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Cadmium in PDB 5cvq: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin

Enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin, PDB code: 5cvq was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.84 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.641, 58.641, 265.848, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin (pdb code 5cvq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin, PDB code: 5cvq:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5cvq

Go back to Cadmium Binding Sites List in 5cvq
Cadmium binding site 1 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:27.0
occ:1.00
OE1 A:GLU130 2.2 28.4 1.0
O A:HOH301 2.2 29.6 1.0
OE1 A:GLU128 2.2 28.8 1.0
OE2 A:GLU130 2.3 27.7 1.0
O A:HOH344 2.5 23.1 1.0
CD A:GLU130 2.6 26.6 1.0
OE2 A:GLU128 2.8 36.8 1.0
CD A:GLU128 2.9 30.9 1.0
NH1 A:ARG116 4.1 30.0 1.0
CG A:GLU130 4.2 25.8 1.0
O A:GLU128 4.3 27.4 1.0
CG A:GLU128 4.4 27.6 1.0
N A:GLU130 4.4 24.9 1.0
O A:HOH371 4.5 21.5 1.0
CD A:ARG116 4.5 22.3 1.0
CA A:ARG129 4.7 25.2 1.0
C A:GLU128 4.7 26.4 1.0
C A:ARG129 4.8 24.4 1.0
N A:ARG129 4.9 24.3 1.0

Cadmium binding site 2 out of 3 in 5cvq

Go back to Cadmium Binding Sites List in 5cvq
Cadmium binding site 2 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:30.5
occ:1.00
NE2 A:HIS141 2.2 28.9 1.0
NE2 A:HIS145 2.3 23.9 1.0
O4 A:BB2205 2.4 22.6 1.0
O2 A:BB2205 2.5 25.8 1.0
SG A:CYS99 2.6 27.0 1.0
C3 A:BB2205 2.9 25.7 1.0
N1 A:BB2205 3.0 26.7 1.0
CD2 A:HIS141 3.2 28.0 1.0
CE1 A:HIS145 3.2 21.8 1.0
CE1 A:HIS141 3.2 26.5 1.0
CD2 A:HIS145 3.3 20.9 1.0
NE2 A:GLN51 3.3 16.5 1.0
CB A:CYS99 3.5 29.7 1.0
O A:HOH362 3.7 30.8 1.0
CD A:GLN51 3.8 18.4 1.0
CA A:CYS99 3.8 28.1 1.0
OE1 A:GLN51 4.1 20.9 1.0
C5 A:BB2205 4.3 24.6 1.0
ND1 A:HIS141 4.3 28.0 1.0
CG A:HIS141 4.4 28.1 1.0
ND1 A:HIS145 4.4 22.6 1.0
CG A:HIS145 4.4 21.2 1.0
N A:LEU100 4.4 27.4 1.0
O A:HOH337 4.5 15.7 1.0
C A:CYS99 4.6 28.9 1.0
C6 A:BB2205 4.6 23.4 1.0
OE1 A:GLU142 4.7 21.2 1.0
C7 A:BB2205 4.8 24.2 1.0
CG A:GLN51 4.9 18.1 1.0
O A:GLY98 4.9 29.2 1.0
OE2 A:GLU142 4.9 19.5 1.0

Cadmium binding site 3 out of 3 in 5cvq

Go back to Cadmium Binding Sites List in 5cvq
Cadmium binding site 3 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:44.4
occ:1.00
OE1 A:GLU132 2.2 38.2 1.0
O A:HOH348 2.2 22.1 1.0
OE2 A:GLU132 2.8 40.2 1.0
CD A:GLU132 2.9 37.8 1.0
CG A:GLU132 4.3 30.5 1.0
CE2 A:TYR114 4.9 37.6 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Actinonin To Be Published.
Page generated: Sat Dec 12 08:26:27 2020

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