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Cadmium in PDB 4nt8: Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae

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

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

Protein crystallography data

The structure of Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae, PDB code: 4nt8 was solved by H.P.T.Ngo, J.K.Kim, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.35 / 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 / 23.5

Other elements in 4nt8:

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

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae (pdb code 4nt8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae, PDB code: 4nt8:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 4nt8

Go back to Cadmium Binding Sites List in 4nt8
Cadmium binding site 1 out of 3 in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas 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 Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:41.7
occ:1.00
O A:HOH372 2.2 34.2 1.0
OE2 A:GLU37 2.2 34.7 1.0
O A:HOH366 2.2 31.0 1.0
O A:HOH367 2.2 34.6 1.0
CD A:GLU37 2.9 29.3 1.0
OE1 A:GLU37 2.9 28.1 1.0
N A:MET1 3.9 39.6 1.0
CA A:MET1 4.1 38.0 1.0
CG A:GLU37 4.3 28.7 1.0
N A:ILE2 4.6 30.2 1.0
C A:MET1 4.8 34.3 1.0

Cadmium binding site 2 out of 3 in 4nt8

Go back to Cadmium Binding Sites List in 4nt8
Cadmium binding site 2 out of 3 in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas 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 Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:31.0
occ:1.00
OD2 A:CSD99 2.1 42.5 1.0
O1 A:FME207 2.2 34.0 1.0
NE2 A:HIS145 2.2 22.3 1.0
NE2 A:HIS141 2.3 25.6 1.0
O A:HOH362 2.3 18.4 1.0
CN A:FME207 2.4 43.3 1.0
SG A:CSD99 2.8 34.1 1.0
OD1 A:CSD99 2.9 44.7 1.0
CD2 A:HIS145 3.1 19.8 1.0
CD2 A:HIS141 3.2 24.9 1.0
CE1 A:HIS145 3.2 21.8 1.0
CE1 A:HIS141 3.3 25.0 1.0
NE2 A:GLN51 3.5 24.1 1.0
N A:FME207 3.7 36.2 1.0
OE1 A:GLN51 3.7 24.4 1.0
CB A:CSD99 3.7 31.9 1.0
CD A:GLN51 3.8 23.4 1.0
CA A:CSD99 4.0 28.9 1.0
O A:HOH301 4.0 17.0 1.0
CA A:FME207 4.1 33.5 1.0
CG A:HIS145 4.3 19.6 1.0
ND1 A:HIS145 4.3 21.6 1.0
CG A:HIS141 4.3 24.0 1.0
OE1 A:GLU142 4.4 24.2 1.0
ND1 A:HIS141 4.4 25.0 1.0
N A:LEU100 4.4 29.9 1.0
O A:HOH358 4.7 22.2 1.0
C A:CSD99 4.7 28.5 1.0
O A:GLY98 4.7 21.8 1.0
OE2 A:GLU142 4.8 27.0 1.0
CG A:GLN51 4.9 21.5 1.0
CD A:GLU142 5.0 23.4 1.0

Cadmium binding site 3 out of 3 in 4nt8

Go back to Cadmium Binding Sites List in 4nt8
Cadmium binding site 3 out of 3 in the Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas 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 Formyl-Methionine-Alanine Complex Structure of Peptide Deformylase From Xanthomoonas Oryzae Pv. Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:27.0
occ:1.00
O A:HOH373 2.2 28.6 1.0
OE2 A:GLU130 2.2 28.6 1.0
O A:HOH368 2.2 25.8 1.0
OE1 A:GLU128 2.2 24.6 1.0
OE2 A:GLU128 2.2 30.2 1.0
OE1 A:GLU130 2.3 25.0 1.0
CD A:GLU128 2.6 27.1 1.0
CD A:GLU130 2.6 26.6 1.0
CG A:GLU130 4.1 30.6 1.0
CG A:GLU128 4.1 28.2 1.0
O A:GLU128 4.3 26.4 1.0
CD A:ARG116 4.3 29.0 1.0
O A:HOH369 4.4 30.9 1.0
NH1 A:ARG116 4.5 35.4 1.0
N A:GLU130 4.5 24.9 1.0
CA A:ARG129 4.7 25.6 1.0
C A:GLU128 4.7 24.7 1.0
C A:ARG129 4.8 25.2 1.0
N A:ARG129 4.9 24.2 1.0

Reference:

H.P.T.Ngo, J.K.Kim, L.W.Kang. Substrate Complex Structure of XOO1075, A Peptide Deformylase, From Xanthomonas Oryzae Pv. Oryzae To Be Published.
Page generated: Sat Dec 12 08:25:20 2020

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