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Nickel in PDB 3cu2: Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution

Enzymatic activity of Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution

All present enzymatic activity of Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution:
5.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution, PDB code: 3cu2 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) 28.92 / 1.91
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.010, 85.010, 140.160, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 20.5

Other elements in 3cu2:

The structure of Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution (pdb code 3cu2). 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 Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution, PDB code: 3cu2:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3cu2

Go back to Nickel Binding Sites List in 3cu2
Nickel binding site 1 out of 2 in the Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 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 Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni238

b:14.0
occ:1.00
 OD1 A:ASP45 2.1 15.1 1.0
NE2 A:HIS43 2.2 8.0 1.0
OD2 A:ASP192 2.2 16.7 1.0
ND1 A:HIS74 2.2 11.1 1.0
O A:HOH272 2.4 22.8 1.0
O A:HOH247 2.4 15.7 1.0
CG A:ASP45 3.1 15.4 1.0
CD2 A:HIS43 3.1 11.4 1.0
CG A:ASP192 3.1 18.8 1.0
CE1 A:HIS74 3.1 12.2 1.0
CE1 A:HIS43 3.2 10.2 1.0
CG A:HIS74 3.3 11.0 1.0
OD2 A:ASP45 3.3 19.9 1.0
OD1 A:ASP192 3.4 16.5 1.0
CB A:HIS74 3.6 11.7 1.0
NE2 A:GLN152 4.2 11.9 1.0
CG A:HIS43 4.2 12.7 1.0
ND1 A:HIS43 4.3 12.4 1.0
NE2 A:HIS74 4.3 14.4 1.0
CD2 A:HIS74 4.4 13.6 1.0
CB A:ASP192 4.4 14.8 1.0
CB A:ASP45 4.5 10.9 1.0
CE A:MSE76 4.5 20.1 1.0
CG1 A:VAL214 4.8 13.2 1.0
CA A:ASP45 4.8 14.6 1.0
OE1 A:GLN152 5.0 11.0 1.0
CD A:GLN152 5.0 15.8 1.0
O A:HOH252 5.0 17.2 1.0

Nickel binding site 2 out of 2 in 3cu2

Go back to Nickel Binding Sites List in 3cu2
Nickel binding site 2 out of 2 in the Crystal Structure of Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 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 Ribulose-5-Phosphate 3-Epimerase (YP_718263.1) From Haemophilus Somnus 129PT at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni238

b:13.8
occ:1.00
 O B:HOH302 2.0 22.2 1.0
OD1 B:ASP45 2.1 13.4 1.0
NE2 B:HIS43 2.1 13.3 1.0
OD2 B:ASP192 2.2 15.5 1.0
ND1 B:HIS74 2.3 13.6 1.0
O B:HOH276 2.4 17.4 1.0
CG B:ASP45 3.1 15.4 1.0
CD2 B:HIS43 3.1 14.8 1.0
CE1 B:HIS43 3.1 12.3 1.0
CG B:ASP192 3.1 16.6 1.0
CE1 B:HIS74 3.2 12.4 1.0
CG B:HIS74 3.3 15.7 1.0
OD1 B:ASP192 3.3 16.0 1.0
OD2 B:ASP45 3.4 15.9 1.0
CB B:HIS74 3.6 13.5 1.0
NE2 B:GLN152 4.1 13.3 1.0
ND1 B:HIS43 4.2 17.2 1.0
CG B:HIS43 4.2 12.7 1.0
NE2 B:HIS74 4.3 17.0 1.0
CD2 B:HIS74 4.4 14.5 1.0
CB B:ASP45 4.4 11.0 1.0
CE B:MSE76 4.5 10.4 1.0
CB B:ASP192 4.5 9.2 1.0
CG1 B:VAL214 4.6 14.1 1.0
CA B:ASP45 4.8 12.6 1.0
CD B:GLN152 4.9 15.0 1.0
O B:HOH314 4.9 23.7 1.0
OE1 B:GLN152 4.9 12.8 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Oct 9 17:14:04 2024

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