Atomistry » Nickel » PDB 6ikt-6lrx » 6jff
Atomistry »
  Nickel »
    PDB 6ikt-6lrx »
      6jff »

Nickel in PDB 6jff: K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

Enzymatic activity of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

Protein crystallography data

The structure of K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jff 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 6jff:

The structure of K3U 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 K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 6jff). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jff:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6jff

Go back to Nickel Binding Sites List in 6jff
Nickel binding site 1 out of 4 in the K3U 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 K3U 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 6jff

Go back to Nickel Binding Sites List in 6jff
Nickel binding site 2 out of 4 in the K3U 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 K3U 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 6jff

Go back to Nickel Binding Sites List in 6jff
Nickel binding site 3 out of 4 in the K3U 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 K3U 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 6jff

Go back to Nickel Binding Sites List in 6jff
Nickel binding site 4 out of 4 in the K3U 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 K3U 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. K3U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.
Page generated: Thu Oct 10 08:34:00 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy