Nickel in PDB 3d82: Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
Protein crystallography data
The structure of Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution, PDB code: 3d82
was solved by
Joint Center For Structural Genomics (Jcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.85 /
2.05
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.920,
95.140,
237.370,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.6 /
21.2
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
(pdb code 3d82). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the
Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution, PDB code: 3d82:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
Nickel binding site 1 out
of 5 in 3d82
Go back to
Nickel Binding Sites List in 3d82
Nickel binding site 1 out
of 5 in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
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 Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni500
b:81.4
occ:1.00
|
O9
|
A:UNL501
|
2.1
|
62.4
|
0.5
|
OE1
|
A:GLU51
|
2.3
|
66.7
|
1.0
|
NE2
|
A:HIS44
|
2.3
|
51.2
|
1.0
|
NE2
|
A:HIS46
|
2.4
|
59.6
|
1.0
|
NE2
|
A:HIS85
|
2.5
|
52.9
|
1.0
|
O8
|
A:UNL501
|
2.8
|
65.2
|
0.5
|
O7
|
A:UNL501
|
2.9
|
65.7
|
0.5
|
CD
|
A:GLU51
|
3.1
|
60.1
|
1.0
|
CE1
|
A:HIS44
|
3.2
|
50.5
|
1.0
|
OE2
|
A:GLU51
|
3.2
|
70.0
|
1.0
|
CD2
|
A:HIS46
|
3.3
|
56.2
|
1.0
|
CE1
|
A:HIS85
|
3.3
|
54.6
|
1.0
|
CD2
|
A:HIS44
|
3.3
|
51.3
|
1.0
|
CE1
|
A:HIS46
|
3.4
|
58.7
|
1.0
|
CD2
|
A:HIS85
|
3.6
|
50.8
|
1.0
|
CZ
|
A:PHE53
|
4.3
|
58.2
|
1.0
|
ND1
|
A:HIS44
|
4.3
|
51.5
|
1.0
|
O6
|
A:UNL501
|
4.3
|
65.1
|
0.5
|
CE1
|
A:PHE53
|
4.4
|
59.4
|
1.0
|
CG
|
A:HIS44
|
4.4
|
49.3
|
1.0
|
CG
|
A:HIS46
|
4.5
|
53.9
|
1.0
|
ND1
|
A:HIS85
|
4.5
|
57.1
|
1.0
|
ND1
|
A:HIS46
|
4.5
|
58.4
|
1.0
|
CG
|
A:GLU51
|
4.6
|
61.1
|
1.0
|
CG
|
A:HIS85
|
4.7
|
52.7
|
1.0
|
O5
|
A:UNL501
|
5.0
|
63.3
|
0.5
|
CD1
|
A:ILE79
|
5.0
|
62.4
|
1.0
|
|
Nickel binding site 2 out
of 5 in 3d82
Go back to
Nickel Binding Sites List in 3d82
Nickel binding site 2 out
of 5 in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
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 Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni500
b:81.3
occ:1.00
|
O8
|
B:UNL501
|
2.3
|
59.2
|
0.5
|
NE2
|
B:HIS46
|
2.4
|
59.9
|
1.0
|
OE1
