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Magnesium in PDB 4z3w: Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa

Protein crystallography data

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa, PDB code: 4z3w was solved by T.Weinert, J.Kung, S.Weidenweber, S.Huwiler, M.Boll, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.63 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 125.340, 116.300, 144.160, 90.00, 110.48, 90.00
R / Rfree (%) 17.8 / 22.2

Other elements in 4z3w:

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Iron (Fe) 64 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa (pdb code 4z3w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa, PDB code: 4z3w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4z3w

Go back to Magnesium Binding Sites List in 4z3w
Magnesium binding site 1 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:30.4
occ:1.00
O A:HOH807 1.9 27.2 1.0
O A:HOH853 2.0 28.0 1.0
O A:MET94 2.0 31.0 1.0
O3P A:MTE702 2.1 26.0 1.0
O2P A:MTE703 2.1 31.0 1.0
O A:SER183 2.2 31.4 1.0
P A:MTE703 3.2 28.7 1.0
C A:MET94 3.2 32.6 1.0
O3P A:MTE703 3.3 21.2 1.0
P A:MTE702 3.4 25.2 1.0
C A:SER183 3.4 30.9 1.0
O A:HOH815 3.5 28.2 1.0
C4' A:MTE703 3.7 24.7 1.0
O1P A:MTE702 3.8 18.0 1.0
O4' A:MTE703 3.9 30.5 1.0
OG A:SER185 4.1 38.0 1.0
N A:MET95 4.1 29.9 1.0
CA A:ALA184 4.1 32.1 1.0
CA A:MET95 4.2 28.2 1.0
N A:ALA184 4.2 30.2 1.0
N A:SER185 4.2 31.3 1.0
CA A:MET94 4.2 30.9 1.0
O4' A:MTE702 4.3 39.7 1.0
C4' A:MTE702 4.3 29.4 1.0
N A:MET94 4.3 30.6 1.0
O1P A:MTE703 4.4 30.8 1.0
O2P A:MTE702 4.5 26.9 1.0
CA A:SER183 4.6 36.0 1.0
CB A:MET94 4.6 25.8 1.0
C A:ALA184 4.7 31.5 1.0
CB A:SER185 4.7 35.5 1.0
N A:SER183 4.7 38.5 1.0
OG A:SER93 4.9 28.3 1.0
C3' A:MTE703 5.0 22.6 1.0
CB A:SER183 5.0 35.2 1.0

Magnesium binding site 2 out of 4 in 4z3w

Go back to Magnesium Binding Sites List in 4z3w
Magnesium binding site 2 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:47.8
occ:1.00
O3P B:MTE702 2.0 61.1 1.0
O B:MET94 2.0 65.0 1.0
O B:SER183 2.3 65.8 1.0
O1P B:MTE703 2.5 63.3 1.0
O B:HOH807 2.5 38.9 1.0
O B:HOH829 2.5 41.2 1.0
C B:MET94 3.2 63.6 1.0
P B:MTE702 3.2 58.1 1.0
O2P B:MTE703 3.4 64.7 1.0
P B:MTE703 3.5 64.9 1.0
C B:SER183 3.5 66.7 1.0
O1P B:MTE702 3.5 49.0 1.0
O B:HOH821 3.6 40.0 1.0
C4' B:MTE702 3.9 43.1 1.0
C4' B:MTE703 3.9 48.4 1.0
O4' B:MTE702 4.0 42.5 1.0
N B:MET95 4.0 63.7 1.0
CA B:MET95 4.0 63.8 1.0
O4' B:MTE703 4.2 48.1 1.0
OG B:SER185 4.2 75.1 1.0
CA B:MET94 4.2 64.0 1.0
CA B:ALA184 4.2 68.3 1.0
N B:ALA184 4.3 67.5 1.0
O2P B:MTE702 4.3 54.4 1.0
N B:MET94 4.4 67.1 1.0
N B:SER185 4.4 70.1 1.0
CB B:MET94 4.6 60.4 1.0
CA B:SER183 4.6 67.8 1.0
N B:SER183 4.7 65.0 1.0
O3P B:MTE703 4.7 67.6 1.0
CB B:SER185 4.9 71.7 1.0
C B:ALA184 4.9 70.7 1.0
CB B:MET95 4.9 66.8 1.0

Magnesium binding site 3 out of 4 in 4z3w

Go back to Magnesium Binding Sites List in 4z3w
Magnesium binding site 3 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg704

b:37.7
occ:1.00
O C:MET94 2.0 40.2 1.0
O3P C:MTE702 2.1 32.7 1.0
O2P C:MTE703 2.1 35.4 1.0
O C:SER183 2.1 38.9 1.0
O C:HOH837 2.2 41.2 1.0
O C:HOH860 2.2 35.2 1.0
C C:MET94 3.2 38.0 1.0
P C:MTE702 3.3 32.3 1.0
C C:SER183 3.3 36.8 1.0
P C:MTE703 3.3 39.6 1.0
O2P C:MTE702 3.4 28.1 1.0
O1P C:MTE703 3.5 39.7 1.0
C4' C:MTE703 3.8 40.6 1.0
O C:HOH859 3.9 32.9 1.0
CA C:ALA184 4.0 32.9 1.0
CA C:MET95 4.0 40.7 1.0
N C:ALA184 4.1 33.0 1.0
N C:MET95 4.1 38.7 1.0
OG C:SER185 4.1 40.2 1.0
O4' C:MTE703 4.1 42.3 1.0
N C:SER185 4.1 35.3 1.0
O4' C:MTE702 4.2 31.2 1.0
CA C:MET94 4.3 34.9 1.0
C4' C:MTE702 4.3 31.3 1.0
O1P C:MTE702 4.4 33.5 1.0
N C:MET94 4.4 36.4 1.0
CA C:SER183 4.4 36.2 1.0
O3P C:MTE703 4.5 39.9 1.0
N C:SER183 4.6 36.5 1.0
C C:ALA184 4.6 32.1 1.0
CB C:SER185 4.7 41.3 1.0
CB C:MET94 4.7 35.2 1.0
CB C:MET95 4.7 40.2 1.0
OG C:SER93 4.8 37.3 1.0
CB C:SER183 4.9 36.8 1.0

Magnesium binding site 4 out of 4 in 4z3w

Go back to Magnesium Binding Sites List in 4z3w
Magnesium binding site 4 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with 1,5 Dienoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:32.9
occ:1.00
O D:MET94 2.1 36.8 1.0
O3P D:MTE703 2.1 32.7 1.0
O2P D:MTE704 2.1 47.8 1.0
O D:HOH838 2.1 28.5 1.0
O D:SER183 2.2 40.0 1.0
O D:HOH836 2.2 35.3 1.0
O1P D:MTE704 3.2 28.9 1.0
P D:MTE704 3.2 36.0 1.0
C D:MET94 3.3 41.2 1.0
P D:MTE703 3.4 31.6 1.0
C D:SER183 3.4 38.9 1.0
O2P D:MTE703 3.5 19.7 1.0
C4' D:MTE704 3.7 29.1 1.0
OG D:SER185 3.8 32.9 1.0
O D:HOH828 3.9 31.7 1.0
O4' D:MTE704 3.9 35.9 1.0
CA D:ALA184 4.1 41.6 1.0
N D:MET95 4.1 41.5 1.0
N D:SER185 4.1 35.8 1.0
N D:ALA184 4.2 42.4 1.0
C4' D:MTE703 4.2 37.4 1.0
CA D:MET95 4.2 42.6 1.0
O4' D:MTE703 4.2 39.5 1.0
CA D:MET94 4.3 39.5 1.0
N D:MET94 4.4 42.0 1.0
O1P D:MTE703 4.4 34.5 1.0
CA D:SER183 4.5 37.0 1.0
O3P D:MTE704 4.5 36.4 1.0
N D:SER183 4.6 37.9 1.0
C D:ALA184 4.7 43.1 1.0
CB D:MET94 4.7 38.9 1.0
CB D:SER185 4.7 34.1 1.0
CB D:SER183 4.9 34.4 1.0
C3' D:MTE704 4.9 30.5 1.0
OG D:SER93 5.0 42.3 1.0

Reference:

T.Weinert, S.G.Huwiler, J.W.Kung, S.Weidenweber, P.Hellwig, H.J.Stark, T.Biskup, S.Weber, J.J.Cotelesage, G.N.George, U.Ermler, M.Boll. Structural Basis of Enzymatic Benzene Ring Reduction. Nat.Chem.Biol. V. 11 586 2015.
ISSN: ESSN 1552-4469
PubMed: 26120796
DOI: 10.1038/NCHEMBIO.1849
Page generated: Mon Dec 14 19:56:12 2020

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