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Cadmium in PDB 5cwy: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83

Enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83, PDB code: 5cwy 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) 30.40 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.974, 58.974, 263.790, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.8

Other elements in 5cwy:

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83 (pdb code 5cwy). 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 Oryze Pv Oryzae, in Complex with Fragment 83, PDB code: 5cwy:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5cwy

Go back to Cadmium Binding Sites List in 5cwy
Cadmium binding site 1 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83


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 Oryze Pv Oryzae, in Complex with Fragment 83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:59.4
occ:1.00
O A:HOH301 2.3 19.5 1.0
SG A:CYS99 2.3 26.0 1.0
NE2 A:HIS141 2.5 19.1 1.0
NE2 A:HIS145 2.6 20.8 1.0
CB A:CYS99 3.2 23.5 1.0
CE1 A:HIS145 3.3 18.1 1.0
O3 A:4WL205 3.3 56.6 1.0
CD2 A:HIS141 3.3 20.3 1.0
O A:HOH328 3.4 29.1 1.0
C1 A:4WL205 3.6 61.0 1.0
CA A:CYS99 3.6 21.7 1.0
CE1 A:HIS141 3.6 19.7 1.0
O A:HOH377 3.7 20.7 1.0
NE2 A:GLN51 3.7 16.7 1.0
CD2 A:HIS145 3.8 21.0 1.0
O2 A:4WL205 3.8 56.0 1.0
CD A:GLN51 4.0 17.7 1.0
OE1 A:GLN51 4.1 20.6 1.0
OE1 A:GLU142 4.2 22.0 1.0
N A:LEU100 4.4 23.9 1.0
O A:GLY98 4.4 27.4 1.0
C A:CYS99 4.4 22.4 1.0
ND1 A:HIS145 4.5 20.1 1.0
CG A:HIS141 4.5 20.4 1.0
C4 A:4WL205 4.6 60.3 1.0
O A:HOH340 4.6 19.0 1.0
ND1 A:HIS141 4.7 19.8 1.0
OE2 A:GLU142 4.7 23.8 1.0
CG A:HIS145 4.8 21.0 1.0
N A:CYS99 4.8 26.9 1.0
CD A:GLU142 4.9 22.0 1.0

Cadmium binding site 2 out of 3 in 5cwy

Go back to Cadmium Binding Sites List in 5cwy
Cadmium binding site 2 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83


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 Oryze Pv Oryzae, in Complex with Fragment 83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:30.0
occ:1.00
OE1 A:GLU128 2.1 26.7 1.0
OE1 A:GLU130 2.3 22.5 1.0
CD A:GLU128 2.9 32.4 1.0
OE2 A:GLU128 3.0 28.5 1.0
CD A:GLU130 3.0 22.8 1.0
OE2 A:GLU130 3.0 24.1 1.0
NE A:ARG116 4.3 24.1 1.0
CG A:GLU128 4.3 30.8 1.0
O A:GLU128 4.4 25.5 1.0
O A:HOH310 4.4 44.2 1.0
CG A:GLU130 4.5 20.4 1.0
N A:GLU130 4.7 22.4 1.0
C A:GLU128 4.8 26.8 1.0
CA A:ARG129 4.8 26.3 1.0
O A:HOH402 4.8 29.8 1.0
CD A:ARG116 4.9 22.5 1.0
C A:ARG129 4.9 25.2 1.0
N A:ARG129 5.0 27.8 1.0

Cadmium binding site 3 out of 3 in 5cwy

Go back to Cadmium Binding Sites List in 5cwy
Cadmium binding site 3 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83


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 Oryze Pv Oryzae, in Complex with Fragment 83 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:63.4
occ:0.70
O A:HOH305 1.7 16.1 1.0
OE1 A:GLU132 2.0 43.8 1.0
CD A:GLU132 3.1 44.1 1.0
OE2 A:GLU132 3.4 50.1 1.0
CG A:GLU132 4.4 35.5 1.0
CE2 A:TYR114 4.5 44.2 1.0
OH A:TYR114 4.7 50.1 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryzae, in Complex with Fragment 83 To Be Published.
Page generated: Sat Dec 12 08:26:28 2020

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