|
B:GLU51
|
2.4
|
69.1
|
1.0
|
NE2
|
B:HIS44
|
2.5
|
49.6
|
1.0
|
NE2
|
B:HIS85
|
2.5
|
56.1
|
1.0
|
O9
|
B:UNL501
|
2.7
|
59.3
|
0.5
|
O7
|
B:UNL501
|
2.9
|
64.0
|
0.5
|
CD2
|
B:HIS46
|
3.2
|
56.0
|
1.0
|
CD
|
B:GLU51
|
3.3
|
61.2
|
1.0
|
CE1
|
B:HIS44
|
3.3
|
50.1
|
1.0
|
CE1
|
B:HIS85
|
3.3
|
54.5
|
1.0
|
OE2
|
B:GLU51
|
3.4
|
70.8
|
1.0
|
CD2
|
B:HIS44
|
3.5
|
50.9
|
1.0
|
CE1
|
B:HIS46
|
3.5
|
59.7
|
1.0
|
CD2
|
B:HIS85
|
3.5
|
52.1
|
1.0
|
CZ
|
B:PHE53
|
4.1
|
58.2
|
1.0
|
CE1
|
B:PHE53
|
4.3
|
61.9
|
1.0
|
O6
|
B:UNL501
|
4.4
|
59.4
|
0.5
|
ND1
|
B:HIS44
|
4.4
|
51.0
|
1.0
|
CG
|
B:HIS46
|
4.4
|
54.9
|
1.0
|
ND1
|
B:HIS85
|
4.5
|
54.6
|
1.0
|
ND1
|
B:HIS46
|
4.6
|
58.1
|
1.0
|
CG
|
B:HIS44
|
4.6
|
49.8
|
1.0
|
CG
|
B:HIS85
|
4.6
|
51.6
|
1.0
|
CG
|
B:GLU51
|
4.7
|
61.9
|
1.0
|
|
Nickel binding site 3 out
of 5 in 3d82
Go back to
Nickel Binding Sites List in 3d82
Nickel binding site 3 out
of 5 in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
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 Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni500
b:56.4
occ:1.00
|
OE1
|
C:GLU51
|
2.2
|
66.5
|
1.0
|
NE2
|
C:HIS46
|
2.3
|
58.9
|
1.0
|
NE2
|
C:HIS44
|
2.3
|
48.7
|
1.0
|
O8
|
C:UNL501
|
2.3
|
38.0
|
0.5
|
NE2
|
C:HIS85
|
2.4
|
48.6
|
1.0
|
O9
|
C:UNL501
|
2.4
|
35.6
|
0.5
|
O7
|
C:UNL501
|
2.7
|
47.8
|
0.5
|
CD
|
C:GLU51
|
3.1
|
61.4
|
1.0
|
CE1
|
C:HIS44
|
3.1
|
50.4
|
1.0
|
CD2
|
C:HIS46
|
3.2
|
56.2
|
1.0
|
CE1
|
C:HIS85
|
3.2
|
50.6
|
1.0
|
CD2
|
C:HIS44
|
3.3
|
51.4
|
1.0
|
CE1
|
C:HIS46
|
3.3
|
58.6
|
1.0
|
OE2
|
C:GLU51
|
3.3
|
68.5
|
1.0
|
CD2
|
C:HIS85
|
3.4
|
49.5
|
1.0
|
O6
|
C:UNL501
|
4.2
|
46.5
|
0.5
|
ND1
|
C:HIS44
|
4.2
|
50.6
|
1.0
|
CG
|
C:HIS46
|
4.3
|
53.3
|
1.0
|
CG
|
C:HIS44
|
4.3
|
48.4
|
1.0
|
ND1
|
C:HIS85
|
4.4
|
49.4
|
1.0
|
ND1
|
C:HIS46
|
4.4
|
56.9
|
1.0
|
CZ
|
C:PHE53
|
4.5
|
60.5
|
1.0
|
CG
|
C:HIS85
|
4.5
|
49.2
|
1.0
|
CG
|
C:GLU51
|
4.5
|
61.6
|
1.0
|
CE1
|
C:PHE53
|
4.6
|
59.0
|
1.0
|
O
|
C:HOH520
|
4.6
|
50.5
|
1.0
|
|
Nickel binding site 4 out
of 5 in 3d82
Go back to
Nickel Binding Sites List in 3d82
Nickel binding site 4 out
of 5 in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
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 Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni500
b:62.3
occ:1.00
|
O9
|
D:UNL501
|
