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Nickel in PDB 3b2y: Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution, PDB code: 3b2y 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) 28.82 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.715, 127.577, 49.303, 90.00, 116.28, 90.00
R / Rfree (%) 17.5 / 21.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution (pdb code 3b2y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution, PDB code: 3b2y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3b2y

Go back to Nickel Binding Sites List in 3b2y
Nickel binding site 1 out of 2 in the Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 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 Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni275

b:30.0
occ:0.70
O A:HOH332 1.8 40.3 1.0
OE1 A:GLU78 2.1 36.8 1.0
OE2 A:GLU78 2.2 36.0 1.0
ND1 A:HIS75 2.2 35.9 1.0
ND1 A:HIS169 2.2 39.1 1.0
O A:HOH310 2.3 34.2 1.0
CD A:GLU78 2.4 36.8 1.0
CE1 A:HIS75 3.0 33.2 1.0
CE1 A:HIS169 3.2 48.6 1.0
CG A:HIS169 3.2 31.5 1.0
CG A:HIS75 3.3 32.8 1.0
CB A:HIS169 3.6 31.8 1.0
CB A:HIS75 3.8 34.0 1.0
O A:HOH283 3.8 26.6 1.0
O A:HOH363 3.9 46.2 1.0
NH1 A:ARG118 3.9 43.8 1.0
CG A:GLU78 4.0 26.8 1.0
O A:GLU170 4.0 36.0 1.0
NE2 A:HIS75 4.2 34.0 1.0
NE2 A:HIS169 4.3 42.1 1.0
CD2 A:HIS169 4.4 40.8 1.0
CD2 A:HIS75 4.4 30.5 1.0
NH2 A:ARG118 4.4 48.2 1.0
N A:GLU170 4.5 30.4 1.0
CA A:HIS169 4.5 28.1 1.0
OE2 A:GLU245 4.6 48.2 1.0
O A:HOH381 4.6 50.1 1.0
CZ A:ARG118 4.6 41.0 1.0
CB A:GLU78 4.8 32.7 1.0
OE1 A:GLU245 4.8 49.3 1.0

Nickel binding site 2 out of 2 in 3b2y

Go back to Nickel Binding Sites List in 3b2y
Nickel binding site 2 out of 2 in the Crystal Structure of A Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 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 Putative Metallopeptidase (SDEN_2526) From Shewanella Denitrificans OS217 at 1.74 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni275

b:29.4
occ:0.70
OE1 B:GLU78 2.1 34.4 1.0
ND1 B:HIS169 2.1 42.8 1.0
ND1 B:HIS75 2.2 32.6 1.0
OE2 B:GLU78 2.3 35.9 1.0
O B:HOH293 2.4 31.0 1.0
CD B:GLU78 2.5 34.0 1.0
CE1 B:HIS75 3.0 42.0 1.0
CE1 B:HIS169 3.1 38.7 1.0
CG B:HIS169 3.2 37.9 1.0
CG B:HIS75 3.4 33.9 1.0
CB B:HIS169 3.5 31.9 1.0
O B:HOH361 3.7 48.2 1.0
CB B:HIS75 3.9 29.3 1.0
NH1 B:ARG118 3.9 40.5 1.0
O B:HOH284 3.9 25.7 1.0
CG B:GLU78 4.0 26.5 1.0
O B:GLU170 4.0 30.7 1.0
NE2 B:HIS75 4.2 34.1 1.0
NE2 B:HIS169 4.2 44.3 1.0
CD2 B:HIS169 4.3 41.5 1.0
NH2 B:ARG118 4.3 47.9 1.0
CD2 B:HIS75 4.4 31.9 1.0
CA B:HIS169 4.5 27.7 1.0
CZ B:ARG118 4.5 39.0 1.0
OE2 B:GLU245 4.6 52.4 1.0
N B:GLU170 4.6 28.8 1.0
OE1 B:GLU245 4.6 45.6 1.0
CB B:GLU78 4.7 30.0 1.0

Reference:

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