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Zinc 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
Manganese (Mn) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5m45

Go back to Zinc Binding Sites List in 5m45
Zinc 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 Zinc with other atoms in the Zn binding site number 1 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:28.6
occ:1.00
 SG C:CYS127 2.3 24.6 1.0
SG C:CYS74 2.4 22.0 1.0
SG C:CYS76 2.4 22.3 1.0
SG C:CYS124 2.4 20.4 1.0
CB C:CYS124 3.2 19.6 1.0
CB C:CYS74 3.3 20.0 1.0
CB C:CYS76 3.3 22.4 1.0
CB C:CYS127 3.5 23.9 1.0
N C:CYS127 3.8 24.3 1.0
N C:CYS76 4.1 20.6 1.0
CA C:CYS127 4.2 23.6 1.0
CA C:CYS76 4.3 22.0 1.0
CB C:HIS78 4.6 21.8 1.0
CB C:GLU126 4.6 30.6 1.0
CA C:CYS74 4.7 19.1 1.0
CA C:CYS124 4.7 19.2 1.0
NE2 C:HIS131 4.8 15.7 1.0
C C:GLU126 4.8 26.1 1.0
OG1 C:THR129 4.9 18.6 1.0
CB C:THR129 4.9 18.1 1.0
C C:CYS74 4.9 19.5 1.0
N C:GLU126 5.0 25.6 1.0

Zinc binding site 2 out of 4 in 5m45

Go back to Zinc Binding Sites List in 5m45
Zinc 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 Zinc with other atoms in the Zn binding site number 2 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:28.4
occ:1.00
 SG F:CYS74 2.3 22.7 1.0
SG F:CYS124 2.4 18.3 1.0
SG F:CYS127 2.4 21.4 1.0
SG F:CYS76 2.4 19.5 1.0
CB F:CYS124 3.1 16.9 1.0
CB F:CYS74 3.2 21.4 1.0
CB F:CYS76 3.4 21.0 1.0
CB F:CYS127 3.5 21.2 1.0
N F:CYS127 3.9 21.0 1.0
N F:CYS76 4.2 20.3 1.0
CA F:CYS127 4.3 20.3 1.0
CA F:CYS76 4.3 21.1 1.0
CB F:HIS78 4.6 17.7 1.0
CA F:CYS74 4.6 19.4 1.0
CA F:CYS124 4.6 16.4 1.0
CB F:GLU126 4.7 27.8 1.0
NE2 F:HIS131 4.7 16.1 1.0
OG1 F:THR129 4.9 16.1 1.0
C F:GLU126 4.9 22.8 1.0
CB F:THR129 4.9 15.6 1.0
C F:CYS74 4.9 20.3 1.0
N F:GLU126 5.0 22.8 1.0

Zinc binding site 3 out of 4 in 5m45

Go back to Zinc Binding Sites List in 5m45
Zinc 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 Zinc with other atoms in the Zn binding site number 3 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:26.6
occ:1.00
 SG I:CYS74 2.3 20.5 1.0
SG I:CYS76 2.4 21.3 1.0
SG I:CYS124 2.4 19.4 1.0
SG I:CYS127 2.4 23.9 1.0
CB I:CYS74 3.2 19.7 1.0
CB I:CYS124 3.2 18.4 1.0
CB I:CYS76 3.3 21.8 1.0
CB I:CYS127 3.6 23.5 1.0
N I:CYS127 3.9 23.4 1.0
N I:CYS76 4.1 20.4 1.0
CA I:CYS76 4.3 21.5 1.0
CA I:CYS127 4.3 22.9 1.0
CB I:HIS78 4.5 22.2 1.0
CA I:CYS74 4.6 18.7 1.0
CB I:GLU126 4.6 27.8 1.0
CA I:CYS124 4.7 18.0 1.0
NE2 I:HIS131 4.8 16.3 1.0
O I:HOH395 4.9 29.0 1.0
C I:GLU126 4.9 24.4 1.0
C I:CYS74 4.9 19.0 1.0
CB I:THR129 4.9 17.4 1.0
OG1 I:THR129 5.0 17.6 1.0
N I:GLU126 5.0 23.9 1.0
C I:CYS76 5.0 22.2 1.0

Zinc binding site 4 out of 4 in 5m45

Go back to Zinc Binding Sites List in 5m45
Zinc 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 Zinc with other atoms in the Zn binding site number 4 of Structure of Acetone Carboxylase Purified From Xanthobacter Autotrophicus within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:30.7
occ:1.00
 SG L:CYS74 2.3 29.6 1.0
SG L:CYS76 2.4 25.2 1.0
SG L:CYS124 2.4 21.2 1.0
SG L:CYS127 2.4 24.6 1.0
CB L:CYS74 3.2 27.9 1.0
CB L:CYS124 3.2 20.7 1.0
CB L:CYS76 3.3 24.5 1.0
CB L:CYS127 3.6 24.8 1.0
N L:CYS127 3.9 25.7 1.0
N L:CYS76 4.1 22.1 1.0
CA L:CYS76 4.3 23.6 1.0
CA L:CYS127 4.3 24.8 1.0
CB L:HIS78 4.5 22.1 1.0
CB L:GLU126 4.6 32.6 1.0
CA L:CYS74 4.6 26.6 1.0
CA L:CYS124 4.7 20.4 1.0
O L:HOH335 4.8 35.1 1.0
NE2 L:HIS131 4.8 17.2 1.0
C L:GLU126 4.9 27.5 1.0
C L:CYS74 4.9 28.9 1.0
N L:GLU126 5.0 27.6 1.0
OG1 L:THR129 5.0 19.9 1.0
C L:CYS76 5.0 23.3 1.0
CB L:THR129 5.0 19.4 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 27 21:42:17 2024

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