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Magnesium in PDB 5vcp: Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.54 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.110, 90.330, 140.210, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 5vcp:

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin (pdb code 5vcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5vcp

Go back to Magnesium Binding Sites List in 5vcp
Magnesium binding site 1 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:50.2
occ:1.00
 O A:HOH386 2.0 68.5 1.0
OD1 A:ASP21 2.7 56.2 1.0
OD2 A:ASP21 2.7 74.1 1.0
O A:HOH340 2.7 41.9 1.0
CG A:ASP21 3.1 66.7 1.0
CB A:ASP21 4.6 44.7 1.0
CG A:PRO19 4.6 41.0 1.0
O A:HOH304 4.7 61.1 1.0
O A:HOH367 4.9 43.4 0.5
O A:HOH346 4.9 41.1 1.0

Magnesium binding site 2 out of 3 in 5vcp

Go back to Magnesium Binding Sites List in 5vcp
Magnesium binding site 2 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:52.0
occ:1.00
 O C:HOH338 2.1 63.9 1.0
O C:HOH362 2.2 68.7 1.0
O B:HOH343 2.6 43.2 1.0
OD1 B:ASP21 2.7 82.7 1.0
OD1 C:ASN156 2.7 63.5 1.0
O C:HOH366 3.1 70.6 1.0
OD2 B:ASP21 3.3 84.2 1.0
CG B:ASP21 3.3 77.6 1.0
CG C:ASN156 3.9 69.1 1.0
O C:HOH336 4.3 28.8 0.3
O A:HOH396 4.4 59.6 1.0
O C:ILE155 4.5 42.4 1.0
CG B:PRO19 4.6 40.1 1.0
CD B:PRO19 4.6 36.8 1.0
ND2 C:ASN156 4.7 78.7 1.0
O C:MET153 4.7 39.3 1.0
O B:PRO19 4.8 34.1 1.0
CB B:ASP21 4.8 58.1 1.0
CB B:PRO19 4.8 35.7 1.0
O B:HOH321 4.9 44.1 1.0

Magnesium binding site 3 out of 3 in 5vcp

Go back to Magnesium Binding Sites List in 5vcp
Magnesium binding site 3 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:47.4
occ:1.00
 O B:HOH384 2.3 50.2 1.0
O B:MET92 2.4 45.3 1.0
O B:HOH312 2.8 49.2 1.0
C B:MET92 3.5 44.4 1.0
N B:MET92 4.1 44.2 1.0
N B:GLU93 4.4 38.8 1.0
CA B:MET92 4.4 41.0 1.0
CA B:GLU93 4.4 45.0 1.0
CB B:GLU93 4.7 59.2 1.0
OG B:SER113 4.8 56.8 1.0
O B:HOH355 4.9 50.6 1.0
C B:ASP91 5.0 45.1 1.0

Reference:

D.G.Conrady, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin To Be Published.
Page generated: Tue Aug 12 21:05:53 2025

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