4.1 18.1 1.0
CZ D:ARG27 4.1 20.2 1.0
CG D:GLU26 4.1 18.6 1.0
OD2 D:ASP29 4.1 24.1 1.0
N D:ARG30 4.3 21.0 1.0
OE1 D:GLU26 4.3 17.2 1.0
CA D:ASP29 4.3 20.3 1.0
CA D:ALA28 4.3 20.5 1.0
CG D:ARG30 4.3 21.5 1.0
CB D:ASP29 4.4 20.6 1.0
C D:ALA28 4.4 20.6 1.0
O D:ARG27 4.4 19.0 1.0
NH2 D:ARG27 4.4 21.8 1.0
CB D:ASP25 4.5 21.3 1.0
NE D:ARG27 4.5 16.9 1.0
CG D:ARG27 4.5 16.7 1.0
C D:ASP29 4.6 20.1 1.0
CB D:HIS266 4.7 18.6 1.0
CB D:GLU26 4.7 18.9 1.0
O D:HIS266 4.9 18.8 1.0
CD D:ARG30 4.9 23.4 1.0
OD2 D:ASP25 5.0 29.1 1.0
O D:GLU26 5.0 17.4 1.0
N D:ASP25 5.0 21.4 1.0

Sodium binding site 3 out of 3 in 3iqe

Go back to Sodium Binding Sites List in 3iqe
Sodium binding site 3 out of 3 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na286

b:42.2
occ:1.00
OD1 E:ASP66 2.3 22.2 1.0
CG E:ASP66 3.2 21.5 1.0
O E:HOH323 3.3 25.9 1.0
OD2 E:ASP66 3.4 23.0 1.0
O E:HOH428 3.6 41.9 1.0
O E:HOH595 4.1 65.3 1.0
CE E:LYS5 4.4 24.1 1.0
CB E:ASP66 4.6 21.3 1.0
NZ E:LYS5 4.6 25.7 1.0
OD2 E:ASP171 4.6 56.1 1.0
O E:GLU64 4.6 23.5 1.0
O E:VAL3 4.9 21.7 1.0
O E:HOH697 5.0 29.2 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: Tue Dec 15 06:15:15 2020

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