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Nickel in PDB 4wxl: Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin

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

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin, PDB code: 4wxl 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) 26.69 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.201, 79.850, 98.168, 90.00, 97.99, 90.00
R / Rfree (%) 17.2 / 24.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin (pdb code 4wxl). 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 Complex with Actinonin, PDB code: 4wxl:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4wxl

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Nickel binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin


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 Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:24.9
occ:1.00
O2 A:BB2202 1.9 41.2 1.0
NE2 A:HIS137 2.0 27.2 1.0
NE2 A:HIS133 2.2 26.8 1.0
SG A:CYS91 2.2 30.1 1.0
N1 A:BB2202 2.6 53.9 1.0
O4 A:BB2202 2.7 69.2 1.0
C3 A:BB2202 2.9 68.4 1.0
CD2 A:HIS133 3.0 25.6 1.0
CE1 A:HIS137 3.0 28.4 1.0
CD2 A:HIS137 3.1 29.5 1.0
CE1 A:HIS133 3.2 28.3 1.0
CB A:CYS91 3.2 27.6 1.0
O A:HOH317 3.5 24.6 1.0
NE2 A:GLN51 3.5 29.3 1.0
CA A:CYS91 3.9 29.2 1.0
CD A:GLN51 3.9 29.7 1.0
OE1 A:GLN51 3.9 31.0 1.0
ND1 A:HIS137 4.1 29.1 1.0
CG A:HIS133 4.1 26.4 1.0
CG A:HIS137 4.2 27.7 1.0
ND1 A:HIS133 4.2 28.4 1.0
C5 A:BB2202 4.3 70.9 1.0
O A:HOH318 4.4 33.3 1.0
OE2 A:GLU134 4.5 29.5 1.0
N A:LEU92 4.6 29.4 1.0
C6 A:BB2202 4.6 69.7 1.0
C A:CYS91 4.7 30.1 1.0
OE1 A:GLU134 4.7 27.1 1.0
C7 A:BB2202 4.7 64.5 1.0
O A:GLY90 4.8 31.2 1.0
CD A:GLU134 4.9 27.1 1.0
CG A:GLN51 5.0 29.1 1.0

Nickel binding site 2 out of 4 in 4wxl

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Nickel binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin


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 Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:32.5
occ:1.00
O2 B:BB2202 1.8 48.9 1.0
NE2 B:HIS133 2.1 38.7 1.0
NE2 B:HIS137 2.1 33.7 1.0
SG B:CYS91 2.2 37.7 1.0
N1 B:BB2202 2.6 66.7 1.0
CD2 B:HIS133 2.9 38.0 1.0
CD2 B:HIS137 3.0 37.4 1.0
CE1 B:HIS137 3.1 33.8 1.0
CE1 B:HIS133 3.2 40.1 1.0
C3 B:BB2202 3.2 66.8 1.0
O B:HOH306 3.2 26.2 1.0
O4 B:BB2202 3.2 62.1 1.0
CB B:CYS91 3.3 33.7 1.0
NE2 B:GLN51 3.6 31.5 1.0
OE2 B:GLU134 3.9 34.4 1.0
CA B:CYS91 4.0 35.9 1.0
CD B:GLN51 4.0 32.7 1.0
OE1 B:GLN51 4.0 39.6 1.0
CG B:HIS133 4.1 37.3 1.0
CG B:HIS137 4.2 38.6 1.0
ND1 B:HIS133 4.2 38.0 1.0
ND1 B:HIS137 4.2 35.7 1.0
O B:HOH311 4.4 29.2 1.0
C5 B:BB2202 4.6 76.2 1.0
CD B:GLU134 4.6 37.0 1.0
OE1 B:GLU134 4.6 36.4 1.0
O B:GLY90 4.7 43.2 1.0
C B:CYS91 4.8 35.5 1.0
N B:LEU92 4.9 36.7 1.0
C6 B:BB2202 4.9 78.6 1.0
C8 B:BB2202 4.9 60.8 1.0

