Atomistry » Nickel » PDB 1t6u-1xmk » 1zle
Atomistry »
  Nickel »
    PDB 1t6u-1xmk »
      1zle »

Nickel in PDB 1zle: Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa

Protein crystallography data

The structure of Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa, PDB code: 1zle was solved by G.N.Sarma, V.A.Manning, L.M.Ciuffetti, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.500, 74.500, 137.330, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa (pdb code 1zle). 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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa, PDB code: 1zle:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 1 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1003

b:59.5
occ:0.30
OD2 A:ASP83 2.6 62.5 1.0
OD2 A:ASP85 2.7 42.1 1.0
OD1 A:ASP83 3.0 45.5 1.0
CG A:ASP83 3.2 52.7 1.0
CG A:ASP85 3.4 47.6 1.0
NH2 A:ARG173 3.5 38.0 1.0
OD1 A:ASN171 3.7 46.4 1.0
CB A:ASP85 3.9 41.0 1.0
CA A:ASN171 4.1 28.5 1.0
NH1 A:ARG173 4.1 38.6 1.0
O A:HOH1061 4.2 56.1 1.0
CZ A:ARG173 4.3 45.4 1.0
OD1 A:ASP85 4.3 38.7 1.0
N A:ASN171 4.5 28.8 1.0
CB A:ASP83 4.6 42.1 1.0
CG A:ASN171 4.6 48.6 1.0
CB A:ASN171 4.8 29.2 1.0
O A:HOH1058 4.8 54.3 1.0

Nickel binding site 2 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 2 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1005

b:61.6
occ:0.30
OD2 A:ASP135 3.7 88.3 1.0
OE2 A:GLU145 3.8 68.9 1.0
OE1 A:GLU145 4.0 43.5 1.0
CD A:GLU145 4.0 56.9 1.0
OE1 A:GLN133 4.3 33.2 1.0
CG A:ASP135 4.4 63.1 1.0
OD1 A:ASP135 4.5 68.8 1.0
OG C:SER63 4.7 58.0 1.0
CG A:ARG169 4.8 47.3 1.0
CG A:GLU145 4.9 45.5 1.0

Nickel binding site 3 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 3 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1008

b:45.2
occ:0.20
O A:ASN178 2.6 41.9 1.0
ND2 A:ASN101 2.9 38.5 1.0
OXT A:ASN178 3.2 64.6 1.0
C A:ASN178 3.3 61.8 1.0
O A:HOH1062 3.5 54.5 1.0
CD1 A:LEU176 3.6 34.0 1.0
CB A:ASN101 3.7 41.4 1.0
CG A:ASN101 3.8 51.2 1.0
O A:HOH1070 4.0 70.9 1.0
CB A:LEU176 4.3 32.0 1.0
ND2 A:ASN127 4.5 30.5 1.0
CG A:LEU176 4.6 32.6 1.0
O A:HOH1013 4.7 34.7 1.0
CA A:ASN178 4.8 52.8 1.0
O A:LEU100 4.8 39.6 1.0
OD1 A:ASN101 4.9 40.3 1.0

Nickel binding site 4 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 4 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1001

b:49.3
occ:0.50
O B:HOH1019 2.0 37.0 0.5
OD2 B:ASP83 2.6 68.5 1.0
CG B:ASP83 3.6 60.6 1.0
OD1 B:ASP83 4.0 55.1 1.0
OD2 B:ASP85 4.1 43.2 1.0
OD1 B:ASN171 4.2 47.4 1.0
NH1 B:ARG173 4.5 37.8 0.5
NH2 B:ARG173 4.6 36.8 0.5
CG B:ASP85 4.8 55.2 1.0
CB B:ASP85 4.8 43.1 1.0
CB B:ASP83 5.0 35.3 1.0
CZ B:ARG173 5.0 37.5 0.5

Nickel binding site 5 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 5 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1004

b:62.9
occ:0.50
OE2 B:GLU99 2.8 74.7 1.0
CD B:GLU99 3.4 73.7 1.0
OE1 B:GLU99 3.6 69.5 1.0
ND2 B:ASN77 4.1 51.6 0.5
OD1 B:ASN77 4.4 71.1 0.5
CG B:ASN77 4.6 55.9 0.5
CG B:GLU99 4.6 42.7 1.0
CB B:SER75 4.8 72.7 0.5
OG B:SER75 4.9 73.9 0.5

Nickel binding site 6 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 6 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1006

b:39.8
occ:0.20
O A:HOH1027 2.2 38.8 1.0
O A:HOH1050 2.2 48.9 1.0
O C:HOH1034 2.5 53.8 1.0
O B:ASP149 2.8 30.2 1.0
OD2 B:ASP149 3.5 46.5 1.0
CG B:ASP149 3.8 34.5 1.0
OD1 B:ASP149 3.9 39.1 1.0
C B:ASP149 3.9 27.8 1.0
N B:ASP149 3.9 25.0 1.0
O A:ASP149 4.2 26.6 1.0
O C:HOH1018 4.2 47.7 1.0
OE A:PCA61 4.3 55.3 1.0
CA B:ASP149 4.4 26.0 1.0
O A:HOH1021 4.4 35.9 1.0
CB B:ASP149 4.7 27.9 1.0
NH1 B:ARG128 4.7 36.1 1.0
OD2 C:ASP149 4.8 46.5 1.0
O A:HOH1039 5.0 45.6 1.0
OE B:PCA61 5.0 64.7 1.0
C B:GLY148 5.0 30.3 1.0

Nickel binding site 7 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 7 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1007

b:70.7
occ:0.40
OD1 B:ASP135 2.1 69.1 1.0
CG B:ASP135 3.2 77.0 1.0
OD2 B:ASP135 3.6 75.9 1.0
O B:ASN136 3.9 48.5 1.0
N B:ASN136 3.9 48.2 1.0
CB B:ASP135 4.4 45.9 1.0
CA B:ASP135 4.5 37.4 1.0
C B:ASN136 4.6 52.3 1.0
C B:ASP135 4.8 42.2 1.0
CA B:ASN136 4.8 43.4 1.0

Nickel binding site 8 out of 8 in 1zle

Go back to Nickel Binding Sites List in 1zle
Nickel binding site 8 out of 8 in the Crystal Structure of A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa


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 A Rgd-Containing Host-Selective Toxin: Pyrenophora Tritici-Repentis Ptr Toxa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1002

b:48.6
occ:0.50
OD2 C:ASP83 2.6 69.9 1.0
O C:HOH1046 3.4 45.8 0.5
CG C:ASP83 3.8 69.3 1.0
OD1 C:ASP83 4.2 61.9 1.0
OD2 C:ASP85 4.2 58.3 1.0
OD1 C:ASN171 4.6 58.3 1.0
NH2 C:ARG173 4.7 65.2 1.0
CG C:ASP85 4.9 60.8 1.0
CB C:ASP85 4.9 52.2 1.0
NH1 C:ARG173 5.0 49.6 1.0

Reference:

G.N.Sarma, V.A.Manning, L.M.Ciuffetti, P.A.Karplus. Structure of Ptr Toxa: An Rgd-Containing Host-Selective Toxin From Pyrenophora Tritici-Repentis Plant Cell V. 17 3190 2005.
ISSN: ISSN 1040-4651
PubMed: 16214901
DOI: 10.1105/TPC.105.034918
Page generated: Fri Sep 25 08:04:58 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy