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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

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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

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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

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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

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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

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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.
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