Atomistry » Nickel » PDB 3a1f-3ds9 » 3cu2
Atomistry »
  Nickel »
    PDB 3a1f-3ds9 »
      3cu2 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy