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Magnesium in PDB 4z3z: Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc

Protein crystallography data

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc, PDB code: 4z3z was solved by T.Weinert, J.W.Kung, S.Weidenweber, S.G.Huwiler, M.Boll, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.51 / 2.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 124.240, 117.430, 143.080, 90.00, 111.04, 90.00
R / Rfree (%) 23.2 / 27.4

Other elements in 4z3z:

The structure of Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Zinc (Zn) 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 Zinc (pdb code 4z3z). 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 Zinc, PDB code: 4z3z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4z3z

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Magnesium binding site 1 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:0.3
occ:1.00
O2P A:MTE704 1.9 0.4 1.0
O3P A:MTE703 2.0 93.4 1.0
O A:SER183 2.0 0.9 1.0
O A:MET94 2.2 0.8 1.0
P A:MTE704 3.1 0.0 1.0
P A:MTE703 3.2 84.8 1.0
C A:SER183 3.2 0.7 1.0
O1P A:MTE703 3.4 82.7 1.0
C A:MET94 3.4 0.6 1.0
O3P A:MTE704 3.4 0.3 1.0
C4' A:MTE704 3.7 92.4 1.0
OG A:SER185 3.7 0.6 1.0
O4' A:MTE704 3.8 94.7 1.0
O4' A:MTE703 3.9 68.5 1.0
C4' A:MTE703 4.0 74.1 1.0
CA A:MET95 4.0 0.0 1.0
N A:ALA184 4.1 0.4 1.0
CA A:ALA184 4.1 0.2 1.0
N A:SER185 4.1 0.4 1.0
N A:MET95 4.2 0.8 1.0
O1P A:MTE704 4.3 1.0 1.0
CA A:SER183 4.3 0.3 1.0
O2P A:MTE703 4.4 81.8 1.0
N A:SER183 4.4 0.0 1.0
CA A:MET94 4.5 0.7 1.0
CB A:SER185 4.6 0.4 1.0
N A:MET94 4.6 0.5 1.0
C A:ALA184 4.6 0.6 1.0
CB A:SER183 4.7 0.4 1.0
CB A:MET95 4.7 0.4 1.0
OG A:SER93 4.8 0.8 1.0
CB A:MET94 4.9 0.5 1.0
O3' A:MTE703 5.0 82.2 1.0

Magnesium binding site 2 out of 4 in 4z3z

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Magnesium binding site 2 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:64.2
occ:1.00
O3P B:MTE703 2.0 67.0 1.0
O B:SER183 2.1 64.0 1.0
O2P B:MTE704 2.1 69.5 1.0
O B:MET94 2.2 72.0 1.0
O2P B:MTE703 2.6 58.7 1.0
P B:MTE703 2.8 61.5 1.0
C B:SER183 3.3 63.4 1.0
C B:MET94 3.4 69.6 1.0
P B:MTE704 3.6 67.6 1.0
C4' B:MTE703 3.7 34.9 1.0
C4' B:MTE704 3.8 67.7 1.0
O4' B:MTE703 3.8 31.5 1.0
OG B:SER185 3.9 59.3 1.0
CA B:MET95 3.9 71.5 1.0
O1P B:MTE703 4.0 57.9 1.0
N B:MET95 4.1 70.8 1.0
N B:ALA184 4.2 62.1 1.0
O4' B:MTE704 4.2 65.9 1.0
O1P B:MTE704 4.2 73.2 1.0
CA B:SER183 4.3 63.7 1.0
CA B:ALA184 4.3 58.4 1.0
N B:SER183 4.3 65.3 1.0
N B:SER185 4.4 60.3 1.0
CA B:MET94 4.5 63.7 1.0
O3P B:MTE704 4.6 62.9 1.0
CB B:MET95 4.6 73.9 1.0
CB B:SER183 4.7 62.9 1.0
N B:MET94 4.7 61.4 1.0
CB B:SER185 4.8 61.8 1.0
C B:ALA184 4.9 57.5 1.0
CB B:MET94 4.9 62.9 1.0
C3' B:MTE703 5.0 44.1 1.0

