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Nickel in PDB 3bjd: Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa

Protein crystallography data

The structure of Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa, PDB code: 3bjd was solved by J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.M.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.90 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.566, 156.904, 136.022, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa (pdb code 3bjd). 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 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa, PDB code: 3bjd:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3bjd

Go back to Nickel Binding Sites List in 3bjd
Nickel binding site 1 out of 3 in the Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa


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 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:24.3
occ:1.00
ND1 A:HIS191 2.1 14.5 1.0
OE1 A:GLU181 2.1 18.1 1.0
NE2 A:HIS274 2.2 23.2 1.0
O A:HOH532 2.2 18.3 1.0
O A:HOH632 2.4 36.6 1.0
O A:HOH756 2.6 38.0 1.0
CD A:GLU181 2.9 22.5 1.0
CE1 A:HIS191 3.0 14.7 1.0
OE2 A:GLU181 3.1 24.6 1.0
CE1 A:HIS274 3.1 23.4 1.0
CG A:HIS191 3.1 15.8 1.0
CD2 A:HIS274 3.2 25.1 1.0
CB A:HIS191 3.5 13.8 1.0
NE2 A:HIS191 4.1 17.0 1.0
CD2 A:HIS191 4.2 15.8 1.0
ND1 A:HIS274 4.2 26.6 1.0
CG A:HIS274 4.3 26.7 1.0
CG A:GLU181 4.3 17.2 1.0
CA A:GLU181 4.7 14.4 1.0
O A:HOH641 4.8 35.0 1.0
CB A:GLU181 4.8 14.2 1.0
CE1 A:TYR270 4.9 21.7 1.0

Nickel binding site 2 out of 3 in 3bjd

Go back to Nickel Binding Sites List in 3bjd
Nickel binding site 2 out of 3 in the Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa


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 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni502

b:24.0
occ:1.00
ND1 B:HIS191 2.0 16.6 1.0
OE1 B:GLU181 2.1 18.3 1.0
NE2 B:HIS274 2.1 31.8 1.0
O1 B:EDO407 2.2 28.6 1.0
O2 B:EDO407 2.3 24.4 1.0
O B:HOH590 2.5 30.5 1.0
CD B:GLU181 2.9 21.8 1.0
CE1 B:HIS191 2.9 18.2 1.0
CE1 B:HIS274 3.1 30.1 1.0
C1 B:EDO407 3.1 29.2 1.0
C2 B:EDO407 3.1 29.7 1.0
CG B:HIS191 3.1 16.9 1.0
CD2 B:HIS274 3.1 31.6 1.0
OE2 B:GLU181 3.2 22.7 1.0
CB B:HIS191 3.6 15.8 1.0
NE2 B:HIS191 4.1 17.6 1.0
CD2 B:HIS191 4.2 16.6 1.0
ND1 B:HIS274 4.2 30.5 1.0
CG B:HIS274 4.3 31.4 1.0
CG B:GLU181 4.4 18.6 1.0
O B:HOH805 4.5 23.0 0.4
CA B:GLU181 4.7 15.8 1.0
CB B:GLU181 4.8 15.4 1.0
OE2 B:GLU244 4.9 35.0 0.6
OE1 B:GLU244 5.0 34.8 0.6

Nickel binding site 3 out of 3 in 3bjd

Go back to Nickel Binding Sites List in 3bjd
Nickel binding site 3 out of 3 in the Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa


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 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni503

b:21.6
occ:1.00
O2 C:EDO405 1.8 22.7 1.0
ND1 C:HIS191 2.0 12.2 1.0
OE1 C:GLU181 2.1 15.9 1.0
NE2 C:HIS274 2.1 26.0 1.0
O1 C:EDO405 2.2 16.7 1.0
O C:HOH636 2.3 22.0 1.0
CE1 C:HIS191 2.9 13.7 1.0
C2 C:EDO405 2.9 23.4 1.0
C1 C:EDO405 3.1 20.3 1.0
CE1 C:HIS274 3.1 25.1 1.0
CD C:GLU181 3.1 16.3 1.0
CG C:HIS191 3.1 12.8 1.0
CD2 C:HIS274 3.1 23.1 1.0
OE2 C:GLU181 3.3 16.2 1.0
CB C:HIS191 3.5 14.4 1.0
NE2 C:HIS191 4.1 15.9 1.0
CD2 C:HIS191 4.2 12.8 1.0
ND1 C:HIS274 4.2 25.9 1.0
OE2 C:GLU244 4.2 27.6 1.0
CG C:HIS274 4.2 24.8 1.0
CG C:GLU181 4.5 13.9 1.0
CA C:GLU181 4.6 13.4 1.0
O C:HOH826 4.6 44.5 1.0
CB C:GLU181 4.7 12.8 1.0
OE1 C:GLU244 4.9 31.8 1.0
OH C:TYR177 5.0 19.0 1.0

Reference:

J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.M.Edwards, A.Joachimiak. Crystal Structure of Putative 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase From Pseudomonas Aeruginosa. To Be Published.
Page generated: Fri Sep 25 08:19:57 2020
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