Nickel binding site 3 out of 4 in 4wxl

Go back to Nickel Binding Sites List in 4wxl
Nickel binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin


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 Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni201

b:27.2
occ:1.00
O2 C:BB2202 1.9 47.5 1.0
NE2 C:HIS137 2.0 23.9 1.0
NE2 C:HIS133 2.1 31.5 1.0
SG C:CYS91 2.2 33.7 1.0
O4 C:BB2202 2.7 65.2 1.0
N1 C:BB2202 2.8 56.1 1.0
CE1 C:HIS137 3.0 26.5 1.0
CD2 C:HIS133 3.0 31.5 1.0
CD2 C:HIS137 3.0 26.5 1.0
C3 C:BB2202 3.0 63.4 1.0
CE1 C:HIS133 3.1 31.7 1.0
CB C:CYS91 3.4 32.4 1.0
O C:HOH311 3.7 28.5 1.0
NE2 C:GLN51 3.7 29.8 1.0
OE1 C:GLN51 3.8 34.5 1.0
CA C:CYS91 3.9 31.2 1.0
CD C:GLN51 3.9 29.9 1.0
ND1 C:HIS137 4.1 26.9 1.0
CG C:HIS137 4.1 27.2 1.0
CG C:HIS133 4.2 31.3 1.0
ND1 C:HIS133 4.2 32.4 1.0
O C:HOH312 4.4 7.4 0.5
OE2 C:GLU134 4.4 36.4 1.0
C5 C:BB2202 4.5 68.4 1.0
OE1 C:GLU134 4.6 35.9 1.0
N C:LEU92 4.6 29.3 1.0
C C:CYS91 4.7 29.7 1.0
C6 C:BB2202 4.8 67.3 1.0
O C:GLY90 4.8 33.4 1.0
CD C:GLU134 4.8 36.4 1.0
C8 C:BB2202 4.9 50.3 1.0

Nickel binding site 4 out of 4 in 4wxl

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


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 Complex with Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni201

b:29.8
occ:1.00
O2 D:BB2202 1.9 40.4 1.0
NE2 D:HIS133 2.1 30.5 1.0
NE2 D:HIS137 2.1 32.8 1.0
SG D:CYS91 2.2 32.4 1.0
O4 D:BB2202 2.4 44.9 1.0
N1 D:BB2202 2.7 41.3 1.0
C3 D:BB2202 2.8 46.8 1.0
NE2 D:GLN51 3.0 38.3 1.0
CD2 D:HIS133 3.1 33.1 1.0
CE1 D:HIS137 3.1 31.6 1.0
CE1 D:HIS133 3.1 32.0 1.0
CD2 D:HIS137 3.1 32.2 1.0
CB D:CYS91 3.5 36.2 1.0
O D:HOH314 3.6 17.6 0.5
CD D:GLN51 3.8 36.0 1.0
CA D:CYS91 3.9 36.7 1.0
ND1 D:HIS133 4.2 31.8 1.0
ND1 D:HIS137 4.2 32.8 1.0
CG D:HIS133 4.2 33.5 1.0
OE1 D:GLN51 4.2 30.2 1.0
CG D:HIS137 4.2 31.0 1.0
C5 D:BB2202 4.3 46.4 1.0
N D:LEU92 4.4 32.5 1.0
C6 D:BB2202 4.6 51.2 1.0
C D:CYS91 4.6 32.4 1.0
OE1 D:GLU134 4.6 36.5 1.0
O D:HOH315 4.7 28.9 1.0
CG D:GLN51 4.9 34.7 1.0
C7 D:BB2202 4.9 54.4 1.0
OE2 D:GLU134 5.0 32.6 1.0
O D:GLY90 5.0 46.4 1.0

Reference:

C.Kishor, A.Addlagatta. Crystal Structure of A Peptide Deformylase From Haemophilus Influenzae Complex with Actinonin To Be Published.
Page generated: Wed Dec 16 01:37:40 2020

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