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Nickel in PDB 4i74: Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion

Enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion

All present enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion, PDB code: 4i74 was solved by F.Giannese, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.91 / 1.68
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.120, 69.420, 130.230, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.8

Other elements in 4i74:

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion (pdb code 4i74). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion, PDB code: 4i74:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 4i74

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Nickel binding site 1 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


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 the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:13.6
occ:0.50
 O A:HOH764 1.1 19.2 1.0
O A:HOH696 1.5 27.2 1.0
O A:HOH661 1.8 29.5 1.0
O A:HOH751 1.9 30.3 1.0
NE2 A:HIS58 2.1 18.9 1.0
O A:HOH704 2.2 33.3 1.0
CE1 A:HIS58 3.0 19.9 1.0
CD2 A:HIS58 3.1 17.7 1.0
ND1 A:HIS58 4.2 18.6 1.0
O A:HOH563 4.2 24.9 1.0
CG A:HIS58 4.3 16.3 1.0
O A:HOH585 4.3 39.0 1.0
O A:HOH675 4.7 35.6 1.0
CD1 A:LEU65 4.8 19.4 1.0

Nickel binding site 2 out of 8 in 4i74

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Nickel binding site 2 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


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 the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:14.1
occ:0.50
 NE2 A:HIS115 2.1 18.9 1.0
CD2 A:HIS115 3.0 16.5 1.0
CE1 A:HIS115 3.1 16.8 1.0
O A:HOH550 4.1 32.8 1.0
CG A:HIS115 4.2 15.5 1.0
ND1 A:HIS115 4.2 14.9 1.0
O A:HOH731 4.4 20.6 1.0
OE2 A:GLU111 4.6 40.2 1.0
CB A:PRO67 4.8 15.3 1.0
CD1 A:LEU120 5.0 13.6 1.0

Nickel binding site 3 out of 8 in 4i74

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Nickel binding site 3 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


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 the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:27.6
occ:0.50
 O A:HOH725 1.9 33.7 1.0
O A:HOH772 2.3 41.4 1.0
CE1 A:HIS317 2.3 27.7 1.0
NE2 A:HIS317 2.8 30.1 1.0
ND1 A:HIS317 3.5 27.7 1.0
CD2 A:HIS317 4.1 23.6 1.0
O A:HOH690 4.1 39.2 1.0
CG A:HIS317 4.4 22.0 1.0
O A:HOH697 4.5 39.2 1.0
OD1 A:ASP222 4.7 30.9 1.0

Nickel binding site 4 out of 8 in 4i74

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Nickel binding site 4 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:21.9
occ:0.50
 N A:SER-1 1.9 40.5 1.0
ND1 A:HIS0 2.0 33.1 1.0
N A:HIS0 2.0 37.5 1.0
N A:GLY-2 2.2 41.5 1.0
CA A:SER-1 2.8 40.5 1.0
C A:SER-1 2.8 39.2 1.0
C A:GLY-2 2.9 41.1 1.0
CE1 A:HIS0 3.0 35.9 1.0
CG A:HIS0 3.0 35.8 1.0
CA A:GLY-2 3.0 41.3 1.0
CA A:HIS0 3.1 36.5 1.0
CB A:HIS0 3.3 36.5 1.0
N A:MET1 3.5 34.7 1.0
OG A:SER-1 3.8 42.5 1.0
C A:HIS0 3.8 35.7 1.0
CB A:SER-1 3.9 40.9 1.0
O A:SER-1 4.0 39.4 1.0
O A:GLY-2 4.0 40.7 1.0
NE2 A:HIS0 4.1 35.6 1.0
CD2 A:HIS0 4.1 34.8 1.0
O A:HOH746 4.1 36.2 1.0
O A:MET1 4.6 31.9 1.0
CA A:MET1 4.8 34.1 1.0
O A:HIS0 5.0 36.0 1.0

Nickel binding site 5 out of 8 in 4i74

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Nickel binding site 5 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni406

