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Cadmium in PDB 5cpd: Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

Enzymatic activity of Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae

All present enzymatic activity of Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae:
3.5.1.88;

Protein crystallography data

The structure of Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae, PDB code: 5cpd 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 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.584, 58.584, 266.188, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 24.7

Other elements in 5cpd:

The structure of Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 3 in 5cpd

Go back to Cadmium Binding Sites List in 5cpd
Cadmium binding site 1 out of 3 in the Methionine-Alanine 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 Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:41.2
occ:1.00
 OE2 A:GLU37 2.2 34.3 1.0
O A:HOH374 2.2 35.0 1.0
CD A:GLU37 2.9 30.1 1.0
OE1 A:GLU37 3.0 29.2 1.0
N A:MET1 3.9 33.2 1.0
CA A:MET1 4.1 34.5 1.0
O A:HOH345 4.1 34.2 1.0
CG A:GLU37 4.4 27.4 1.0
N A:ILE2 4.5 27.9 1.0
C A:MET1 4.7 32.2 1.0

Cadmium binding site 2 out of 3 in 5cpd

Go back to Cadmium Binding Sites List in 5cpd
Cadmium binding site 2 out of 3 in the Methionine-Alanine 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 Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:30.7
occ:1.00
 OD2 A:CSD99 2.2 41.9 1.0
O A:HOH313 2.2 27.9 1.0
NE2 A:HIS141 2.2 25.0 1.0
NE2 A:HIS145 2.2 20.6 1.0
O A:HOH326 2.6 17.6 1.0
SG A:CSD99 2.7 34.1 1.0
CD2 A:HIS145 3.1 17.6 1.0
CD2 A:HIS141 3.2 24.4 1.0
CE1 A:HIS141 3.2 21.9 1.0
CE1 A:HIS145 3.3 21.4 1.0
NE2 A:GLN51 3.5 23.2 1.0
OE1 A:GLN51 3.7 24.0 1.0
OD1 A:CSD99 3.8 40.6 1.0
CD A:GLN51 3.8 23.3 1.0
CB A:CSD99 3.8 31.7 1.0
N A:MET208 3.9 26.5 1.0
CA A:CSD99 4.0 28.4 1.0
O A:HOH304 4.0 19.9 1.0
CA A:MET208 4.1 30.9 1.0
ND1 A:HIS141 4.3 21.9 1.0
CG A:HIS145 4.3 18.6 1.0
CG A:HIS141 4.4 22.6 1.0
ND1 A:HIS145 4.4 19.7 1.0
OE1 A:GLU142 4.4 26.4 1.0
N A:LEU100 4.5 28.6 1.0
O A:HOH353 4.7 22.5 1.0
OE2 A:GLU142 4.8 29.5 1.0
C A:CSD99 4.8 27.3 1.0
O A:GLY98 4.8 21.4 1.0
CG A:GLN51 5.0 19.9 1.0

Cadmium binding site 3 out of 3 in 5cpd

Go back to Cadmium Binding Sites List in 5cpd
Cadmium binding site 3 out of 3 in the Methionine-Alanine 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 Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:27.2
occ:1.00
 O A:HOH303 2.2 29.0 1.0
O A:HOH312 2.2 27.1 1.0
OE2 A:GLU130 2.2 24.2 1.0
OE1 A:GLU128 2.3 25.9 1.0
OE1 A:GLU130 2.3 26.3 1.0
OE2 A:GLU128 2.3 31.1 1.0
CD A:GLU130 2.6 25.7 1.0
CD A:GLU128 2.6 27.5 1.0
CG A:GLU130 4.1 30.2 1.0
CG A:GLU128 4.2 28.1 1.0
O A:GLU128 4.3 25.1 1.0
CD A:ARG116 4.3 29.1 1.0
O A:HOH378 4.4 40.1 1.0
N A:GLU130 4.4 25.9 1.0
NH1 A:ARG116 4.4 32.1 1.0
CA A:ARG129 4.7 26.5 1.0
C A:GLU128 4.8 25.0 1.0
C A:ARG129 4.8 25.0 1.0
N A:ARG129 5.0 23.5 1.0

Reference:

H.P.T.Ngo, L.W.Kang. Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomonas Oryzae Pv. Oryzae To Be Published.
Page generated: Fri Jul 19 18:17:42 2024

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