Atomistry » Sodium » PDB 3icf-3ivu » 3iqe
Atomistry »
  Sodium »
    PDB 3icf-3ivu »
      3iqe »

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: Mon Oct 7 11:00:48 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy