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Magnesium in PDB 5m45: Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus

Enzymatic activity of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus

All present enzymatic activity of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus:
6.4.1.6;

Protein crystallography data

The structure of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus, PDB code: 5m45 was solved by B.V.Kabasakal, J.N.Wells, B.C.Nwaobi, B.J.Eilers, J.W.Peters, J.W.Murray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 126.06 / 1.87
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 86.915, 139.733, 165.827, 65.89, 86.54, 88.69
R / Rfree (%) 19.2 / 21.7

Other elements in 5m45:

The structure of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus (pdb code 5m45). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus, PDB code: 5m45:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in 5m45

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Magnesium binding site 1 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:18.9
occ:1.00
O A:VAL768 2.3 16.9 1.0
O A:HOH1194 2.3 22.4 1.0
O A:SER763 2.5 19.2 1.0
O A:HOH1395 3.1 37.5 1.0
C A:SER763 3.5 17.9 1.0
C A:VAL768 3.6 17.0 1.0
CB A:SER763 3.7 18.4 1.0
CA A:SER763 3.8 17.4 1.0
CA A:VAL768 4.5 16.1 1.0
N A:HIS769 4.5 17.6 1.0
CA A:HIS769 4.6 18.2 1.0
O A:LEU765 4.6 16.3 1.0
N A:VAL768 4.6 16.0 1.0
OG A:SER763 4.6 19.5 1.0
N A:GLU764 4.7 17.9 1.0
CB A:VAL768 4.7 15.6 1.0

Magnesium binding site 2 out of 24 in 5m45

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Magnesium binding site 2 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:23.7
occ:1.00
O A:HOH1356 2.2 32.9 1.0
O A:HOH1087 2.4 43.3 1.0
O A:HOH1222 2.4 20.5 1.0
OG A:SER759 2.6 18.2 1.0
O A:SER759 2.6 15.9 1.0
C A:SER759 3.4 16.4 1.0
CB A:SER759 3.7 17.1 1.0
CA A:SER759 3.8 17.0 1.0
N A:SER759 3.8 17.3 1.0
OD2 A:ASP391 4.4 16.5 1.0
N A:MET760 4.4 15.4 1.0
OE2 A:GLU764 4.6 21.6 1.0
O A:ASP391 4.8 14.1 1.0
CA A:MET760 4.8 15.5 1.0

Magnesium binding site 3 out of 24 in 5m45

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Magnesium binding site 3 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:16.2
occ:1.00
O B:HOH1111 2.2 34.1 1.0
O2P B:AMP801 2.2 28.2 1.0
O B:HOH1011 2.4 29.3 1.0
OD2 B:ASP24 2.5 28.5 1.0
O B:MET22 2.6 30.4 1.0
O B:HOH1066 2.6 20.0 1.0
O3P B:AMP801 2.7 28.2 1.0
P B:AMP801 3.0 28.7 1.0
CG B:ASP24 3.5 26.9 1.0
C B:MET22 3.7 29.1 1.0
OD1 B:ASP24 3.8 28.6 1.0
O5' B:AMP801 3.9 24.4 1.0
CB B:MET22 4.2 33.7 1.0
O1P B:AMP801 4.2 27.4 1.0
O B:HOH947 4.3 23.6 1.0
N B:MET22 4.3 29.4 1.0
CA B:MET22 4.3 30.9 1.0
O B:HOH923 4.4 25.9 1.0
O B:ALA498 4.5 22.3 1.0
OD2 B:ASP17 4.5 25.6 1.0
O B:HOH901 4.5 18.0 1.0
O B:HOH1113 4.6 37.9 1.0
O B:ASP17 4.7 22.0 1.0
N B:THR23 4.8 27.1 1.0
C5' B:AMP801 4.8 23.9 1.0
O B:HOH1017 4.8 30.0 1.0
CB B:ASP24 4.9 25.5 1.0
N B:ASP24 5.0 24.5 1.0

Magnesium binding site 4 out of 24 in 5m45

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Magnesium binding site 4 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:16.4
occ:1.00
O B:HOH1166 2.0 28.0 1.0
O B:HOH901 2.2 18.0 1.0
O B:HOH947 2.4 23.6 1.0
OD1 B:ASP309 2.4 18.7 1.0
O B:HOH923 2.4 25.9 1.0
OD2 B:ASP309 2.6 18.6 1.0
O B:HOH1150 2.6 19.1 1.0
CG B:ASP309 2.8 18.5 1.0
O B:HOH1141 3.7 33.5 1.0
O3P B:AMP801 3.9 28.2 1.0
O B:HOH988 4.0 28.3 1.0
OD2 B:ASP316 4.2 20.3 1.0
N B:GLY311 4.2 18.9 1.0
O B:HOH984 4.3 22.5 1.0
CA B:GLY311 4.3 19.1 1.0
CB B:ASP309 4.3 18.1 1.0
CA B:GLY472 4.4 18.5 1.0
C B:ILE310 4.4 18.8 1.0
O B:HOH1066 4.4 20.0 1.0
O B:ILE310 4.4 18.8 1.0
O B:HOH1113 4.5 37.9 1.0
O B:HOH1019 4.5 30.2 1.0
OD2 B:ASP17 4.8 25.6 1.0
C B:ASP309 4.9 17.9 1.0

Magnesium binding site 5 out of 24 in 5m45

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Magnesium binding site 5 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:25.5
occ:1.00
O B:HOH1244 2.3 35.4 1.0
O B:HOH1161 2.4 37.1 1.0
O B:HOH1114 2.5 25.2 1.0
O B:ACT805 2.5 41.1 1.0
OXT B:ACT805 2.7 42.5 1.0
C B:ACT805 3.0 42.6 1.0
O B:HOH965 4.4 23.5 1.0
NZ B:LYS328 4.5 48.1 1.0
CH3 B:ACT805 4.5 40.2 1.0
OD1 B:ASP332 4.5 22.3 1.0
O B:HOH1156 4.6 27.3 1.0
OE2 A:GLU73 4.7 20.6 1.0
NH1 B:ARG123 4.8 28.8 1.0
O B:HOH1108 4.8 31.6 1.0
NZ B:LYS459 4.9 34.8 1.0

Magnesium binding site 6 out of 24 in 5m45

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Magnesium binding site 6 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg806

b:31.5
occ:1.00
O B:HOH1132 2.4 37.2 1.0
O C:HOH399 2.5 44.1 1.0
O B:HOH1061 2.7 22.0 1.0
OD1 C:ASP19 2.7 39.6 1.0
O C:HOH402 2.9 33.1 1.0
OD1 B:ASP447 2.9 31.4 1.0
CG B:ASP447 3.8 28.9 1.0
O C:HOH315 3.8 14.5 1.0
CG C:ASP19 3.9 37.9 1.0
O B:HOH1224 4.1 36.1 1.0
OD2 B:ASP447 4.4 33.2 1.0
CA B:ASP447 4.6 22.2 1.0
ND1 C:HIS22 4.7 28.1 1.0
O B:HOH1239 4.7 36.0 1.0
CB B:ASP447 4.7 24.9 1.0
CB C:ASP19 4.8 34.8 1.0
OD2 C:ASP19 4.8 40.9 1.0
CA C:ASP19 4.9 31.6 1.0
OD2 B:ASP450 4.9 38.9 1.0
O B:ASP447 4.9 19.7 1.0
O B:HOH1223 4.9 43.5 1.0

Magnesium binding site 7 out of 24 in 5m45

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Magnesium binding site 7 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:19.5
occ:1.00
O D:HOH1364 2.3 40.1 1.0
O D:HOH1116 2.4 24.1 1.0
O D:VAL768 2.4 17.1 1.0
O D:SER763 2.5 17.1 1.0
O D:HOH1404 2.9 38.0 1.0
C D:SER763 3.5 17.2 1.0
C D:VAL768 3.7 17.3 1.0
CB D:SER763 3.7 18.0 1.0
CA D:SER763 3.9 17.0 1.0
N D:HIS769 4.6 17.8 1.0
CA D:VAL768 4.6 16.8 1.0
CA D:HIS769 4.6 18.7 1.0
OG D:SER763 4.7 19.7 1.0
N D:GLU764 4.7 17.0 1.0
O D:LEU765 4.7 15.9 1.0
N D:VAL768 4.8 17.1 1.0
CB D:VAL768 4.8 16.6 1.0
O D:HOH1480 4.9 43.0 1.0

