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Cadmium in PDB 5cvk: Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493

Enzymatic activity of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493

All present enzymatic activity of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493, PDB code: 5cvk 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) 26.95 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.002, 59.002, 264.653, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.4

Other elements in 5cvk:

The structure of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 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 Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 (pdb code 5cvk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493, PDB code: 5cvk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5cvk

Go back to Cadmium Binding Sites List in 5cvk
Cadmium binding site 1 out of 5 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


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 Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:19.9
occ:0.50
 CD A:CD204 1.8 29.0 0.5
SG A:CYS99 2.2 23.8 1.0
NE2 A:HIS141 2.2 19.8 1.0
NE2 A:HIS145 2.3 16.4 1.0
CE1 A:HIS145 3.0 16.5 1.0
CB A:CYS99 3.1 22.2 1.0
CE1 A:HIS141 3.1 21.0 1.0
O A:HOH427 3.1 26.2 1.0
CD2 A:HIS141 3.2 19.8 1.0
CD2 A:HIS145 3.4 15.1 1.0
NE2 A:GLN51 3.5 16.9 1.0
O A:HOH411 3.6 21.4 1.0
CA A:CYS99 3.6 20.6 1.0
OE1 A:GLN51 3.9 18.7 1.0
CD A:GLN51 3.9 19.0 1.0
OE2 A:GLU142 4.3 20.3 1.0
ND1 A:HIS145 4.3 13.6 1.0
ND1 A:HIS141 4.3 16.8 1.0
CG A:HIS141 4.4 17.4 1.0
N A:LEU100 4.4 20.2 1.0
C A:CYS99 4.5 19.7 1.0
CG A:HIS145 4.5 15.1 1.0
OE1 A:GLU142 4.5 21.5 1.0
O A:HOH405 4.5 15.7 1.0
C12 A:56E205 4.6 32.1 1.0
O A:GLY98 4.6 21.3 1.0
CD A:GLU142 4.8 19.4 1.0
O11 A:56E205 4.8 37.9 1.0
N A:CYS99 4.9 22.4 1.0

Cadmium binding site 2 out of 5 in 5cvk

Go back to Cadmium Binding Sites List in 5cvk
Cadmium binding site 2 out of 5 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


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 Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:42.4
occ:0.50
 O A:HOH446 2.2 42.8 1.0
OE1 A:GLU132 2.5 37.1 1.0
OE2 A:GLU132 3.0 50.3 1.0
CD A:GLU132 3.1 39.4 1.0
CE2 A:TYR114 4.3 30.3 1.0
CG A:GLU132 4.5 29.1 1.0
OH A:TYR114 4.9 37.4 1.0

Cadmium binding site 3 out of 5 in 5cvk

Go back to Cadmium Binding Sites List in 5cvk
Cadmium binding site 3 out of 5 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


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 Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:25.3
occ:1.00
 O A:HOH429 2.4 27.4 1.0
OE1 A:GLU128 2.5 25.8 1.0
OE1 A:GLU130 2.5 18.0 1.0
OE2 A:GLU128 2.6 23.8 1.0
OE2 A:GLU130 2.6 17.0 1.0
CD A:GLU130 2.9 17.6 1.0
CD A:GLU128 2.9 26.6 1.0
O A:GLU128 4.4 18.8 1.0
O A:HOH430 4.4 26.8 1.0
CG A:GLU130 4.4 18.7 1.0
NE A:ARG116 4.4 20.7 1.0
CG A:GLU128 4.4 26.4 1.0
N A:GLU130 4.5 17.1 1.0
C A:GLU128 4.7 19.6 1.0
CA A:ARG129 4.7 19.0 1.0
C A:ARG129 4.8 16.9 1.0
N A:ARG129 4.9 18.0 1.0
O A:HOH321 4.9 30.7 1.0
CD A:ARG116 4.9 22.9 1.0

Cadmium binding site 4 out of 5 in 5cvk

Go back to Cadmium Binding Sites List in 5cvk
Cadmium binding site 4 out of 5 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:29.0
occ:0.50
 CD A:CD201 1.8 19.9 0.5
NE2 A:HIS145 2.4 16.4 1.0
O A:HOH427 2.6 26.2 1.0
NE2 A:HIS141 2.7 19.8 1.0
OE1 A:GLN51 2.8 18.7 1.0
OE2 A:GLU142 2.8 20.3 1.0
OE1 A:GLU142 2.9 21.5 1.0
CD2 A:HIS145 3.0 15.1 1.0
CD2 A:HIS141 3.1 19.8 1.0
CD A:GLU142 3.2 19.4 1.0
CD A:GLN51 3.3 19.0 1.0
NE2 A:GLN51 3.4 16.9 1.0
CE1 A:HIS145 3.6 16.5 1.0
SG A:CYS99 3.8 23.8 1.0
CE1 A:HIS141 4.0 21.0 1.0
C12 A:56E205 4.1 32.1 1.0
CG A:HIS145 4.3 15.1 1.0
O A:GLY46 4.3 13.0 1.0
CG A:HIS141 4.4 17.4 1.0
ND1 A:HIS145 4.5 13.6 1.0
CG A:GLN51 4.6 14.2 1.0
CG A:GLU142 4.6 17.5 1.0
CB A:CYS99 4.7 22.2 1.0
S11 A:56E205 4.8 27.6 1.0
C A:GLY46 4.8 15.0 1.0
N A:ALA48 4.8 14.3 1.0
CA A:LEU47 4.8 14.5 1.0
ND1 A:HIS141 4.8 16.8 1.0
O11 A:56E205 4.8 37.9 1.0
CA A:CYS99 4.9 20.6 1.0

Cadmium binding site 5 out of 5 in 5cvk

Go back to Cadmium Binding Sites List in 5cvk
Cadmium binding site 5 out of 5 in the Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv. Oryze, in Complex with Fragment 493 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:22.2
occ:0.35
 OD1 A:ASP164 2.3 27.9 0.5
O A:HOH438 2.3 31.8 1.0
OD2 A:ASP164 2.4 28.7 0.5
O A:LEU105 2.5 22.8 1.0
O A:HOH424 2.6 33.8 1.0
CG A:ASP164 2.7 27.6 0.5
C A:LEU105 3.4 19.8 1.0
N A:LEU105 3.7 20.6 1.0
CB A:ASP164 3.9 25.5 0.5
C A:GLY104 3.9 22.3 1.0
CA A:LEU105 4.1 20.0 1.0
CB A:ARG106 4.1 21.7 1.0
CB A:ASP164 4.2 25.2 0.5
N A:ARG106 4.3 18.2 1.0
N A:GLY104 4.3 21.1 1.0
CG A:ASP164 4.4 25.1 0.5
O A:GLY104 4.4 23.4 1.0
O A:HOH322 4.4 17.9 1.0
CA A:GLY98 4.4 18.7 1.0
CA A:GLY104 4.5 23.1 1.0
CA A:ARG106 4.6 20.1 1.0
CG A:ARG106 4.6 22.6 1.0
OD1 A:ASP164 4.8 27.2 0.5
O A:HOH313 4.8 49.5 1.0
C4 A:56E205 4.8 38.1 1.0
OD2 A:ASP164 4.9 25.5 0.5
CA A:ASP164 5.0 26.2 0.5
O A:HOH353 5.0 28.8 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformyase From Xanthomonas Oryzae Pv.Oryze, in Complex with Fragment 493 To Be Published.
Page generated: Thu Jul 10 14:14:31 2025

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