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Manganese 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:

Magnesium (Mg) 24 atoms
Zinc (Zn) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus, PDB code: 5m45:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5m45

Go back to Manganese Binding Sites List in 5m45
Manganese binding site 1 out of 4 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn801

b:11.3
occ:1.00
OD1 A:ASP153 2.0 11.7 1.0
O A:ACT802 2.2 13.1 1.0
OXT A:ACT802 2.3 13.9 1.0
ND1 A:HIS175 2.3 10.7 1.0
NE2 A:HIS150 2.3 11.6 1.0
C A:ACT802 2.6 13.5 1.0
CG A:ASP153 2.7 11.7 1.0
OD2 A:ASP153 2.7 11.7 1.0
CE1 A:HIS150 3.2 11.7 1.0
CE1 A:HIS175 3.2 10.8 1.0
CG A:HIS175 3.3 10.7 1.0
CD2 A:HIS150 3.4 11.6 1.0
CB A:HIS175 3.7 10.8 1.0
CB A:ASP153 4.1 11.6 1.0
CH3 A:ACT802 4.1 13.6 1.0
O A:HOH1213 4.3 29.2 1.0
NE1 A:TRP401 4.3 11.6 1.0
ND1 A:HIS150 4.4 11.7 1.0
NE2 A:HIS175 4.4 10.8 1.0
N A:ASP153 4.4 11.8 1.0
CA A:HIS175 4.4 10.8 1.0
CD2 A:HIS175 4.4 10.8 1.0
CG A:HIS150 4.5 11.5 1.0
CA A:ASP153 4.5 11.7 1.0
C A:CYS152 4.6 12.1 1.0
CZ2 A:TRP401 4.8 11.7 1.0
O A:CYS152 4.8 12.1 1.0
CB A:CYS152 4.9 12.6 1.0
CE A:MET187 5.0 13.6 1.0
CE2 A:TRP401 5.0 11.7 1.0

Manganese binding site 2 out of 4 in 5m45

Go back to Manganese Binding Sites List in 5m45
Manganese binding site 2 out of 4 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn801

b:11.8
occ:1.00
OD1 D:ASP153 2.1 11.5 1.0
O D:ACT802 2.1 14.8 1.0
ND1 D:HIS175 2.3 10.4 1.0
NE2 D:HIS150 2.3 12.0 1.0
OXT D:ACT802 2.4 15.9 1.0
C D:ACT802 2.6 15.3 1.0
OD2 D:ASP153 2.6 11.3 1.0
CG D:ASP153 2.6 11.3 1.0
CE1 D:HIS150 3.2 12.2 1.0
CE1 D:HIS175 3.2 10.5 1.0
CG D:HIS175 3.4 10.4 1.0
CD2 D:HIS150 3.4 12.0 1.0
CB D:HIS175 3.7 10.3 1.0
CB D:ASP153 4.1 11.2 1.0
CH3 D:ACT802 4.1 14.9 1.0
O D:HOH1089 4.2 34.8 1.0
NE1 D:TRP401 4.4 12.1 1.0
ND1 D:HIS150 4.4 12.2 1.0
NE2 D:HIS175 4.4 10.6 1.0
N D:ASP153 4.4 11.4 1.0
CA D:HIS175 4.4 10.3 1.0
CD2 D:HIS175 4.5 10.4 1.0
CG D:HIS150 4.5 11.9 1.0
CA D:ASP153 4.6 11.2 1.0
C D:CYS152 4.7 11.8 1.0
CZ2 D:TRP401 4.7 12.2 1.0
O D:CYS152 4.9 11.7 1.0
CE2 D:TRP401 5.0 12.0 1.0
CE D:MET187 5.0 12.6 1.0
CB D:CYS152 5.0 12.3 1.0

Manganese binding site 3 out of 4 in 5m45

Go back to Manganese Binding Sites List in 5m45
Manganese binding site 3 out of 4 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn801

b:11.6
occ:1.00
OD1 G:ASP153 2.1 11.3 1.0
OXT G:ACT802 2.2 13.3 1.0
ND1 G:HIS175 2.3 11.1 1.0
NE2 G:HIS150 2.3 10.9 1.0
O G:ACT802 2.4 14.1 1.0
C G:ACT802 2.6 14.1 1.0
OD2 G:ASP153 2.7 11.4 1.0
CG G:ASP153 2.7 11.2 1.0
CE1 G:HIS150 3.2 10.9 1.0
CE1 G:HIS175 3.2 11.2 1.0
CG G:HIS175 3.3 11.1 1.0
CD2 G:HIS150 3.4 10.9 1.0
CB G:HIS175 3.7 11.1 1.0
CH3 G:ACT802 4.1 14.2 1.0
CB G:ASP153 4.1 11.2 1.0
O G:HOH1016 4.2 35.4 1.0
NE2 G:HIS175 4.4 11.2 1.0
ND1 G:HIS150 4.4 11.0 1.0
NE1 G:TRP401 4.4 11.9 1.0
CA G:HIS175 4.4 11.0 1.0
N G:ASP153 4.4 11.1 1.0
CD2 G:HIS175 4.4 11.2 1.0
CG G:HIS150 4.5 11.0 1.0
CA G:ASP153 4.6 11.1 1.0
C G:CYS152 4.7 11.3 1.0
CZ2 G:TRP401 4.8 12.0 1.0
O G:CYS152 4.9 11.2 1.0
CB G:CYS152 4.9 11.9 1.0
CE G:MET187 4.9 11.6 1.0
CE2 G:TRP401 5.0 11.9 1.0

Manganese binding site 4 out of 4 in 5m45

Go back to Manganese Binding Sites List in 5m45
Manganese binding site 4 out of 4 in the Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn801

b:13.9
occ:1.00
OD1 J:ASP153 2.0 12.3 1.0
OXT J:ACT802 2.1 15.3 1.0
ND1 J:HIS175 2.3 11.9 1.0
NE2 J:HIS150 2.4 11.8 1.0
O J:ACT802 2.4 15.1 1.0
C J:ACT802 2.6 15.6 1.0
CG J:ASP153 2.7 12.1 1.0
OD2 J:ASP153 2.7 12.5 1.0
CE1 J:HIS150 3.2 11.9 1.0
CE1 J:HIS175 3.2 12.1 1.0
CG J:HIS175 3.3 11.9 1.0
CD2 J:HIS150 3.4 11.6 1.0
CB J:HIS175 3.7 11.8 1.0
CB J:ASP153 4.1 11.8 1.0
CH3 J:ACT802 4.1 15.3 1.0
NE1 J:TRP401 4.4 10.9 1.0
NE2 J:HIS175 4.4 12.1 1.0
ND1 J:HIS150 4.4 11.8 1.0
N J:ASP153 4.4 11.8 1.0
CA J:HIS175 4.4 11.5 1.0
O J:HOH1273 4.4 37.8 1.0
CD2 J:HIS175 4.4 12.1 1.0
CG J:HIS150 4.5 11.8 1.0
CA J:ASP153 4.5 11.8 1.0
C J:CYS152 4.6 12.1 1.0
CZ2 J:TRP401 4.8 11.1 1.0
O J:CYS152 4.8 12.1 1.0
CB J:CYS152 4.9 12.5 1.0
CE J:MET187 5.0 14.9 1.0
CE2 J:TRP401 5.0 11.1 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: Sun Oct 6 01:53:59 2024

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