Atomistry » Calcium » PDB 3ij7-3isv » 3iqe
Atomistry »
  Calcium »
    PDB 3ij7-3isv »
      3iqe »

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: Sat Dec 12 04:15:57 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy