Atomistry » Nickel » PDB 3l1m-3n6n » 3n0q
Atomistry »
  Nickel »
    PDB 3l1m-3n6n »
      3n0q »

Nickel in PDB 3n0q: Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution, PDB code: 3n0q 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) 28.16 / 1.80
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 97.533, 97.533, 96.522, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 18.6

Other elements in 3n0q:

The structure of Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution (pdb code 3n0q). 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 Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution, PDB code: 3n0q:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3n0q

Go back to Nickel Binding Sites List in 3n0q
Nickel binding site 1 out of 2 in the Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 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 Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:22.3
occ:1.00
OD1 A:ASP356 2.0 22.7 1.0
O3 A:TRS504 2.1 26.7 1.0
NE2 A:HIS206 2.1 22.0 1.0
NE2 A:HIS201 2.1 21.7 1.0
O1 A:TRS504 2.2 24.8 1.0
N A:TRS504 2.4 32.7 1.0
C A:TRS504 2.9 31.2 1.0
CG A:ASP356 3.0 21.6 1.0
C3 A:TRS504 3.0 27.6 1.0
C1 A:TRS504 3.0 30.7 1.0
CD2 A:HIS206 3.1 23.2 1.0
CE1 A:HIS201 3.1 23.5 1.0
CE1 A:HIS206 3.1 25.6 1.0
CD2 A:HIS201 3.1 21.7 1.0
OD2 A:ASP356 3.2 22.7 1.0
ND2 A:ASN195 4.0 21.4 1.0
ND1 A:HIS206 4.2 22.8 1.0
CG A:HIS206 4.2 24.0 1.0
ND1 A:HIS201 4.2 22.7 1.0
CG A:HIS201 4.3 21.7 1.0
CB A:ASP356 4.4 22.4 1.0
C2 A:TRS504 4.4 34.3 1.0
SG A:CYS202 4.6 31.2 1.0
O A:ASN195 4.7 22.2 1.0
CG2 A:THR352 4.8 19.8 1.0
CG A:ASN195 4.8 21.7 1.0
O A:HOH511 4.8 21.3 1.0
O A:GLU198 4.8 21.7 1.0
CA A:ASP356 4.9 21.3 1.0
OD1 A:ASN195 4.9 24.0 1.0
O2 A:TRS504 5.0 41.5 1.0

Nickel binding site 2 out of 2 in 3n0q

Go back to Nickel Binding Sites List in 3n0q
Nickel binding site 2 out of 2 in the Crystal Structure of A Putative Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 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 Aromatic-Ring Hydroxylating Dioxygenase (TM1040_3219) From Silicibacter Sp. TM1040 at 1.80 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni502

b:34.0
occ:1.00
O3 A:TRS505 1.7 41.6 1.0
O A:HOH589 2.0 30.4 1.0
NE2 A:HIS16 2.2 26.6 1.0
O A:HOH663 2.2 36.2 1.0
O2 A:TRS505 2.3 26.9 1.0
O1 A:TRS505 2.3 39.6 1.0
C3 A:TRS505 2.9 46.5 1.0
CE1 A:HIS16 3.1 27.3 1.0
C2 A:TRS505 3.1 37.2 1.0
CD2 A:HIS16 3.2 25.9 1.0
C A:TRS505 3.2 42.4 1.0
C1 A:TRS505 3.3 43.9 1.0
O A:HOH627 4.2 33.8 1.0
O A:HOH901 4.2 51.8 1.0
ND1 A:HIS16 4.2 26.8 1.0
CG A:HIS16 4.3 25.9 1.0
CD A:PRO376 4.5 24.6 1.0
CG A:PRO376 4.6 26.4 1.0
CD A:ARG13 4.6 34.0 0.5
N A:TRS505 4.7 46.7 1.0
NE A:ARG13 4.7 36.2 0.5
CB A:PRO376 4.9 26.0 1.0
N A:PRO376 4.9 23.5 1.0
CD A:ARG13 5.0 34.1 0.5

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Thu Oct 29 06:21:07 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy