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Nickel in PDB 3no4: Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution, PDB code: 3no4 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) 29.70 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.085, 89.085, 211.563, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution (pdb code 3no4). 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 A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution, PDB code: 3no4:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3no4

Go back to Nickel Binding Sites List in 3no4
Nickel binding site 1 out of 3 in the Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 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 Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni300

b:29.1
occ:1.00
O A:HOH531 2.1 41.5 1.0
OE1 A:GLU172 2.1 23.6 1.0
OD1 A:ASP40 2.1 21.4 1.0
NE2 A:HIS31 2.2 21.8 1.0
O A:HOH645 2.7 48.2 1.0
CD A:GLU172 2.9 23.3 1.0
CG A:ASP40 3.0 20.9 1.0
O A:HOH532 3.0 28.2 1.0
OE2 A:GLU172 3.1 25.0 1.0
OD2 A:ASP40 3.1 21.7 1.0
CE1 A:HIS31 3.2 22.3 1.0
CD2 A:HIS31 3.2 26.7 1.0
O A:HOH438 4.0 21.7 1.0
CG2 A:THR39 4.1 20.8 1.0
O A:GLY109 4.2 22.6 1.0
ND1 A:HIS31 4.3 20.9 1.0
CG A:GLU172 4.3 24.4 1.0
OE2 A:GLU29 4.3 28.7 1.0
CG A:HIS31 4.3 23.7 1.0
ND1 A:HIS167 4.3 24.9 1.0
O A:HOH534 4.3 39.7 1.0
CE1 A:HIS167 4.3 24.7 1.0
O A:HOH536 4.4 49.9 1.0
CB A:ASP40 4.4 21.8 1.0
N A:ASP40 4.7 21.2 1.0
CB A:THR39 4.8 21.4 1.0
CA A:ASP40 4.8 21.8 1.0
CB A:GLU172 4.9 24.2 1.0

Nickel binding site 2 out of 3 in 3no4

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Nickel binding site 2 out of 3 in the Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 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 Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni300

b:30.7
occ:1.00
OE1 B:GLU172 2.0 24.0 1.0
OD1 B:ASP40 2.1 24.3 1.0
O B:HOH742 2.1 54.4 1.0
NE2 B:HIS31 2.1 26.1 1.0
O B:HOH739 2.5 42.4 1.0
O B:HOH736 2.9 26.1 1.0
CD B:GLU172 2.9 24.5 1.0
CG B:ASP40 2.9 21.2 1.0
CE1 B:HIS31 3.1 23.9 1.0
OD2 B:ASP40 3.1 23.1 1.0
OE2 B:GLU172 3.1 24.4 1.0
CD2 B:HIS31 3.2 25.6 1.0
O B:HOH738 4.0 33.0 1.0
CG2 B:THR39 4.1 20.1 1.0
O B:HOH719 4.1 27.6 1.0
OE2 B:GLU29 4.1 30.6 1.0
O B:GLY109 4.2 23.4 1.0
ND1 B:HIS31 4.2 24.1 1.0
CE1 B:HIS167 4.2 23.8 1.0
CG B:HIS31 4.3 23.1 1.0
ND1 B:HIS167 4.3 25.2 1.0
CG B:GLU172 4.3 25.3 1.0
CB B:ASP40 4.4 22.6 1.0
O1 B:UNL350 4.6 51.0 1.0
O B:HOH740 4.7 43.9 1.0
CB B:THR39 4.7 23.6 1.0
N B:ASP40 4.7 22.2 1.0
CA B:ASP40 4.8 21.8 1.0
CB B:GLU172 4.9 25.3 1.0
N B:ALA168 5.0 26.3 1.0

Nickel binding site 3 out of 3 in 3no4

Go back to Nickel Binding Sites List in 3no4
Nickel binding site 3 out of 3 in the Crystal Structure of A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution


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 A Creatinine Amidohydrolase (NPUN_F1913) From Nostoc Punctiforme Pcc 73102 at 2.00 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni300

b:29.6
occ:1.00
O C:HOH911 2.0 39.9 1.0
OD1 C:ASP40 2.0 24.4 1.0
OE1 C:GLU172 2.1 23.9 1.0
NE2 C:HIS31 2.1 24.1 1.0
O C:HOH913 2.5 37.9 1.0
CD C:GLU172 2.9 25.5 1.0
O C:HOH909 2.9 27.1 1.0
CG C:ASP40 2.9 21.8 1.0
OE2 C:GLU172 3.1 23.7 1.0
CE1 C:HIS31 3.1 24.4 1.0
OD2 C:ASP40 3.1 22.5 1.0
CD2 C:HIS31 3.2 23.1 1.0
O C:HOH868 3.9 26.7 1.0
O C:HOH910 4.1 31.5 1.0
OE2 C:GLU29 4.2 29.1 1.0
O C:GLY109 4.2 21.6 1.0
ND1 C:HIS31 4.2 24.0 1.0
CG2 C:THR39 4.2 23.0 1.0
ND1 C:HIS167 4.3 24.5 1.0
CG C:GLU172 4.3 25.6 1.0
CG C:HIS31 4.3 22.7 1.0
CE1 C:HIS167 4.3 25.3 1.0
CB C:ASP40 4.3 21.9 1.0
N C:ASP40 4.7 22.4 1.0
CB C:THR39 4.7 22.1 1.0
CA C:ASP40 4.8 22.5 1.0
O C:HOH912 4.8 45.8 1.0
CB C:GLU172 4.9 25.0 1.0
O3 C:UNL350 5.0 65.0 1.0
N C:ALA168 5.0 23.9 1.0
O C:HOH842 5.0 20.7 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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