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Magnesium in PDB 1u6k: Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri

Enzymatic activity of Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri

All present enzymatic activity of Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri:
1.5.99.9;

Protein crystallography data

The structure of Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri, PDB code: 1u6k was solved by E.Warkentin, C.H.Hagemeier, S.Shima, R.K.Thauer, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.55
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 (%) 17.8 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri (pdb code 1u6k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri, PDB code: 1u6k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1u6k

Go back to Magnesium Binding Sites List in 1u6k
Magnesium binding site 1 out of 4 in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri


Mono view


Stereo pair view

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

b:19.2
occ:1.00
 O A:HOH4034 1.9 22.2 1.0
O A:HOH4014 1.9 22.0 1.0
O A:HOH4009 2.1 18.9 1.0
OE1 A:GLU175 3.9 26.1 1.0
O A:HOH4004 4.2 17.1 1.0
O A:GLU91 4.3 24.8 1.0
O A:HOH4030 4.3 20.4 1.0
O A:SER90 4.4 26.1 1.0
O A:HOH4124 4.5 26.8 1.0
C A:GLU91 4.6 24.9 1.0
CG A:GLU175 4.7 25.2 1.0
CD A:GLU175 4.7 26.0 1.0
N A:PRO93 4.9 21.4 1.0
CA A:GLU91 4.9 26.9 1.0
CA A:PRO93 5.0 21.2 1.0
O A:HOH4036 5.0 21.9 1.0
O A:HOH4077 5.0 26.4 1.0
C A:TYR92 5.0 21.7 1.0

Magnesium binding site 2 out of 4 in 1u6k

Go back to Magnesium Binding Sites List in 1u6k
Magnesium binding site 2 out of 4 in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri


Mono view


Stereo pair view

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

b:23.5
occ:1.00
 O A:HOH4036 1.9 21.9 1.0
O A:HOH4190 2.0 29.0 1.0
O A:HOH4488 2.0 27.1 1.0
O A:HOH4089 2.2 28.5 1.0
O A:GLU111 4.1 27.3 1.0
OE1 A:GLU175 4.2 26.1 1.0
O A:HOH4124 4.3 26.8 1.0
OE2 A:GLU175 4.4 29.1 1.0
O A:HOH4204 4.4 29.7 1.0
O A:HOH4491 4.6 38.2 1.0
CD A:GLU175 4.7 26.0 1.0
C A:GLN112 5.0 24.2 1.0

Magnesium binding site 3 out of 4 in 1u6k

Go back to Magnesium Binding Sites List in 1u6k
Magnesium binding site 3 out of 4 in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5003

b:30.3
occ:1.00
 O A:HOH4091 2.0 29.9 1.0
O A:HOH4213 2.0 34.8 1.0
O A:HOH4510 2.1 30.9 1.0
O A:HOH4210 2.2 31.0 1.0
OE1 A:GLU91 4.1 42.1 1.0
O A:HOH4346 4.2 33.6 1.0
O A:GLU91 4.4 24.8 1.0
O A:HOH4092 4.4 26.9 1.0
O A:HOH4570 4.4 41.7 1.0
OD2 A:ASP171 4.6 36.1 1.0
O A:HOH4302 4.9 38.5 1.0

Magnesium binding site 4 out of 4 in 1u6k

Go back to Magnesium Binding Sites List in 1u6k
Magnesium binding site 4 out of 4 in the Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tls Refinement of the Structure of Se-Methionine Labelled Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase (Mtd) From Methanopyrus Kandleri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5004

b:37.2
occ:1.00
 O A:HOH4180 2.0 32.2 1.0
O A:HOH4178 2.1 34.7 1.0
O A:HOH4279 2.1 34.0 1.0
O A:HOH4361 2.2 33.8 1.0
O A:HOH4471 3.9 35.1 1.0
OD1 A:ASP177 4.0 31.4 1.0
OD2 A:ASP177 4.2 29.9 1.0
O A:GLU172 4.2 33.5 1.0
O A:HOH4409 4.3 40.7 1.0
OE2 A:GLU172 4.4 42.3 1.0
CG A:ASP177 4.5 27.9 1.0
CB A:GLU172 4.6 35.9 1.0

Reference:

E.Warkentin, C.H.Hagemeier, S.Shima, R.K.Thauer, U.Ermler. The Structure of F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase: A Crystallographic 'Superstructure' of the Selenomethionine-Labelled Protein Crystal Structure. Acta Crystallogr.,Sect.D V. 61 198 2005.
ISSN: ISSN 0907-4449
PubMed: 15681872
DOI: 10.1107/S0907444904030732
Page generated: Mon Dec 14 06:52:37 2020

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