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Cadmium in PDB 5cy7: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275

Enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275, PDB code: 5cy7 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 (°) 58.823, 58.823, 264.034, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.2

Other elements in 5cy7:

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
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 Oryze, in Complex with Fragment 275 (pdb code 5cy7). 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 Oryze, in Complex with Fragment 275, PDB code: 5cy7:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5cy7

Go back to Cadmium Binding Sites List in 5cy7
Cadmium binding site 1 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275


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 Oryze, in Complex with Fragment 275 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:56.2
occ:1.00
O A:HOH304 2.1 4.8 1.0
NE2 A:HIS141 2.4 20.8 1.0
SG A:CYS99 2.5 26.0 1.0
NE2 A:HIS145 2.5 22.0 1.0
CE1 A:HIS145 3.2 18.7 1.0
O A:HOH381 3.2 32.3 1.0
CD2 A:HIS141 3.3 21.4 1.0
CB A:CYS99 3.4 24.9 1.0
CE1 A:HIS141 3.5 21.5 1.0
NE2 A:GLN51 3.5 17.0 1.0
CD2 A:HIS145 3.6 22.3 1.0
CA A:CYS99 3.8 24.1 1.0
O A:HOH379 3.8 19.1 1.0
OE1 A:GLN51 3.8 19.7 1.0
CD A:GLN51 3.8 17.7 1.0
OE2 A:GLU142 4.1 20.3 1.0
OE1 A:GLU142 4.3 21.4 1.0
O A:GLY98 4.4 29.3 1.0
ND1 A:HIS145 4.4 20.5 1.0
CG A:HIS141 4.5 18.8 1.0
N A:LEU100 4.5 24.5 1.0
O A:HOH354 4.5 19.6 1.0
ND1 A:HIS141 4.5 19.9 1.0
C A:CYS99 4.6 23.7 1.0
CG A:HIS145 4.6 22.2 1.0
CD A:GLU142 4.7 20.4 1.0
C4 A:56U205 4.7 50.5 1.0
N9 A:56U205 4.8 57.8 1.0
C3 A:56U205 4.9 60.8 1.0
N A:CYS99 5.0 26.2 1.0
CG A:GLN51 5.0 17.7 1.0

Cadmium binding site 2 out of 3 in 5cy7

Go back to Cadmium Binding Sites List in 5cy7
Cadmium binding site 2 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275


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 Oryze, in Complex with Fragment 275 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:29.1
occ:1.00
OE1 A:GLU128 2.1 28.1 1.0
OE1 A:GLU130 2.4 23.7 1.0
O A:HOH394 2.4 22.9 1.0
CD A:GLU128 2.9 33.9 1.0
OE2 A:GLU130 2.9 25.7 1.0
OE2 A:GLU128 3.0 32.6 1.0
CD A:GLU130 3.0 24.6 1.0
O A:GLU128 4.2 22.5 1.0
CG A:GLU128 4.3 30.8 1.0
NH1 A:ARG116 4.5 33.7 1.0
CG A:GLU130 4.5 23.9 1.0
CD A:ARG116 4.5 26.4 1.0
O A:HOH389 4.6 22.3 1.0
N A:GLU130 4.7 23.6 1.0
C A:GLU128 4.7 24.9 1.0
CA A:ARG129 4.9 23.6 1.0
C A:ARG129 5.0 23.9 1.0

Cadmium binding site 3 out of 3 in 5cy7

Go back to Cadmium Binding Sites List in 5cy7
Cadmium binding site 3 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275


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 Oryze, in Complex with Fragment 275 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:0.4
occ:1.00
O A:HOH325 2.4 34.8 1.0
OE1 A:GLU132 2.7 55.2 1.0
OE2 A:GLU132 3.3 56.9 1.0
CD A:GLU132 3.3 52.8 1.0
CE2 A:TYR114 4.5 34.6 1.0
CG A:GLU132 4.7 39.8 1.0
OH A:TYR114 4.8 36.0 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 To Be Published.
Page generated: Sat Dec 12 08:26:30 2020

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