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Nickel in PDB 6jfd: K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

Enzymatic activity of K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa

All present enzymatic activity of K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa:
3.5.1.88;

Protein crystallography data

The structure of K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfd 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) 49.99 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.330, 146.356, 65.306, 90.00, 109.90, 90.00
R / Rfree (%) 22.5 / 28.4

Nickel Binding Sites:

The binding sites of Nickel atom in the K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa (pdb code 6jfd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa, PDB code: 6jfd:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6jfd

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Nickel binding site 1 out of 6 in the K1U 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 K1U 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:76.2
occ:1.00
 SG A:CYS103 2.2 35.2 1.0
NE2 A:HIS149 2.4 28.5 1.0
NE2 A:HIS145 2.5 32.0 1.0
CE1 A:HIS149 3.0 29.9 1.0
CB A:CYS103 3.2 35.2 1.0
CD2 A:HIS145 3.5 31.2 1.0
O A:HOH304 3.5 31.0 1.0
CE1 A:HIS145 3.5 34.5 1.0
NE2 A:GLN55 3.5 30.9 1.0
CD2 A:HIS149 3.7 28.6 1.0
CA A:CYS103 3.9 33.9 1.0
CD A:GLN55 4.1 31.7 1.0
OE1 A:GLN55 4.2 35.1 1.0
ND1 A:HIS149 4.3 31.2 1.0
N A:LEU104 4.5 42.6 1.0
ND1 A:HIS145 4.6 33.0 1.0
CG A:HIS145 4.6 30.4 1.0
CG A:HIS149 4.6 28.0 1.0
C A:CYS103 4.6 36.3 1.0
O A:GLY102 4.7 36.1 1.0
O A:HOH303 4.8 26.3 1.0
OE2 A:GLU146 4.8 44.2 1.0

Nickel binding site 2 out of 6 in 6jfd

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Nickel binding site 2 out of 6 in the K1U 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 K1U 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:0.5
occ:1.00
 NE2 B:HIS149 2.1 40.6 1.0
NE2 B:HIS145 2.5 35.0 1.0
SG B:CYS103 2.5 36.7 1.0
CE1 B:HIS149 3.1 40.5 1.0
CD2 B:HIS149 3.2 39.2 1.0
CD2 B:HIS145 3.3 34.6 1.0
CE1 B:HIS145 3.3 37.1 1.0
CB B:CYS103 3.6 37.1 1.0
O B:HOH305 3.6 25.6 1.0
O B:HOH303 3.8 31.6 1.0
NE2 B:GLN55 3.8 32.5 1.0
OE2 B:GLU146 3.8 52.7 1.0
OE1 B:GLN55 4.1 33.5 1.0
CA B:CYS103 4.1 36.9 1.0
ND1 B:HIS149 4.2 37.9 1.0
CD B:GLN55 4.2 36.1 1.0
CG B:HIS149 4.3 38.8 1.0
CG B:HIS145 4.3 34.5 1.0
ND1 B:HIS145 4.3 34.9 1.0
O B:GLY102 4.5 45.9 1.0
CD B:GLU146 4.7 49.3 1.0
O B:HIS145 4.9 29.6 1.0
N B:LEU104 5.0 40.1 1.0

Nickel binding site 3 out of 6 in 6jfd

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Nickel binding site 3 out of 6 in the K1U 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 K1U 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:Ni202

b:91.7
occ:1.00
 OE2 D:GLU31 2.5 55.0 1.0
OE2 B:GLU25 2.8 49.6 1.0
OE1 B:GLU25 2.8 43.9 1.0
CD B:GLU25 3.2 46.9 1.0
CD D:GLU31 3.3 56.4 1.0
OE1 D:GLU31 3.4 66.4 1.0
OG B:SER24 3.7 45.6 1.0
CB B:PRO23 4.6 44.5 1.0
N B:SER24 4.7 40.6 1.0
CG B:GLU25 4.7 45.9 1.0
CG D:GLU31 4.8 50.8 1.0
CB B:SER24 5.0 41.4 1.0
N D:GLU30 5.0 44.0 1.0

