Atomistry » Magnesium » PDB 4doa-4dv5 » 4dpm
Atomistry »
  Magnesium »
    PDB 4doa-4dv5 »
      4dpm »

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

Go back to Magnesium Binding Sites List in 4dpm
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

Go back to Magnesium Binding Sites List in 4dpm
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

Go back to Magnesium Binding Sites List in 4dpm
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

Go back to Magnesium Binding Sites List in 4dpm
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

Go back to Magnesium Binding Sites List in 4dpm
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

Go back to Magnesium Binding Sites List in 4dpm
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: Thu Aug 15 17:19:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy