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Magnesium in PDB 1qv9: Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure

Enzymatic activity of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure

All present enzymatic activity of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure:
1.5.99.9;

Protein crystallography data

The structure of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure, PDB code: 1qv9 was solved by C.H.Hagemeier, S.Shima, R.K.Thauer, G.Bourenkov, H.D.Bartunik, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 120.100, 151.200, 110.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure (pdb code 1qv9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure, PDB code: 1qv9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1qv9

Go back to Magnesium Binding Sites List in 1qv9
Magnesium binding site 1 out of 4 in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5001

b:18.8
occ:1.00
 O A:HOH4034 1.9 21.3 1.0
O A:HOH4014 1.9 21.2 1.0
O A:HOH4009 2.1 18.7 1.0
OE1 A:GLU175 3.9 22.1 1.0
O A:HOH4004 4.2 16.9 1.0
O A:GLU91 4.3 21.4 1.0
O A:HOH4030 4.3 21.2 1.0
O A:SER90 4.4 24.7 1.0
O A:HOH4124 4.5 27.4 1.0
C A:GLU91 4.6 23.8 1.0
CG A:GLU175 4.7 21.6 1.0
CD A:GLU175 4.7 23.4 1.0
N A:PRO93 4.9 18.6 1.0
CA A:GLU91 4.9 26.2 1.0
CA A:PRO93 5.0 19.6 1.0
O A:HOH4036 5.0 21.7 1.0
O A:HOH4077 5.0 25.0 1.0
C A:TYR92 5.0 18.1 1.0

Magnesium binding site 2 out of 4 in 1qv9

Go back to Magnesium Binding Sites List in 1qv9
Magnesium binding site 2 out of 4 in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5002

b:23.7
occ:1.00
 O A:HOH4036 1.9 21.7 1.0
O A:HOH4190 2.0 28.0 1.0
O A:HOH4488 2.0 27.6 1.0
O A:HOH4089 2.2 28.9 1.0
O A:GLU111 4.1 25.3 1.0
OE1 A:GLU175 4.2 22.1 1.0
O A:HOH4124 4.3 27.4 1.0
OE2 A:GLU175 4.4 25.9 1.0
O A:HOH4204 4.4 30.0 1.0
O A:HOH4491 4.6 44.5 1.0
CD A:GLU175 4.7 23.4 1.0
C A:GLN112 5.0 22.5 1.0

Magnesium binding site 3 out of 4 in 1qv9

Go back to Magnesium Binding Sites List in 1qv9
Magnesium binding site 3 out of 4 in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5004

b:46.4
occ:1.00
 O A:HOH4180 2.0 32.2 1.0
O A:HOH4178 2.1 35.7 1.0
O A:HOH4279 2.1 33.9 1.0
O A:HOH4361 2.2 32.1 1.0
O A:HOH4471 3.9 36.9 1.0
OD1 A:ASP177 4.0 29.9 1.0
OD2 A:ASP177 4.2 28.3 1.0
O A:GLU172 4.2 33.6 1.0
O A:HOH4409 4.3 43.7 1.0
OE2 A:GLU172 4.4 44.5 1.0
CG A:ASP177 4.5 28.9 1.0
CB A:GLU172 4.6 36.0 1.0

Magnesium binding site 4 out of 4 in 1qv9

Go back to Magnesium Binding Sites List in 1qv9
Magnesium binding site 4 out of 4 in the Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5003

b:30.3
occ:1.00
 O B:HOH4299 2.0 34.7 1.0
O B:HOH4184 2.0 29.6 1.0
OE2 B:GLU228 4.2 32.5 1.0
O B:HOH4114 4.2 30.4 1.0
OE1 B:GLU228 4.3 43.0 1.0
CD B:GLU228 4.6 38.7 1.0
O B:HOH4163 4.7 32.6 1.0

Reference:

C.H.Hagemeier, S.Shima, R.K.Thauer, G.Bourenkov, H.D.Bartunik, U.Ermler. Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri: A Methanogenic Enzyme with An Unusual Quarternary Structure J.Mol.Biol. V. 332 1047 2003.
ISSN: ISSN 0022-2836
PubMed: 14499608
DOI: 10.1016/S0022-2836(03)00949-5
Page generated: Tue Aug 13 11:56:11 2024

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