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Nickel in PDB 6jfe: K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

Enzymatic activity of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

Protein crystallography data

The structure of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfe was solved by I.H.Lee, T.H.Ho, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 44.682, 121.818, 146.314, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Other elements in 6jfe:

The structure of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 6jfe). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfe:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6jfe

Go back to Nickel Binding Sites List in 6jfe
Nickel binding site 1 out of 4 in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:61.2
occ:1.00
 NE2 A:HIS149 2.2 34.0 1.0
SG A:CYS103 2.3 39.5 1.0
O A:HOH303 2.4 40.9 1.0
NE2 A:HIS145 2.5 37.5 1.0
CE1 A:HIS149 2.9 39.4 1.0
CD2 A:HIS145 3.2 40.1 1.0
CD2 A:HIS149 3.3 33.9 1.0
CB A:CYS103 3.4 38.1 1.0
O A:HOH337 3.5 32.7 1.0
NE2 A:GLN55 3.5 35.3 1.0
CE1 A:HIS145 3.5 40.6 1.0
CD A:GLN55 4.0 40.5 1.0
CA A:CYS103 4.1 37.7 1.0
OE1 A:GLN55 4.1 36.8 1.0
OE2 A:GLU146 4.1 41.0 1.0
ND1 A:HIS149 4.1 37.0 1.0
CG A:HIS149 4.3 31.4 1.0
O A:HOH322 4.4 40.4 1.0
CG A:HIS145 4.4 33.6 1.0
ND1 A:HIS145 4.5 35.5 1.0
O A:GLY102 4.7 38.8 1.0
CD A:GLU146 4.7 49.7 1.0
OE1 A:GLU146 4.8 50.4 1.0
N A:LEU104 4.9 36.3 1.0
C A:CYS103 4.9 38.1 1.0
O A:HIS145 5.0 31.0 1.0

Nickel binding site 2 out of 4 in 6jfe

Go back to Nickel Binding Sites List in 6jfe
Nickel binding site 2 out of 4 in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:72.8
occ:1.00
 CE1 A:HIS44 2.4 69.9 1.0
NE2 A:HIS44 3.0 64.9 1.0
ND1 A:HIS44 3.4 62.9 1.0
CD2 A:HIS44 4.2 59.9 1.0
CG A:HIS44 4.4 58.9 1.0

Nickel binding site 3 out of 4 in 6jfe

Go back to Nickel Binding Sites List in 6jfe
Nickel binding site 3 out of 4 in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:93.3
occ:1.00
 OE2 A:GLU25 2.5 47.2 1.0
OE1 A:GLU25 3.0 43.3 1.0
CD A:GLU25 3.1 48.1 1.0
CG A:GLU25 4.6 40.5 1.0
OG A:SER24 4.7 48.4 1.0
N A:SER24 4.9 36.7 1.0

Nickel binding site 4 out of 4 in 6jfe

Go back to Nickel Binding Sites List in 6jfe
Nickel binding site 4 out of 4 in the K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:63.4
occ:1.00
 NE2 B:HIS149 2.1 34.4 1.0
F1 B:K3U202 2.1 0.7 1.0
SG B:CYS103 2.4 45.2 1.0
NE2 B:HIS145 2.4 42.1 1.0
F B:K3U202 2.5 59.4 1.0
C12 B:K3U202 2.8 98.9 1.0
CE1 B:HIS149 2.9 33.2 1.0
CD2 B:HIS145 3.2 41.9 1.0
CB B:CYS103 3.3 44.0 1.0
CD2 B:HIS149 3.3 31.9 1.0
O B:HOH326 3.4 32.3 1.0
CE1 B:HIS145 3.5 39.5 1.0
F2 B:K3U202 3.5 98.9 1.0
NE2 B:GLN55 3.9 34.0 1.0
ND1 B:HIS149 4.1 31.4 1.0
C11 B:K3U202 4.1 95.4 1.0
OE1 B:GLN55 4.2 37.8 1.0
CA B:CYS103 4.2 39.3 1.0
CD B:GLN55 4.2 37.7 1.0
CG B:HIS149 4.3 31.3 1.0
OE2 B:GLU146 4.3 57.6 1.0
CG B:HIS145 4.4 39.7 1.0
O B:HOH316 4.4 29.7 1.0
ND1 B:HIS145 4.5 41.1 1.0
C3 B:K3U202 4.6 95.8 1.0
O B:GLY102 4.7 47.5 1.0
C4 B:K3U202 4.8 84.4 1.0
OE1 B:GLU146 4.8 55.8 1.0
CD B:GLU146 4.9 49.7 1.0
N B:LEU104 4.9 42.3 1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K2U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.
Page generated: Thu Oct 10 08:33:50 2024

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