Magnesium binding site 8 out of 24 in 5m45

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Magnesium binding site 8 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg806

b:32.5
occ:1.00
O F:HOH428 2.4 38.6 1.0
O D:HOH1133 2.4 28.6 1.0
O D:ALA689 2.5 17.0 1.0
O D:HOH1380 3.1 39.2 1.0
C D:ALA689 3.6 16.4 1.0
CA D:ALA689 4.0 16.2 1.0
O D:SER691 4.5 16.3 1.0
NH2 F:ARG92 4.7 21.5 1.0
O D:HOH1383 4.7 35.7 1.0
N D:LYS690 4.7 16.8 1.0
CB D:ALA689 4.7 16.3 1.0
O D:LEU688 4.8 15.4 1.0

Magnesium binding site 9 out of 24 in 5m45

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Magnesium binding site 9 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg802

b:12.3
occ:1.00
O E:HOH922 2.1 16.3 1.0
O E:HOH1217 2.2 30.1 1.0
OD1 E:ASP309 2.4 17.1 1.0
O E:HOH1210 2.4 17.5 1.0
O E:HOH907 2.5 21.8 1.0
O E:HOH1223 2.6 21.9 1.0
OD2 E:ASP309 2.6 16.9 1.0
CG E:ASP309 2.9 16.3 1.0
O E:HOH976 3.9 26.2 1.0
O3P E:AMP801 3.9 25.9 1.0
O E:HOH1283 4.0 24.7 1.0
OD2 E:ASP316 4.2 18.0 1.0
N E:GLY311 4.2 15.4 1.0
CA E:GLY311 4.2 15.9 1.0
O E:HOH952 4.2 22.8 1.0
CB E:ASP309 4.3 15.5 1.0
C E:ILE310 4.3 15.2 1.0
CA E:GLY472 4.4 15.8 1.0
O E:ILE310 4.4 15.6 1.0
O E:HOH1270 4.5 31.3 1.0
O E:HOH1089 4.5 32.2 1.0
O E:HOH1012 4.6 23.3 1.0
OD2 E:ASP17 4.8 20.9 1.0
C E:ASP309 4.9 14.8 1.0

Magnesium binding site 10 out of 24 in 5m45

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Magnesium binding site 10 out of 24 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg803

b:14.2
occ:1.00
O2P E:AMP801 2.2 29.1 1.0
O E:HOH1045 2.2 22.1 1.0
OD2 E:ASP24 2.5 23.5 1.0
O E:MET22 2.6 25.6 1.0
O E:HOH1012 2.6 23.3 1.0
O3P E:AMP801 2.7 25.9 1.0
O E:HOH1114 2.7 29.2 1.0
P E:AMP801 2.9 25.6 1.0
CG E:ASP24 3.5 22.0 1.0
C E:MET22 3.7 24.8 1.0
OD1 E:ASP24 3.9 22.8 1.0
O5' E:AMP801 4.0 24.0 1.0
O1P E:AMP801 4.1 25.3 1.0
CB E:MET22 4.2 28.4 1.0
N E:MET22 4.3 24.9 1.0
CA E:MET22 4.3 26.2 1.0
O E:HOH907 4.4 21.8 1.0
OD2 E:ASP17 4.5 20.9 1.0
O E:ALA498 4.5 17.1 1.0
O E:HOH1089 4.6 32.2 1.0
O E:ASP17 4.6 19.2 1.0
O E:HOH1223 4.7 21.9 1.0
O E:HOH922 4.7 16.3 1.0
N E:THR23 4.7 22.7 1.0
C5' E:AMP801 4.8 21.9 1.0
CB E:ASP24 4.8 21.2 1.0
N E:ASP24 4.9 20.7 1.0
O E:HOH937 4.9 21.8 1.0
CA E:GLY20 4.9 25.1 1.0
CG E:ASP17 5.0 20.1 1.0

Reference:

F.Mus, B.J.Eilers, A.B.Alleman, B.V.Kabasakal, J.N.Wells, J.W.Murray, B.P.Nocek, J.L.Dubois, J.W.Peters. Structural Basis For the Mechanism of Atp-Dependent Acetone Carboxylation. Sci Rep V. 7 7234 2017.
ISSN: ESSN 2045-2322
PubMed: 28775283
DOI: 10.1038/S41598-017-06973-8
Page generated: Mon Dec 14 20:50:25 2020

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