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Magnesium in PDB 1u6j: The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A Resolution

Enzymatic activity of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A Resolution

All present enzymatic activity of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A Resolution:
1.5.99.9;

Protein crystallography data

The structure of The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A Resolution, PDB code: 1u6j 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 / 2.40
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 (%) 17.5 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A Resolution (pdb code 1u6j). 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 2.4A Resolution, PDB code: 1u6j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1u6j

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Magnesium binding site 1 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6001

b:29.1
occ:1.00
 O A:HOH9013 2.0 13.1 1.0
O A:HOH9010 2.2 18.4 1.0
O A:HOH9014 2.3 25.5 1.0
O A:HOH9008 2.3 33.3 1.0
O A:HOH9011 2.5 12.2 1.0
O A:SER90 3.9 44.0 1.0
OE1 A:GLU175 4.0 33.0 1.0
O A:GLU91 4.2 39.3 1.0
O A:HOH8414 4.3 29.8 1.0
C A:GLU91 4.4 39.5 1.0
CA A:GLU91 4.6 41.0 1.0
O A:HOH9087 4.8 36.0 1.0
O A:HOH8060 4.8 21.6 1.0
C A:SER90 4.9 42.1 1.0

Magnesium binding site 2 out of 8 in 1u6j

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Magnesium binding site 2 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg6002

b:25.8
occ:1.00
 O A:HOH9087 1.8 36.0 1.0
O A:HOH8387 2.0 26.1 1.0
O A:HOH9089 2.2 30.3 1.0
O A:HOH9090 2.2 32.1 1.0
O A:HOH9088 2.3 38.1 1.0
O A:HOH9091 3.0 46.0 1.0
O A:HOH8414 3.8 29.8 1.0
OE1 A:GLU175 4.1 33.0 1.0
OE2 A:GLU175 4.3 35.3 1.0
O A:GLU111 4.4 43.0 1.0
CD A:GLU175 4.6 33.4 1.0
O A:HOH9014 4.7 25.5 1.0
C A:GLN112 4.8 37.6 1.0
N A:GLY113 4.8 37.1 1.0
O A:GLN112 4.9 37.9 1.0
CA A:GLY113 4.9 35.8 1.0

Magnesium binding site 3 out of 8 in 1u6j

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Magnesium binding site 3 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6003

b:25.5
occ:1.00
 O B:HOH9018 1.8 30.9 1.0
O B:HOH9017 2.0 48.2 1.0
O B:HOH9009 2.0 26.6 1.0
O B:HOH9015 2.2 26.2 1.0
O B:HOH9019 2.4 30.2 1.0
O B:SER90 4.0 32.0 1.0
O B:GLU91 4.1 33.7 1.0
O B:HOH8030 4.2 14.4 1.0
C B:GLU91 4.3 32.6 1.0
OE1 B:GLU175 4.4 33.1 1.0
CA B:GLU91 4.4 33.1 1.0
O B:HOH9092 4.6 26.0 1.0
O B:HOH8038 4.8 22.5 1.0
O B:HOH8109 5.0 13.6 1.0
C B:SER90 5.0 31.0 1.0
N B:TYR92 5.0 31.8 1.0

Magnesium binding site 4 out of 8 in 1u6j

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Magnesium binding site 4 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg6004

b:30.2
occ:1.00
 O B:HOH8239 2.1 12.0 1.0
O B:HOH9092 2.6 26.0 1.0
OE1 B:GLU175 3.7 33.1 1.0
OE2 B:GLU175 3.9 37.0 1.0
CD B:GLU175 4.2 35.0 1.0
O B:GLU111 4.4 30.6 1.0
N B:GLY113 4.7 26.4 1.0
C B:GLN112 4.7 26.4 1.0
CA B:GLY113 4.7 25.5 1.0
O B:GLN112 4.8 26.3 1.0

Magnesium binding site 5 out of 8 in 1u6j

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Magnesium binding site 5 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6005

b:35.5
occ:1.00
 O G:HOH9025 1.8 52.1 1.0
O G:HOH9020 2.0 44.9 1.0
O G:HOH8421 2.0 25.3 1.0
O G:HOH9021 2.2 62.3 1.0
O G:HOH9024 2.5 53.0 1.0
O G:HOH9023 2.9 29.3 1.0
O G:HOH9022 3.7 27.4 1.0
O G:HOH8321 4.0 17.2 1.0
OE1 G:GLU175 4.2 33.5 1.0
OE2 G:GLU175 4.6 37.8 1.0
O G:GLU111 4.7 42.6 1.0
CD G:GLU175 4.8 35.3 1.0
O G:HOH8235 4.9 16.4 1.0
O G:HOH8021 4.9 25.9 1.0

Magnesium binding site 6 out of 8 in 1u6j

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Magnesium binding site 6 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg6006

b:21.7
occ:1.00
 O G:HOH8243 1.9 32.4 1.0
O G:HOH8236 2.2 7.2 1.0
O G:HOH8235 2.7 16.4 1.0
O G:HOH8021 2.8 25.9 1.0
O G:GLU91 3.6 36.3 1.0
C G:GLU91 4.0 35.5 1.0
O G:SER90 4.3 37.0 1.0
OE1 G:GLU175 4.3 33.5 1.0
CA G:GLU91 4.4 36.6 1.0
O G:HOH8049 4.8 20.9 1.0
N G:TYR92 4.8 35.4 1.0
C G:TYR92 4.8 33.8 1.0
N G:PRO93 4.9 34.0 1.0
O G:TYR92 5.0 33.5 1.0

Magnesium binding site 7 out of 8 in 1u6j

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Magnesium binding site 7 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg6007

b:34.0
occ:1.00
 O H:HOH9029 2.2 31.8 1.0
O H:HOH9028 2.2 50.0 1.0
O H:HOH9030 2.4 45.3 1.0
O H:HOH9031 3.6 29.9 1.0
OE1 H:GLU175 3.7 28.2 1.0
OE2 H:GLU175 4.0 27.0 1.0
CD H:GLU175 4.3 28.6 1.0
O H:GLU111 4.6 31.5 1.0
O H:GLN112 4.9 24.2 1.0
C H:GLN112 4.9 26.4 1.0
N H:GLY113 4.9 25.1 1.0
CA H:GLY113 4.9 26.1 1.0

Magnesium binding site 8 out of 8 in 1u6j

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Magnesium binding site 8 out of 8 in the The Structure of Native Coenzyme F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase at 2.4A 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 2.4A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg6008

b:27.8
occ:1.00
 O H:HOH9105 2.0 46.5 1.0
O H:HOH9104 2.2 48.6 1.0
O H:HOH9102 2.3 30.7 1.0
O H:HOH8240 2.3 45.3 1.0
O H:HOH9031 3.2 29.9 1.0
O H:SER90 3.9 27.1 1.0
O H:GLU91 4.3 32.8 1.0
OE1 H:GLU175 4.3 28.2 1.0
CA H:GLU91 4.4 30.3 1.0
C H:GLU91 4.4 31.1 1.0
O H:HOH9106 4.6 28.5 1.0
C H:SER90 4.9 25.8 1.0
O H:HOH8265 5.0 12.7 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: Tue Aug 13 14:44:53 2024

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