Atomistry » Cadmium » PDB 5an6-5gu0 » 5cy8
Atomistry »
  Cadmium »
    PDB 5an6-5gu0 »
      5cy8 »

Cadmium in PDB 5cy8: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244

Enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244, PDB code: 5cy8 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) 28.65 / 2.38
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.661, 58.661, 263.749, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.7

Other elements in 5cy8:

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244 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 Oryzae Pv Oryze, in Complex with Fragment 244 (pdb code 5cy8). 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 Oryze, in Complex with Fragment 244, PDB code: 5cy8:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5cy8

Go back to Cadmium Binding Sites List in 5cy8
Cadmium binding site 1 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244


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 Oryze, in Complex with Fragment 244 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:33.4
occ:1.00
OE1 A:GLU128 2.2 27.9 1.0
OE2 A:GLU130 2.3 23.2 1.0
OE2 A:GLU128 2.8 39.0 1.0
CD A:GLU128 2.9 37.2 1.0
CD A:GLU130 3.1 24.6 1.0
OE1 A:GLU130 3.2 24.9 1.0
NE A:ARG116 4.3 27.9 1.0
O A:GLU128 4.4 24.2 1.0
CG A:GLU128 4.4 34.4 1.0
CG A:GLU130 4.5 21.3 1.0
N A:GLU130 4.6 25.9 1.0
O A:HOH387 4.6 34.7 1.0
C A:GLU128 4.8 27.9 1.0
CA A:ARG129 4.8 27.7 1.0
CD A:ARG116 4.9 30.8 1.0
C A:ARG129 4.9 27.6 1.0

Cadmium binding site 2 out of 3 in 5cy8

Go back to Cadmium Binding Sites List in 5cy8
Cadmium binding site 2 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244


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 Oryze, in Complex with Fragment 244 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:49.9
occ:1.00
O A:HOH302 1.6 3.4 1.0
NE2 A:HIS145 2.5 20.9 1.0
NE2 A:HIS141 2.5 26.8 1.0
SG A:CYS99 2.5 26.4 1.0
O A:HOH341 2.8 38.5 1.0
CD2 A:HIS145 3.2 21.7 1.0
CD2 A:HIS141 3.2 26.8 1.0
OE1 A:GLN51 3.4 20.3 1.0
NE2 A:GLN51 3.5 19.8 1.0
OE1 A:GLU142 3.5 21.1 1.0
CD A:GLN51 3.6 20.8 1.0
CE1 A:HIS145 3.6 25.6 1.0
CE1 A:HIS141 3.6 27.5 1.0
CB A:CYS99 3.8 28.6 1.0
OE2 A:GLU142 3.9 21.4 1.0
CD A:GLU142 4.1 19.0 1.0
CA A:CYS99 4.2 25.4 1.0
O A:HOH350 4.3 28.6 1.0
N7 A:56V201 4.4 47.1 1.0
CG A:HIS145 4.4 23.1 1.0
CG A:HIS141 4.5 25.4 1.0
ND1 A:HIS145 4.6 25.7 1.0
O A:HOH354 4.6 30.5 1.0
ND1 A:HIS141 4.6 25.8 1.0
N A:LEU100 4.7 27.4 1.0
CG A:GLN51 4.8 18.4 1.0
O A:GLY98 4.9 28.1 1.0
C8 A:56V201 4.9 47.8 1.0
C A:CYS99 4.9 25.2 1.0

Cadmium binding site 3 out of 3 in 5cy8

Go back to Cadmium Binding Sites List in 5cy8
Cadmium binding site 3 out of 3 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244


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 Oryze, in Complex with Fragment 244 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:41.5
occ:0.50
O A:HOH301 1.8 20.0 1.0
OE2 A:GLU132 2.3 42.8 1.0
OE1 A:GLU132 2.6 42.3 1.0
O A:HOH400 2.6 35.1 1.0
CD A:GLU132 2.8 43.9 1.0
CG A:GLU132 4.3 35.7 1.0
CE2 A:TYR114 4.8 39.4 1.0
CB A:GLU132 4.9 29.6 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryze, in Complex with Fragment 244 To Be Published.
Page generated: Fri Jul 19 18:20:42 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy