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Cadmium in PDB 5cp0: Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae

Enzymatic activity of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae

All present enzymatic activity of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae:
3.5.1.88;

Protein crystallography data

The structure of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, PDB code: 5cp0 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) 29.37 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.736, 58.736, 265.360, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.7

Other elements in 5cp0:

The structure of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae also contains other interesting chemical elements:

Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae (pdb code 5cp0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, PDB code: 5cp0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5cp0

Go back to Cadmium Binding Sites List in 5cp0
Cadmium binding site 1 out of 5 in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae


Mono view


Stereo pair view

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

b:26.1
occ:1.00
 O A:HOH402 2.2 26.6 1.0
OE1 A:GLU128 2.3 28.4 1.0
OE1 A:GLU130 2.3 22.3 1.0
OE2 A:GLU128 2.3 27.4 1.0
CD A:GLU128 2.7 29.3 1.0
OE2 A:GLU130 2.9 22.2 1.0
CD A:GLU130 3.0 21.8 1.0
O A:HOH347 3.0 57.3 1.0
CG A:GLU128 4.2 32.9 1.0
NE A:ARG116 4.3 20.4 1.0
O A:GLU128 4.3 19.7 1.0
O A:HOH361 4.4 43.2 1.0
CG A:GLU130 4.5 20.4 1.0
O A:HOH421 4.6 31.4 1.0
C A:GLU128 4.7 20.7 1.0
N A:GLU130 4.7 18.5 1.0
CA A:ARG129 4.8 20.2 1.0
CD A:ARG116 4.9 23.3 1.0
N A:ARG129 4.9 19.0 1.0
C A:ARG129 4.9 19.4 1.0

Cadmium binding site 2 out of 5 in 5cp0

Go back to Cadmium Binding Sites List in 5cp0
Cadmium binding site 2 out of 5 in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae


Mono view


Stereo pair view

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

b:56.2
occ:0.80
 OE2 A:GLU37 2.2 40.9 1.0
CD A:GLU37 2.8 30.3 1.0
OE1 A:GLU37 2.9 25.5 1.0
O A:HOH439 3.3 42.9 1.0
N A:MET1 4.0 27.5 1.0
CA A:MET1 4.1 28.9 1.0
O A:HOH403 4.3 34.0 1.0
CG A:GLU37 4.3 32.2 1.0
N A:ILE2 4.7 23.9 1.0
C A:MET1 4.8 28.7 1.0

Cadmium binding site 3 out of 5 in 5cp0

Go back to Cadmium Binding Sites List in 5cp0
Cadmium binding site 3 out of 5 in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:24.0
occ:1.00
 NE2 A:HIS141 2.2 15.9 1.0
O C:HOH101 2.2 19.6 1.0
NE2 A:HIS145 2.2 16.8 1.0
O A:HOH306 2.3 20.5 1.0
SG A:CYS99 2.4 37.4 1.0
CD2 A:HIS141 3.1 18.6 1.0
CE1 A:HIS141 3.2 17.9 1.0
CE1 A:HIS145 3.2 18.6 1.0
CD2 A:HIS145 3.2 17.4 1.0
NE2 A:GLN51 3.5 20.5 1.0
CB A:CYS99 3.5 39.8 1.0
O A:HOH416 3.7 19.6 1.0
CA A:CYS99 3.9 35.5 1.0
N C:MET1 3.9 25.2 1.0
CD A:GLN51 3.9 22.1 1.0
OE1 A:GLN51 4.0 22.1 1.0
CA C:MET1 4.3 29.3 1.0
ND1 A:HIS141 4.3 17.1 1.0
CG A:HIS141 4.3 18.3 1.0
ND1 A:HIS145 4.3 16.5 1.0
CG A:HIS145 4.4 15.8 1.0
N A:LEU100 4.5 38.3 1.0
OE1 A:GLU142 4.6 18.4 1.0
C A:CYS99 4.6 34.1 1.0
O A:HOH401 4.6 16.4 1.0
OE2 A:GLU142 4.7 21.6 1.0
O A:GLY98 4.8 25.6 1.0
CG A:GLN51 5.0 17.6 1.0
N A:SER101 5.0 29.0 1.0

Cadmium binding site 4 out of 5 in 5cp0

Go back to Cadmium Binding Sites List in 5cp0
Cadmium binding site 4 out of 5 in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:48.8
occ:0.50
 O A:HOH414 2.2 39.5 1.0
OG A:SER33 4.6 32.9 1.0
CB A:SER33 4.8 23.4 1.0

Cadmium binding site 5 out of 5 in 5cp0

Go back to Cadmium Binding Sites List in 5cp0
Cadmium binding site 5 out of 5 in the Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae


Mono view


Stereo pair view

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

b:43.8
occ:0.50
 O A:HOH466 2.2 30.9 1.0
O A:LEU105 2.9 29.9 1.0
CB A:ASP164 3.4 44.6 1.0
C A:LEU105 3.6 26.8 1.0
N A:LEU105 3.7 27.7 1.0
C A:GLY104 3.8 27.6 1.0
CG A:ASP164 3.9 57.4 1.0
O A:HOH302 4.0 30.7 1.0
CA A:LEU105 4.1 24.0 1.0
CA A:GLY104 4.2 38.1 1.0
O A:GLY104 4.3 34.6 1.0
N A:GLY104 4.3 31.2 1.0
CB A:ARG106 4.3 28.4 1.0
OD2 A:ASP164 4.4 57.1 1.0
CA A:GLY98 4.4 20.7 1.0
N A:ARG106 4.4 24.9 1.0
O A:HOH310 4.4 33.2 1.0
OD1 A:ASP164 4.5 53.8 1.0
CG A:ARG106 4.5 31.2 1.0
CD A:ARG106 4.6 32.0 1.0
CB C:ALA2 4.7 32.7 1.0
CA A:ASP164 4.7 37.2 1.0
CA A:ARG106 4.8 23.4 1.0
O A:HOH301 4.9 49.2 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Mas Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae To Be Published.
Page generated: Fri Jul 19 18:16:46 2024

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