Magnesium binding site 3 out of 4 in 4z3z

Go back to Magnesium Binding Sites List in 4z3z
Magnesium binding site 3 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:47.2
occ:1.00
O2P C:MTE704 2.0 0.5 1.0
O3P C:MTE703 2.0 86.1 1.0
O C:SER183 2.2 96.0 1.0
O C:MET94 2.6 78.5 1.0
P C:MTE703 3.1 86.2 1.0
P C:MTE704 3.2 94.3 1.0
O2P C:MTE703 3.2 46.6 1.0
C4' C:MTE704 3.2 63.3 1.0
C C:SER183 3.5 93.8 1.0
OG C:SER185 3.5 79.7 1.0
O1P C:MTE704 3.6 87.3 1.0
O4' C:MTE704 3.6 63.0 1.0
C C:MET94 3.8 84.8 1.0
C4' C:MTE703 3.8 59.1 1.0
O4' C:MTE703 3.9 55.3 1.0
N C:SER185 4.2 80.9 1.0
O1P C:MTE703 4.3 87.9 1.0
N C:ALA184 4.3 90.8 1.0
CB C:SER185 4.4 80.5 1.0
CA C:ALA184 4.4 86.8 1.0
O3P C:MTE704 4.4 94.1 1.0
CA C:SER183 4.4 91.8 1.0
CA C:MET95 4.5 84.0 1.0
C3' C:MTE704 4.5 60.7 1.0
N C:SER183 4.6 89.0 1.0
N C:MET95 4.6 87.1 1.0
CB C:SER183 4.7 92.0 1.0
C C:ALA184 4.8 83.7 1.0
CA C:MET94 4.8 91.3 1.0
O3' C:MTE704 4.8 60.4 1.0
N C:MET94 4.9 94.7 1.0
CA C:SER185 5.0 81.2 1.0
OG C:SER183 5.0 93.3 1.0

Magnesium binding site 4 out of 4 in 4z3z

Go back to Magnesium Binding Sites List in 4z3z
Magnesium binding site 4 out of 4 in the Active Site Complex Bambc of Benzoyl Coenzyme A Reductase in Complex with Zinc


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 Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:43.6
occ:1.00
O2P D:MTE704 1.9 82.5 1.0
O D:SER183 2.1 70.0 1.0
O3P D:MTE703 2.1 73.9 1.0
O D:MET94 2.8 69.5 1.0
C4' D:MTE704 3.2 42.7 1.0
P D:MTE704 3.2 74.5 1.0
OG D:SER185 3.3 56.9 1.0
P D:MTE703 3.3 70.0 1.0
C D:SER183 3.3 67.6 1.0
O1P D:MTE703 3.4 64.7 1.0
O4' D:MTE704 3.6 38.2 1.0
C D:MET94 4.0 71.3 1.0
O1P D:MTE704 4.0 76.7 1.0
O4' D:MTE703 4.0 53.9 1.0
N D:SER185 4.1 59.1 1.0
CB D:SER185 4.2 58.0 1.0
C4' D:MTE703 4.2 54.8 1.0
O3P D:MTE704 4.2 75.9 1.0
CA D:SER183 4.2 67.7 1.0
N D:ALA184 4.3 66.9 1.0
CA D:ALA184 4.3 66.5 1.0
N D:SER183 4.4 71.5 1.0
O2P D:MTE703 4.5 70.8 1.0
CB D:SER183 4.5 65.9 1.0
C3' D:MTE704 4.5 41.2 1.0
CA D:MET95 4.6 69.6 1.0
N5 D:MTE704 4.7 51.2 1.0
C D:ALA184 4.7 61.7 1.0
O3' D:MTE704 4.7 42.8 1.0
OG D:SER183 4.8 65.9 1.0
N D:MET95 4.8 72.1 1.0
CA D:SER185 4.8 57.2 1.0
C9 D:MTE704 5.0 55.8 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 19:56:23 2020

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