b:7.2
occ:0.20
 C2' A:MBY408 0.7 13.7 0.8
C1' A:MBY408 1.1 15.8 0.8
O2' A:MBY408 1.4 15.1 0.8
C3' A:MBY408 1.8 13.2 0.8
N4' A:MBY408 1.8 15.0 0.8
O1 A:TRS409 1.8 5.4 0.2
O A:HOH742 1.9 2.9 0.2
N A:TRS409 2.1 6.4 0.2
OD2 A:ASP14 2.2 6.8 0.2
O3 A:TRS409 2.2 5.9 0.2
C4' A:MBY408 2.3 14.8 0.8
C A:TRS409 2.6 6.5 0.2
C1 A:TRS409 2.7 6.8 0.2
O3' A:MBY408 2.7 12.5 0.8
C3 A:TRS409 2.9 6.5 0.2
CG A:ASP14 3.1 11.4 0.2
C7 A:MBY408 3.2 17.1 0.8
OD1 A:ASP14 3.4 9.6 0.2
OD1 A:ASP14 3.4 17.0 0.8
O A:HOH527 3.4 13.9 1.0
C5' A:MBY408 3.5 14.7 0.8
CA A:CA401 3.5 13.2 1.0
OD2 A:ASP40 3.7 13.4 1.0
ND2 A:ASN12 3.8 20.0 1.0
OD2 A:ASP14 3.9 15.4 0.8
C9 A:MBY408 3.9 17.9 0.8
CE3 A:TRP260 4.0 17.0 1.0
CG A:ASP14 4.0 14.7 0.8
OD2 A:ASP261 4.0 12.2 1.0
C2 A:TRS409 4.1 6.8 0.2
N3 A:MBY408 4.2 16.4 0.8
OD1 A:ASP261 4.3 15.1 1.0
CB A:ASN12 4.3 16.4 1.0
CZ3 A:TRP260 4.3 15.2 1.0
C4 A:MBY408 4.3 18.4 0.8
CG A:ASP261 4.5 14.2 1.0
CD2 A:TRP260 4.5 14.3 1.0
CG A:ASN12 4.5 19.0 1.0
OD2 A:ASP15 4.5 13.2 1.0
CB A:ASP14 4.6 12.2 0.2
O5' A:MBY408 4.7 15.1 0.8
CG A:ASP40 4.9 14.3 1.0
C8 A:MBY408 4.9 18.3 0.8
OD1 A:ASN186 5.0 15.8 1.0

Nickel binding site 6 out of 8 in 4i74

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Nickel binding site 6 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni407

b:24.4
occ:0.50
 O A:HOH729 1.9 24.1 1.0
O A:HOH728 2.0 20.6 1.0
OD2 A:ASP190 2.1 17.5 1.0
O A:HOH780 2.1 36.3 1.0
O A:HOH755 2.3 32.0 1.0
O A:HOH540 2.8 26.4 1.0
CG A:ASP190 2.9 16.2 1.0
OD1 A:ASP190 3.2 15.1 1.0
O A:HOH752 3.7 32.1 1.0
O A:HOH547 4.1 20.1 1.0
O A:THR74 4.1 17.7 1.0
OG A:SER141 4.2 14.5 1.0
O A:HOH754 4.2 33.7 1.0
CB A:ASP190 4.2 14.1 1.0
O A:HOH566 4.3 25.3 1.0
CB A:SER141 4.5 14.2 1.0
CB A:ALA193 4.7 15.1 1.0
CG2 A:VAL76 4.8 16.6 1.0
O A:HOH730 5.0 31.9 1.0

Nickel binding site 7 out of 8 in 4i74

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Nickel binding site 7 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni410

b:38.4
occ:0.25
 NI A:NI410 0.0 38.4 0.2
O A:HOH757 2.2 32.6 1.0
NI A:NI410 2.4 40.8 0.2
NE2 A:HIS247 2.8 37.3 1.0
OE1 A:GLU82 2.8 22.2 0.2
CD2 A:HIS247 3.1 36.5 1.0
CD A:GLU82 3.8 22.4 0.2
O A:HOH705 3.9 22.2 1.0
CE1 A:HIS247 4.0 37.0 1.0
OE2 A:GLU82 4.2 22.7 0.2
CG A:HIS247 4.4 32.0 1.0
ND1 A:HIS247 4.9 36.9 1.0

Nickel binding site 8 out of 8 in 4i74

Go back to Nickel Binding Sites List in 4i74
Nickel binding site 8 out of 8 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 and Allosterically Inhibited By A NI2+ Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni410

b:40.8
occ:0.25
 NI A:NI410 0.0 40.8 0.2
NE2 A:HIS247 2.3 37.3 1.0
NI A:NI410 2.4 38.4 0.2
CD2 A:HIS247 3.0 36.5 1.0
CE1 A:HIS247 3.1 37.0 1.0
OE1 A:GLU82 3.6 22.2 0.2
ND1 A:HIS247 3.9 36.9 1.0
CG A:HIS247 4.0 32.0 1.0
O A:HOH720 4.2 38.1 1.0
O A:HOH757 4.3 32.6 1.0
CB A:THR246 4.6 27.5 1.0
CD A:GLU82 4.7 22.4 0.2
CG2 A:THR246 4.9 29.7 1.0
N A:HIS247 4.9 28.6 1.0

Reference:

F.Giannese, M.Berg, P.Van Der Veken, V.Castagna, P.Tornaghi, K.Augustyns, M.Degano. Structures of Purine Nucleosidase From Trypanosoma Brucei Bound to Isozyme-Specific Trypanocidals and A Novel Metalorganic Inhibitor Acta Crystallogr.,Sect.D V. 69 1553 2013.
ISSN: ISSN 0907-4449
PubMed: 23897478
DOI: 10.1107/S0907444913010792
Page generated: Wed Dec 16 01:30:44 2020

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