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Calcium 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:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin and Coenzyme F420, PDB code: 3iqe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3iqe

Go back to Calcium Binding Sites List in 3iqe
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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
B:Ca286

b:23.9
occ:1.00
 OD2 B:ASP89 1.8 22.8 1.0
OE2 B:GLU85 1.9 23.9 1.0
CG B:ASP89 2.6 21.8 1.0
OD1 B:ASP89 2.8 21.4 1.0
CD B:GLU85 2.9 24.2 1.0
CG B:GLU85 3.3 20.7 1.0
CB B:ASP89 4.0 19.4 1.0
OE1 B:GLU85 4.0 27.3 1.0
O B:GLU85 4.6 15.8 1.0
CB B:GLU85 4.7 18.9 1.0

Calcium binding site 2 out of 4 in 3iqe

Go back to Calcium Binding Sites List in 3iqe
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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
B:Ca287

b:61.0
occ:1.00
 OE1 B:GLU34 2.1 36.1 1.0
CD B:GLU34 2.8 29.6 1.0
OE2 B:GLU34 2.8 33.9 1.0
NH1 B:ARG36 3.6 30.2 1.0
CG B:GLU34 4.2 24.4 1.0
CE1 B:PHE63 4.5 20.8 1.0
CZ B:ARG36 4.7 28.3 1.0
CD1 B:PHE63 4.9 23.4 1.0

Calcium binding site 3 out of 4 in 3iqe

Go back to Calcium Binding Sites List in 3iqe
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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
C:Ca286

b:25.1
occ:1.00
 OE1 C:GLU228 1.8 26.5 1.0
O E:HOH751 2.1 26.3 1.0
O E:HOH757 2.1 21.0 1.0
CD C:GLU228 2.8 25.2 1.0
OE2 C:GLU228 3.2 25.3 1.0
O C:HOH748 3.8 36.6 1.0
O E:MET279 3.8 21.0 1.0
CE C:LYS227 3.9 23.3 1.0
NZ C:LYS227 4.2 22.3 1.0
CG C:GLU228 4.2 20.9 1.0
O C:HOH747 4.5 40.2 1.0
CB E:MET279 4.7 23.7 1.0
C E:MET279 4.8 22.3 1.0

Calcium binding site 4 out of 4 in 3iqe

Go back to Calcium Binding Sites List in 3iqe
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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:Ca286

b:36.1
occ:1.00
 OE1 D:GLU54 1.8 24.5 1.0
OE1 D:GLU50 1.9 27.4 1.0
O D:HOH714 2.2 26.1 1.0
CD D:GLU54 2.9 22.5 1.0
CD D:GLU50 2.9 25.2 1.0
OE2 D:GLU54 3.4 21.7 1.0
CG D:GLU50 3.4 22.2 1.0
O D:HOH584 4.0 37.2 1.0
OE2 D:GLU50 4.1 27.9 1.0
CG D:GLU54 4.2 21.4 1.0
CB D:GLU50 4.9 21.6 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: Tue Jul 8 13:27:27 2025

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