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Magnesium in PDB 1u6i: The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution

Enzymatic activity of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution

All present enzymatic activity of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution:
1.5.99.9;

Protein crystallography data

The structure of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution, PDB code: 1u6i 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) 19.35 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.900, 118.900, 219.200, 90.00, 90.01, 90.00
R / Rfree (%) 18.9 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution (pdb code 1u6i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution, PDB code: 1u6i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1u6i

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Magnesium binding site 1 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6001

b:19.9
occ:1.00
 O A:HOH9011 2.3 27.7 1.0
O A:HOH9013 2.3 23.6 1.0
O A:HOH9010 2.4 22.7 1.0
O A:HOH9014 2.5 16.0 1.0
O A:HOH9008 2.5 20.7 1.0
O A:HOH8346 3.0 31.2 1.0
O A:HOH8095 3.4 19.6 1.0
OE1 A:GLU175 3.4 29.6 1.0
CG A:GLU175 4.0 26.9 1.0
CD A:GLU175 4.1 29.2 1.0
O A:HOH8067 4.3 18.7 1.0
O A:GLY113 4.5 24.1 1.0
CA A:PRO93 4.6 26.6 1.0
O A:GLU91 4.7 33.4 1.0
O A:TYR92 4.9 30.5 1.0
N A:PRO93 4.9 27.9 1.0
O A:SER90 4.9 31.2 1.0
O A:HOH9087 5.0 22.2 1.0

Magnesium binding site 2 out of 8 in 1u6i

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Magnesium binding site 2 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6002

b:32.9
occ:1.00
 O A:HOH9088 1.9 30.2 1.0
O A:HOH9087 2.1 22.2 1.0
O A:HOH9089 2.3 31.0 1.0
O A:HOH9090 2.3 34.4 1.0
O A:GLU111 3.8 34.8 1.0
OE1 A:GLU175 4.6 29.6 1.0
C A:GLN112 4.6 27.5 1.0
N A:GLY113 4.7 26.6 1.0
OE2 A:GLU175 4.7 31.8 1.0
O A:GLN112 4.8 28.2 1.0
C A:GLU111 4.8 34.2 1.0
CA A:GLY113 4.9 25.9 1.0
CA A:GLN112 5.0 29.3 1.0

Magnesium binding site 3 out of 8 in 1u6i

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Magnesium binding site 3 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6005

b:17.1
occ:1.00
 O B:HOH9017 1.8 22.6 1.0
O B:HOH9018 2.0 30.0 1.0
O B:HOH9015 2.0 40.1 1.0
O B:HOH9019 2.1 22.5 1.0
O B:HOH8542 2.2 30.1 1.0
O B:GLU91 3.9 28.8 1.0
O B:HOH8087 4.2 10.9 1.0
C B:GLU91 4.3 28.7 1.0
OE1 B:GLU175 4.3 23.4 1.0
O B:SER90 4.3 28.2 1.0
CA B:GLU91 4.5 29.8 1.0
O B:HOH8091 4.5 14.2 1.0
O B:HOH8426 4.7 21.1 1.0
O B:HOH8245 4.8 46.4 1.0
O B:HOH8180 4.9 13.9 1.0
C B:TYR92 4.9 25.1 1.0
N B:PRO93 5.0 25.0 1.0
N B:TYR92 5.0 27.1 1.0
O B:TYR92 5.0 24.7 1.0

Magnesium binding site 4 out of 8 in 1u6i

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Magnesium binding site 4 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6006

b:29.7
occ:1.00
 O B:HOH9095 2.0 40.0 1.0
O B:HOH8080 2.0 14.7 1.0
O B:HOH9096 2.1 33.8 1.0
O B:HOH9092 2.6 38.9 1.0
OE1 B:GLU175 3.9 23.4 1.0
OE2 B:GLU175 4.4 27.5 1.0
CD B:GLU175 4.6 24.9 1.0
O B:HOH8180 4.7 13.9 1.0
O B:GLU111 4.8 32.0 1.0

Magnesium binding site 5 out of 8 in 1u6i

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Magnesium binding site 5 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6008

b:29.1
occ:1.00
 O G:HOH9020 1.8 34.5 1.0
O G:HOH9025 2.1 29.8 1.0
O G:HOH9023 2.5 25.7 1.0
O G:HOH9022 2.7 38.0 1.0
O G:GLU111 4.1 35.5 1.0
OE1 G:GLU175 4.2 29.6 1.0
OE2 G:GLU175 4.4 33.3 1.0
C G:GLN112 4.6 26.9 1.0
N G:GLY113 4.6 24.3 1.0
O G:GLN112 4.7 27.3 1.0
CD G:GLU175 4.7 30.6 1.0
CA G:GLY113 4.8 23.6 1.0
O G:HOH8113 4.9 19.0 1.0

Magnesium binding site 6 out of 8 in 1u6i

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Magnesium binding site 6 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6009

b:47.5
occ:1.00
 O G:HOH9100 2.0 30.6 1.0
O G:HOH8113 2.0 19.0 1.0
O G:HOH8333 2.0 11.7 1.0
O G:HOH9099 2.1 42.3 1.0
O G:HOH8341 2.2 9.9 1.0
O G:HOH9097 2.2 35.2 1.0
OE1 G:GLU175 3.8 29.6 1.0
O G:GLU91 4.2 31.4 1.0
O G:SER90 4.2 30.3 1.0
O G:HOH8089 4.3 15.0 1.0
O G:HOH8094 4.4 19.6 1.0
C G:GLU91 4.6 30.4 1.0
O G:HOH9025 4.7 29.8 1.0
CD G:GLU175 4.7 30.6 1.0
CG G:GLU175 4.8 29.0 1.0
CA G:GLU91 5.0 30.8 1.0

Magnesium binding site 7 out of 8 in 1u6i

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Magnesium binding site 7 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg6011

b:26.6
occ:1.00
 O H:HOH8490 2.2 25.4 1.0
O H:HOH8024 2.5 19.8 1.0
O H:HOH9026 2.7 47.9 1.0
OE1 H:GLU175 3.8 25.6 1.0
OE2 H:GLU175 4.1 24.6 1.0
CD H:GLU175 4.4 25.2 1.0
O H:HOH8391 4.7 12.0 1.0
O H:GLU111 4.7 34.4 1.0

Magnesium binding site 8 out of 8 in 1u6i

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Magnesium binding site 8 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.2A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg6012

b:27.5
occ:1.00
 O H:HOH9105 1.9 22.7 1.0
O H:HOH9104 2.0 39.3 1.0
O H:HOH8334 2.0 12.4 1.0
O H:HOH8539 2.1 24.4 1.0
O H:HOH8478 2.5 30.8 1.0
O H:HOH8537 2.7 23.1 1.0
OE1 H:GLU175 3.8 25.6 1.0
O H:HOH8189 3.9 8.3 1.0
O H:GLU91 4.4 28.2 1.0
CG H:GLU175 4.5 23.9 1.0
O H:HOH8391 4.5 12.0 1.0
CD H:GLU175 4.6 25.2 1.0
O H:HOH8188 4.6 15.0 1.0
O H:SER90 4.7 24.7 1.0
C H:GLU91 4.8 26.2 1.0
O H:HOH8490 4.9 25.4 1.0
O H:HOH8275 4.9 24.6 1.0
CA H:PRO93 5.0 23.4 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: Sun Aug 10 05:01:59 2025

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