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Nickel in PDB 1y1o: X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus

Protein crystallography data

The structure of X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus, PDB code: 1y1o was solved by J.Osipiuk, H.Li, S.Moy, F.Collart, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.10 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.261, 81.018, 106.279, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.8

Nickel Binding Sites:

The binding sites of Nickel atom in the X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus (pdb code 1y1o). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus, PDB code: 1y1o:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1y1o

Go back to Nickel Binding Sites List in 1y1o
Nickel binding site 1 out of 2 in the X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni321

b:27.0
occ:1.00
ND1 A:HIS151 2.1 25.1 1.0
ND1 A:HIS175 2.1 27.8 1.0
OE2 A:GLU171 2.1 31.3 1.0
O A:HOH340 2.2 9.6 1.0
CD A:GLU171 2.9 35.2 1.0
CE1 A:HIS151 3.0 24.5 1.0
OE1 A:GLU171 3.0 32.8 1.0
CE1 A:HIS175 3.0 31.8 1.0
CG A:HIS151 3.0 23.2 1.0
CG A:HIS175 3.1 30.0 1.0
CB A:HIS151 3.4 24.3 1.0
CB A:HIS175 3.5 28.8 1.0
NE2 A:HIS151 4.1 27.3 1.0
CD2 A:HIS151 4.1 22.8 1.0
NE2 A:HIS175 4.2 31.2 1.0
CA A:HIS151 4.2 24.4 1.0
NE1 A:TRP155 4.2 20.3 1.0
CD2 A:HIS175 4.2 29.6 1.0
CG A:GLU171 4.4 34.4 1.0
CB C:ALA127 4.6 25.0 1.0
CD1 A:TRP155 4.6 20.8 1.0
O C:ALA127 4.9 26.0 1.0
O D:GLY48 4.9 31.4 1.0

Nickel binding site 2 out of 2 in 1y1o

Go back to Nickel Binding Sites List in 1y1o
Nickel binding site 2 out of 2 in the X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Crystal Structure of Penicillin-Binding Protein- Related Factor A From Bacillus Stearothermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni322

b:29.3
occ:1.00
ND1 C:HIS151 2.1 19.1 1.0
O C:HOH328 2.1 10.4 1.0
OE2 C:GLU171 2.2 31.7 1.0
ND1 C:HIS175 2.2 33.4 1.0
CD C:GLU171 2.9 37.1 1.0
CE1 C:HIS151 3.0 20.4 1.0
OE1 C:GLU171 3.0 34.5 1.0
CG C:HIS151 3.1 19.8 1.0
CE1 C:HIS175 3.1 32.4 1.0
CG C:HIS175 3.2 30.5 1.0
CB C:HIS151 3.5 21.4 1.0
CB C:HIS175 3.5 27.4 1.0
NE2 C:HIS151 4.0 20.4 1.0
NE1 C:TRP155 4.0 26.4 1.0
CD2 C:HIS151 4.1 22.6 1.0
CA C:HIS151 4.2 22.5 1.0
NE2 C:HIS175 4.3 32.8 1.0
CD2 C:HIS175 4.3 29.6 1.0
CG C:GLU171 4.4 34.2 1.0
CD1 C:TRP155 4.5 27.2 1.0
CB A:ALA127 4.7 22.1 1.0
O B:GLY48 4.8 28.4 1.0
O C:HOH334 5.0 43.5 1.0
CA C:HIS175 5.0 28.2 1.0

Reference:

J.Osipiuk, H.Li, S.Moy, F.Collart, A.Joachimiak. X-Ray Crystal Structure of Penicillin-Binding Protein-Related Factor A From Bacillus Stearothermophilus To Be Published.
Page generated: Wed Dec 16 01:16:41 2020

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