Atomistry » Cadmium » PDB 5an6-5gu1 » 5cpd
Atomistry »
  Cadmium »
    PDB 5an6-5gu1 »
      5cpd »

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: Sat Dec 12 08:26:25 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy