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Magnesium in PDB 4dpm: Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa

Enzymatic activity of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa

All present enzymatic activity of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa:
1.2.1.75; 1.2.1.76;

Protein crystallography data

The structure of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa, PDB code: 4dpm was solved by U.Demmer, E.Warkentin, A.Srivastava, D.Kockelkorn, G.Fuchs, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 111.630, 137.620, 362.010, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa (pdb code 4dpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa, PDB code: 4dpm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4dpm

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Magnesium binding site 1 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:52.3
occ:1.00
 O4A A:COA402 2.2 39.7 1.0
O1A A:COA402 2.4 53.9 1.0
O A:TYR187 2.4 25.7 1.0
O2A A:COA402 3.0 48.8 1.0
P1A A:COA402 3.2 43.4 1.0
C A:TYR187 3.4 21.3 1.0
P2A A:COA402 3.4 33.6 1.0
O3A A:COA402 3.8 38.5 1.0
N A:TYR187 4.0 19.9 1.0
CD A:PRO188 4.1 21.3 1.0
N A:PRO188 4.2 21.9 1.0
O A:HOH626 4.2 39.5 1.0
CA A:TYR187 4.4 19.2 1.0
O5A A:COA402 4.4 32.8 1.0
O5B A:COA402 4.5 43.1 1.0
O6A A:COA402 4.6 32.6 1.0
CB A:TYR187 4.7 19.2 1.0
CCP A:COA402 4.8 38.3 1.0

Magnesium binding site 2 out of 6 in 4dpm

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Magnesium binding site 2 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:48.4
occ:1.00
 O B:HOH693 2.2 39.8 1.0
O2A B:COA402 2.4 53.6 1.0
O4A B:COA402 2.4 44.0 1.0
O B:TYR187 2.4 33.4 1.0
O1A B:COA402 2.5 46.9 1.0
P1A B:COA402 3.0 45.5 1.0
O B:HOH662 3.0 33.6 1.0
P2A B:COA402 3.3 36.3 1.0
O3A B:COA402 3.5 38.3 1.0
C B:TYR187 3.6 23.5 1.0
O B:HOH677 3.8 46.5 1.0
N B:TYR187 4.2 19.8 1.0
CD B:PRO188 4.2 22.6 1.0
O5A B:COA402 4.2 40.3 1.0
O B:HOH645 4.3 33.8 1.0
N B:PRO188 4.4 22.5 1.0
O5B B:COA402 4.5 48.9 1.0
O6A B:COA402 4.5 40.7 1.0
CA B:TYR187 4.6 20.8 1.0
CCP B:COA402 4.8 44.2 1.0
CB B:TYR187 4.9 20.2 1.0
C5B B:COA402 5.0 43.2 1.0
O B:HOH656 5.0 38.2 1.0

Magnesium binding site 3 out of 6 in 4dpm

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Magnesium binding site 3 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:75.8
occ:1.00
 O1A C:COA402 2.2 80.7 1.0
O C:TYR187 2.2 62.3 1.0
O4A C:COA402 2.4 63.5 1.0
C C:TYR187 3.4 60.2 1.0
P1A C:COA402 3.5 70.3 1.0
P2A C:COA402 3.6 65.0 1.0
O3A C:COA402 3.7 65.4 1.0
O C:HOH612 4.1 58.9 1.0
N C:TYR187 4.2 57.7 1.0
O5B C:COA402 4.2 65.8 1.0
CD C:PRO188 4.2 60.8 1.0
N C:PRO188 4.3 60.1 1.0
CA C:TYR187 4.3 59.6 1.0
O6A C:COA402 4.5 63.3 1.0
O2A C:COA402 4.6 76.2 1.0
CB C:TYR187 4.7 60.0 1.0
O5A C:COA402 4.8 63.2 1.0

Magnesium binding site 4 out of 6 in 4dpm

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Magnesium binding site 4 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:0.9
occ:1.00
 O D:TYR187 2.1 0.5 1.0
O1A D:COA402 2.1 1.0 1.0
O D:HOH623 2.3 63.8 1.0
O4A D:COA402 2.6 0.8 1.0
C D:TYR187 3.3 0.0 1.0
P1A D:COA402 3.5 0.5 1.0
P2A D:COA402 3.8 0.3 1.0
O3A D:COA402 3.9 0.9 1.0
CD D:PRO188 4.1 0.2 1.0
N D:PRO188 4.2 0.9 1.0
N D:TYR187 4.2 0.8 1.0
CA D:TYR187 4.3 0.3 1.0
O5B D:COA402 4.3 0.8 1.0
O D:HOH614 4.4 58.0 1.0
O6A D:COA402 4.6 0.1 1.0
O2A D:COA402 4.7 0.7 1.0
CB D:TYR187 4.7 0.8 1.0
O5A D:COA402 4.9 0.3 1.0

Magnesium binding site 5 out of 6 in 4dpm

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Magnesium binding site 5 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:78.9
occ:1.00
 O1A E:COA402 2.1 80.3 1.0
O E:TYR187 2.1 74.3 1.0
O E:HOH611 2.4 53.2 1.0
O4A E:COA402 2.5 74.5 1.0
O E:HOH650 2.7 52.9 1.0
C E:TYR187 3.3 63.0 1.0
P1A E:COA402 3.4 74.8 1.0
P2A E:COA402 3.8 73.1 1.0
O3A E:COA402 3.8 76.3 1.0
CD E:PRO188 4.1 60.0 1.0
O5B E:COA402 4.2 69.4 1.0
N E:PRO188 4.2 61.6 1.0
N E:TYR187 4.2 61.1 1.0
CA E:TYR187 4.3 61.7 1.0
O2A E:COA402 4.6 80.7 1.0
O6A E:COA402 4.6 72.0 1.0
CB E:TYR187 4.6 63.1 1.0
O E:HOH631 4.8 52.5 1.0
O5A E:COA402 4.9 75.7 1.0

Magnesium binding site 6 out of 6 in 4dpm

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Magnesium binding site 6 out of 6 in the Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Malonyl-Coenzyme A Reductase From Crenarchaeota in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:0.7
occ:1.00
 O1A F:COA402 1.9 0.0 1.0
O F:TYR187 2.0 0.2 1.0
O4A F:COA402 2.3 0.4 1.0
C F:TYR187 3.2 0.1 1.0
P1A F:COA402 3.4 0.2 1.0
P2A F:COA402 3.6 0.4 1.0
O3A F:COA402 3.9 0.7 1.0
O F:HOH623 4.0 66.2 1.0
CD F:PRO188 4.1 0.9 1.0
N F:TYR187 4.1 0.8 1.0
N F:PRO188 4.1 0.9 1.0
CA F:TYR187 4.2 0.6 1.0
O5B F:COA402 4.2 0.6 1.0
O2A F:COA402 4.5 0.0 1.0
O6A F:COA402 4.5 0.3 1.0
CB F:TYR187 4.6 0.1 1.0
O5A F:COA402 4.8 0.7 1.0

Reference:

U.Demmer, E.Warkentin, A.Srivastava, D.Kockelkorn, M.Potter, A.Marx, G.Fuchs, U.Ermler. Structural Basis For A Bispecific Nadp+ and Coa Binding Site in An Archaeal Malonyl-Coenzyme A Reductase. J.Biol.Chem. V. 288 6363 2013.
ISSN: ISSN 0021-9258
PubMed: 23325803
DOI: 10.1074/JBC.M112.421263
Page generated: Mon Dec 14 12:48:21 2020

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