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Nickel in PDB 3dkq: Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution

Protein crystallography data

The structure of Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution, PDB code: 3dkq 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) 28.86 / 2.26
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 153.452, 153.452, 84.851, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution (pdb code 3dkq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution, PDB code: 3dkq:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3dkq

Go back to Nickel Binding Sites List in 3dkq
Nickel binding site 1 out of 3 in the Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 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 Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni500

b:43.0
occ:1.00
NE2 A:HIS96 2.2 47.6 1.0
NE2 A:HIS157 2.2 45.9 1.0
OD1 A:ASP98 2.3 52.5 1.0
N1 A:IMD501 2.5 40.1 1.0
N3 A:IMD502 2.6 46.9 1.0
C4 A:IMD502 2.8 48.0 1.0
C5 A:IMD501 2.8 36.6 1.0
CG A:ASP98 3.0 54.1 1.0
OD2 A:ASP98 3.1 55.5 1.0
CD2 A:HIS157 3.1 49.3 1.0
CE1 A:HIS96 3.2 48.5 1.0
CD2 A:HIS96 3.2 47.7 1.0
CE1 A:HIS157 3.3 53.5 1.0
C2 A:IMD501 3.7 43.2 1.0
C2 A:IMD502 3.9 51.5 1.0
C5 A:IMD502 4.1 53.6 1.0
C4 A:IMD501 4.1 45.5 1.0
ND1 A:HIS96 4.3 49.0 1.0
CG A:HIS157 4.3 47.4 1.0
ND1 A:HIS157 4.3 54.7 1.0
CG A:HIS96 4.4 49.3 1.0
CB A:ASP98 4.5 54.0 1.0
N3 A:IMD501 4.6 46.2 1.0
CZ A:PHE171 4.6 47.4 0.5
N1 A:IMD502 4.6 52.0 1.0
OH A:TYR151 4.8 60.1 1.0
CE2 A:PHE171 4.8 50.2 0.5
CA A:ASP98 5.0 54.8 1.0
N A:ASP98 5.0 54.7 1.0
CZ2 A:TRP173 5.0 67.1 1.0

Nickel binding site 2 out of 3 in 3dkq

Go back to Nickel Binding Sites List in 3dkq
Nickel binding site 2 out of 3 in the Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 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 Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni500

b:59.2
occ:0.50
NE2 B:HIS157 2.1 61.9 1.0
NE2 B:HIS96 2.2 62.1 1.0
OD1 B:ASP98 2.3 69.5 1.0
CE1 B:HIS157 3.0 63.3 1.0
O B:HOH551 3.0 59.7 1.0
CD2 B:HIS157 3.1 61.0 1.0
N3 B:IMD501 3.1 87.1 1.0
CD2 B:HIS96 3.1 62.5 1.0
C2 B:IMD501 3.2 88.1 1.0
CG B:ASP98 3.2 62.4 1.0
CE1 B:HIS96 3.3 63.4 1.0
OD2 B:ASP98 3.4 63.9 1.0
ND1 B:HIS157 4.1 61.8 1.0
CG B:HIS157 4.1 56.6 1.0
C4 B:IMD501 4.3 88.8 1.0
N1 B:IMD501 4.3 90.2 1.0
CG B:HIS96 4.3 59.3 1.0
ND1 B:HIS96 4.4 61.6 1.0
CB B:ASP98 4.6 60.0 1.0
OH B:TYR151 4.8 53.9 1.0
C5 B:IMD501 4.9 90.8 1.0

Nickel binding site 3 out of 3 in 3dkq

Go back to Nickel Binding Sites List in 3dkq
Nickel binding site 3 out of 3 in the Crystal Structure of Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 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 Putative Oxygenase (YP_001051978.1) From Shewanella Baltica OS155 at 2.26 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni500

b:53.2
occ:1.00
NE2 C:HIS96 2.2 48.3 1.0
OD1 C:ASP98 2.2 57.1 1.0
NE2 C:HIS157 2.2 44.4 1.0
N1 C:IMD502 2.6 63.6 1.0
N3 C:IMD501 2.6 49.8 1.0
C5 C:IMD502 2.8 62.5 1.0
C4 C:IMD501 2.9 48.3 1.0
CG C:ASP98 3.0 53.9 1.0
OD2 C:ASP98 3.1 52.1 1.0
CE1 C:HIS96 3.1 49.2 1.0
CE1 C:HIS157 3.1 49.8 1.0
CD2 C:HIS157 3.2 48.0 1.0
CD2 C:HIS96 3.2 51.1 1.0
C2 C:IMD501 3.9 52.5 1.0
C2 C:IMD502 3.9 64.8 1.0
C4 C:IMD502 4.1 65.9 1.0
ND1 C:HIS96 4.2 55.7 1.0
ND1 C:HIS157 4.2 51.5 1.0
C5 C:IMD501 4.3 53.3 1.0
CG C:HIS157 4.3 50.5 1.0
CG C:HIS96 4.3 53.9 1.0
CB C:ASP98 4.5 54.6 1.0
N3 C:IMD502 4.7 68.3 1.0
N1 C:IMD501 4.7 53.9 1.0
CZ2 C:TRP173 4.8 61.3 1.0
CZ C:PHE171 4.9 52.8 1.0
CZ C:PHE93 5.0 54.4 1.0
CA C:ASP98 5.0 55.3 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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