Nickel binding site 4 out of 6 in 6jfd

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Nickel binding site 4 out of 6 in the K1U 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 K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni201

b:70.0
occ:1.00
 SG C:CYS103 2.1 33.2 1.0
NE2 C:HIS149 2.4 25.6 1.0
NE2 C:HIS145 2.6 36.2 1.0
O2 C:K1U202 2.7 63.2 1.0
CE1 C:HIS149 3.0 27.8 1.0
CB C:CYS103 3.1 33.2 1.0
C8 C:K1U202 3.1 80.5 1.0
O1 C:K1U202 3.2 81.2 1.0
CD2 C:HIS145 3.3 37.3 1.0
O C:HOH303 3.4 46.7 1.0
CD2 C:HIS149 3.7 25.3 1.0
CE1 C:HIS145 3.7 37.6 1.0
NE2 C:GLN55 3.8 30.4 1.0
CA C:CYS103 3.9 31.6 1.0
OE1 C:GLN55 4.2 35.1 1.0
CD C:GLN55 4.2 30.8 1.0
ND1 C:HIS149 4.3 28.9 1.0
C24 C:K1U202 4.3 82.1 1.0
O C:HOH302 4.5 28.5 1.0
CG C:HIS145 4.5 35.7 1.0
C1 C:K1U202 4.6 67.7 1.0
O C:GLY102 4.6 39.0 1.0
CG C:HIS149 4.6 25.4 1.0
C9 C:K1U202 4.6 77.4 1.0
N C:LEU104 4.6 37.2 1.0
C C:CYS103 4.7 33.4 1.0
ND1 C:HIS145 4.7 36.8 1.0
OE2 C:GLU146 5.0 49.2 1.0

Nickel binding site 5 out of 6 in 6jfd

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Nickel binding site 5 out of 6 in the K1U 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 5 of K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni201

b:92.5
occ:1.00
 NE2 D:HIS149 2.1 33.0 1.0
SG D:CYS103 2.5 39.6 1.0
NE2 D:HIS145 2.6 34.3 1.0
CE1 D:HIS149 3.0 32.0 1.0
CD2 D:HIS149 3.2 33.3 1.0
CD2 D:HIS145 3.3 32.8 1.0
CB D:CYS103 3.4 37.2 1.0
CE1 D:HIS145 3.7 35.1 1.0
O D:HOH305 3.7 23.4 1.0
OE2 D:GLU146 3.7 51.6 1.0
NE2 D:GLN55 3.8 28.0 1.0
CA D:CYS103 4.0 36.4 1.0
OE1 D:GLN55 4.0 31.0 1.0
CD D:GLN55 4.1 32.6 1.0
O D:HOH302 4.1 22.9 1.0
ND1 D:HIS149 4.2 33.4 1.0
CG D:HIS149 4.3 33.5 1.0
CG D:HIS145 4.4 32.8 1.0
ND1 D:HIS145 4.6 33.7 1.0
CD D:GLU146 4.6 50.6 1.0
O D:GLY102 4.6 44.0 1.0
N D:LEU104 4.8 39.1 1.0
C D:CYS103 4.9 36.9 1.0
O D:HIS145 4.9 33.4 1.0

Nickel binding site 6 out of 6 in 6jfd

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Nickel binding site 6 out of 6 in the K1U 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 6 of K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni202

b:94.1
occ:1.00
 OE2 B:GLU31 2.4 66.5 1.0
OE2 D:GLU25 2.7 44.5 1.0
OE1 D:GLU25 3.0 41.6 1.0
CD D:GLU25 3.3 44.3 1.0
CD B:GLU31 3.4 66.4 1.0
OE1 B:GLU31 3.5 76.0 1.0
OG D:SER24 3.8 50.5 1.0
CB B:GLU30 4.5 60.2 1.0
N B:GLU30 4.7 48.6 1.0
CG B:GLU31 4.8 62.5 1.0
CG D:GLU25 4.8 42.3 1.0
CB D:PRO23 4.8 50.3 1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K1U Bound Crystal Structure of Class I Type B Peptide Deformylase From Pseudomonas Aeruginosa To Be Published.
Page generated: Thu Oct 10 08:33:47 2024

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