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
Go back to
Nickel Binding Sites List in 4wxl
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
Go back to
Nickel Binding Sites List in 4wxl
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
Go back to
Nickel Binding Sites List in 4wxl
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 Oct 9 19:19:14 2024
|