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Nickel in PDB 4wxk: Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae, PDB code: 4wxk was solved by C.Kishor, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.37 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.036, 80.961, 98.586, 90.00, 97.81, 90.00
R / Rfree (%) 16.1 / 22.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae (pdb code 4wxk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae, PDB code: 4wxk:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4wxk

Go back to Nickel Binding Sites List in 4wxk
Nickel binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:13.5
occ:1.00
O A:HOH306 2.1 13.9 1.0
NE2 A:HIS133 2.1 18.4 1.0
NE2 A:HIS137 2.1 18.2 1.0
SG A:CYS91 2.2 17.8 1.0
CD2 A:HIS133 3.0 19.2 1.0
CE1 A:HIS137 3.0 17.0 1.0
CD2 A:HIS137 3.1 16.0 1.0
CE1 A:HIS133 3.1 19.4 1.0
CB A:CYS91 3.2 18.9 1.0
O A:HOH367 3.5 22.7 1.0
NE2 A:GLN51 3.7 19.9 1.0
O A:HOH363 3.7 22.4 1.0
OE1 A:GLN51 3.8 19.4 1.0
CA A:CYS91 3.9 19.1 1.0
OE2 A:GLU134 4.0 19.0 1.0
CD A:GLN51 4.0 20.0 1.0
CG A:HIS133 4.1 18.9 1.0
ND1 A:HIS137 4.2 17.6 1.0
ND1 A:HIS133 4.2 18.9 1.0
CG A:HIS137 4.2 16.9 1.0
O A:HOH343 4.3 14.2 1.0
OE1 A:GLU134 4.5 18.6 1.0
CD A:GLU134 4.5 18.1 1.0
O A:GLY90 4.6 18.6 1.0
N A:LEU92 4.7 18.6 1.0
C A:CYS91 4.7 19.3 1.0

Nickel binding site 2 out of 4 in 4wxk

Go back to Nickel Binding Sites List in 4wxk
Nickel binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:13.1
occ:1.00
O B:HOH303 2.0 16.3 1.0
NE2 B:HIS137 2.1 16.2 1.0
NE2 B:HIS133 2.1 21.4 1.0
SG B:CYS91 2.2 17.3 1.0
CD2 B:HIS133 2.9 19.7 1.0
CD2 B:HIS137 3.1 16.0 1.0
CE1 B:HIS137 3.1 15.7 1.0
CE1 B:HIS133 3.2 20.2 1.0
CB B:CYS91 3.3 16.6 1.0
O B:HOH372 3.5 16.9 1.0
NE2 B:GLN51 3.7 15.6 1.0
OE1 B:GLN51 3.8 17.4 1.0
O B:HOH359 3.8 13.9 1.0
CD B:GLN51 3.9 15.2 1.0
OE2 B:GLU134 3.9 18.2 1.0
CA B:CYS91 3.9 15.0 1.0
CG B:HIS133 4.2 19.2 1.0
ND1 B:HIS137 4.2 14.5 1.0
CG B:HIS137 4.2 13.9 1.0
ND1 B:HIS133 4.2 19.1 1.0
O B:HOH361 4.3 17.8 1.0
OE1 B:GLU134 4.4 16.8 1.0
CD B:GLU134 4.5 17.1 1.0
N B:LEU92 4.7 16.7 1.0
O B:GLY90 4.7 15.7 1.0
C B:CYS91 4.7 16.0 1.0
C2 B:GOL202 4.9 32.7 1.0
CG B:GLN51 5.0 15.6 1.0

Nickel binding site 3 out of 4 in 4wxk

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Nickel binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni201

b:16.2
occ:1.00
NE2 C:HIS133 2.0 18.6 1.0
O C:HOH304 2.1 21.0 1.0
NE2 C:HIS137 2.1 17.4 1.0
SG C:CYS91 2.2 20.8 1.0
CD2 C:HIS133 2.9 19.6 1.0
CE1 C:HIS137 3.0 17.4 1.0
CE1 C:HIS133 3.1 19.2 1.0
CD2 C:HIS137 3.1 16.1 1.0
CB C:CYS91 3.3 21.1 1.0
O C:HOH359 3.5 15.8 1.0
O C:HOH358 3.7 22.2 1.0
NE2 C:GLN51 3.8 21.7 1.0
OE1 C:GLN51 3.8 21.8 1.0
CA C:CYS91 3.9 19.0 1.0
OE2 C:GLU134 3.9 21.0 1.0
CD C:GLN51 4.0 21.6 1.0
CG C:HIS133 4.1 17.8 1.0
ND1 C:HIS133 4.1 18.9 1.0
ND1 C:HIS137 4.2 16.9 1.0
CG C:HIS137 4.2 16.9 1.0
O C:HOH324 4.4 19.8 1.0
OE1 C:GLU134 4.5 21.1 1.0
CD C:GLU134 4.5 22.1 1.0
O C:GLY90 4.6 18.8 1.0
N C:LEU92 4.7 22.4 1.0
C C:CYS91 4.7 19.2 1.0
C1 C:GOL202 4.9 40.4 1.0

Nickel binding site 4 out of 4 in 4wxk

Go back to Nickel Binding Sites List in 4wxk
Nickel binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni201

b:13.5
occ:1.00
NE2 D:HIS133 2.0 16.7 1.0
O D:HOH309 2.0 12.4 1.0
NE2 D:HIS137 2.1 17.5 1.0
SG D:CYS91 2.3 18.5 1.0
CD2 D:HIS133 2.9 17.6 1.0
CE1 D:HIS133 3.0 17.6 1.0
CE1 D:HIS137 3.0 17.6 1.0
CD2 D:HIS137 3.1 16.9 1.0
CB D:CYS91 3.2 16.7 1.0
O D:HOH352 3.7 15.3 1.0
NE2 D:GLN51 3.8 17.6 1.0
OE1 D:GLN51 3.8 18.0 1.0
O D:HOH350 3.8 19.2 1.0
CA D:CYS91 3.9 16.4 1.0
CD D:GLN51 4.0 18.9 1.0
OE2 D:GLU134 4.0 20.5 1.0
ND1 D:HIS133 4.1 17.1 1.0
CG D:HIS133 4.1 16.0 1.0
ND1 D:HIS137 4.1 18.1 1.0
CG D:HIS137 4.2 16.6 1.0
O D:HOH339 4.3 16.2 1.0
OE1 D:GLU134 4.4 18.7 1.0
CD D:GLU134 4.5 20.7 1.0
O D:GLY90 4.7 16.5 1.0
C D:CYS91 4.7 18.0 1.0
N D:LEU92 4.8 18.4 1.0
C1 D:GOL202 4.9 32.6 1.0
C3 D:GOL202 5.0 31.8 1.0

Reference:

C.Kishor, A.Addlagatta. Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae To Be Published.
Page generated: Wed Dec 16 01:37:39 2020

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