2.1
|
38.8
|
0.5
|
NE2
|
D:HIS44
|
2.3
|
51.0
|
1.0
|
NE2
|
D:HIS46
|
2.4
|
59.4
|
1.0
|
NE2
|
D:HIS85
|
2.4
|
51.4
|
1.0
|
OE1
|
D:GLU51
|
2.4
|
67.3
|
1.0
|
O8
|
D:UNL501
|
2.4
|
39.8
|
0.5
|
O7
|
D:UNL501
|
2.6
|
47.8
|
0.5
|
OE2
|
D:GLU51
|
3.1
|
68.1
|
1.0
|
CD
|
D:GLU51
|
3.1
|
61.1
|
1.0
|
CD2
|
D:HIS46
|
3.2
|
54.5
|
1.0
|
CE1
|
D:HIS44
|
3.3
|
51.8
|
1.0
|
CE1
|
D:HIS85
|
3.3
|
50.7
|
1.0
|
CD2
|
D:HIS44
|
3.3
|
50.2
|
1.0
|
CD2
|
D:HIS85
|
3.4
|
52.8
|
1.0
|
CE1
|
D:HIS46
|
3.5
|
57.9
|
1.0
|
O6
|
D:UNL501
|
4.1
|
43.6
|
0.5
|
ND1
|
D:HIS44
|
4.4
|
52.1
|
1.0
|
CZ
|
D:PHE53
|
4.4
|
57.1
|
1.0
|
CG
|
D:HIS46
|
4.4
|
54.8
|
1.0
|
CG
|
D:HIS44
|
4.4
|
48.8
|
1.0
|
ND1
|
D:HIS85
|
4.4
|
57.3
|
1.0
|
O
|
D:HOH554
|
4.5
|
61.4
|
1.0
|
O
|
D:HOH545
|
4.5
|
56.2
|
1.0
|
ND1
|
D:HIS46
|
4.5
|
56.6
|
1.0
|
CG
|
D:HIS85
|
4.5
|
52.2
|
1.0
|
CG
|
D:GLU51
|
4.6
|
60.5
|
1.0
|
CE1
|
D:PHE53
|
4.6
|
59.8
|
1.0
|
O5
|
D:UNL501
|
4.9
|
45.1
|
0.5
|
|
Nickel binding site 5 out
of 5 in 3d82
Go back to
Nickel Binding Sites List in 3d82
Nickel binding site 5 out
of 5 in the Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of A Cupin-2 Domain Containing Protein (SFRI_3543) From Shewanella Frigidimarina Ncimb 400 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni500
b:66.6
occ:1.00
|
NE2
|
E:HIS44
|
2.3
|
49.3
|
1.0
|
OE1
|
E:GLU51
|
2.3
|
71.0
|
1.0
|
NE2
|
E:HIS46
|
2.4
|
59.6
|
1.0
|
O8
|
E:UNL501
|
2.5
|
43.9
|
0.5
|
O9
|
E:UNL501
|
2.5
|
41.2
|
0.5
|
NE2
|
E:HIS85
|
2.6
|
49.8
|
1.0
|
O7
|
E:UNL501
|
2.9
|
50.9
|
0.5
|
CE1
|
E:HIS44
|
3.2
|
49.3
|
1.0
|
CD2
|
E:HIS46
|
3.3
|
56.5
|
1.0
|
CE1
|
E:HIS85
|
3.3
|
52.1
|
1.0
|
CD2
|
E:HIS44
|
3.3
|
50.7
|
1.0
|
CD
|
E:GLU51
|
3.3
|
65.8
|
1.0
|
CE1
|
E:HIS46
|
3.5
|
60.5
|
1.0
|
OE2
|
E:GLU51
|
3.6
|
70.9
|
1.0
|
CD2
|
E:HIS85
|
3.7
|
53.2
|
1.0
|
CZ
|
E:PHE53
|
4.2
|
59.6
|
1.0
|
ND1
|
E:HIS44
|
4.3
|
50.7
|
1.0
|
O6
|
E:UNL501
|
4.4
|
48.7
|
0.5
|
CE1
|
E:PHE53
|
4.4
|
61.0
|
1.0
|
CG
|
E:HIS44
|
4.4
|
50.8
|
1.0
|
CG
|
E:HIS46
|
4.5
|
54.4
|
1.0
|
ND1
|
E:HIS85
|
4.5
|
49.1
|
1.0
|
ND1
|
E:HIS46
|
4.5
|
59.2
|
1.0
|
CG
|
E:GLU51
|
4.7
|
60.3
|
1.0
|
CG
|
E:HIS85
|
4.7
|
51.4
|
1.0
|
|
Reference:
Joint Center For Structural Genomics (Jcsg),
Joint Center For Structural Genomics (Jcsg).
N/A N/A.
Page generated: Wed Oct 9 17:14:38 2024
|