Atomistry » Nickel » PDB 3dse-3hy3 » 3foo
Atomistry »
  Nickel »
    PDB 3dse-3hy3 »
      3foo »

Nickel in PDB 3foo: A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form

Protein crystallography data

The structure of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form, PDB code: 3foo was solved by R.J.Radford, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.53 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.339, 107.396, 102.051, 90.00, 105.52, 90.00
R / Rfree (%) 20.9 / 26.8

Other elements in 3foo:

The structure of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Nickel atom in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form (pdb code 3foo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 24 binding sites of Nickel where determined in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form, PDB code: 3foo:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 1 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni107

b:66.2
occ:1.00
O A:ALA1 2.3 45.5 1.0
OD2 A:ASP39 2.6 43.5 1.0
N A:ALA1 2.8 45.8 1.0
O A:HOH166 3.0 35.5 1.0
OD1 A:ASP39 3.1 42.2 1.0
C A:ALA1 3.1 45.8 1.0
CG A:ASP39 3.2 42.2 1.0
CA A:ALA1 3.4 45.8 1.0
CB A:ALA1 4.0 45.8 1.0
N A:ASP2 4.3 45.7 1.0
ND2 A:ASN6 4.4 41.6 1.0
CB A:ASP39 4.6 41.5 1.0
O A:ASP39 4.7 41.1 1.0
CA A:ASP2 5.0 45.6 1.0

Nickel binding site 2 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 2 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni108

b:34.8
occ:1.00
NAK C:PXX151 2.1 31.1 1.0
NAJ C:PXX151 2.1 30.3 1.0
ND1 A:HIS77 2.1 34.9 1.0
O C:HOH125 2.2 37.4 1.0
O C:HOH124 2.7 19.4 1.0
CAR C:PXX151 2.9 30.1 1.0
CAQ C:PXX151 2.9 30.1 1.0
CE1 A:HIS77 3.0 34.0 1.0
CAF C:PXX151 3.1 30.5 1.0
CAE C:PXX151 3.1 31.0 1.0
CG A:HIS77 3.2 35.5 1.0
CB A:HIS77 3.6 36.2 1.0
NE2 A:HIS77 4.1 33.4 1.0
CD2 A:HIS77 4.2 34.3 1.0
CAP C:PXX151 4.2 30.8 1.0
CAO C:PXX151 4.3 30.9 1.0
CA A:HIS77 4.3 36.8 1.0
CAD C:PXX151 4.4 30.7 1.0
CAC C:PXX151 4.4 30.2 1.0
O C:HOH170 4.6 28.8 1.0
O C:LYS42 4.6 40.7 1.0
CAH C:PXX151 4.8 30.1 1.0
CAG C:PXX151 4.9 30.3 1.0

Nickel binding site 3 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 3 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni107

b:76.5
occ:1.00
O B:ALA1 1.9 46.1 1.0
N B:ALA1 2.4 46.4 1.0
OD2 B:ASP39 2.5 42.5 1.0
O B:HOH171 2.7 35.3 1.0
C B:ALA1 2.8 46.0 1.0
CA B:ALA1 3.1 46.3 1.0
CG B:ASP39 3.3 41.6 1.0
OD1 B:ASP39 3.5 42.2 1.0
N B:ASP2 4.0 45.7 1.0
CB B:ALA1 4.1 46.4 1.0
ND2 B:ASN6 4.6 41.4 1.0
CA B:ASP2 4.6 45.6 1.0
CB B:ASP39 4.6 41.3 1.0
O B:ASP39 4.6 40.9 1.0

Nickel binding site 4 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 4 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni108

b:31.7
occ:1.00
NAJ A:PXX151 2.1 28.9 1.0
NAK A:PXX151 2.1 29.0 1.0
ND1 B:HIS77 2.1 33.7 1.0
CAQ A:PXX151 2.9 29.1 1.0
CAR A:PXX151 2.9 28.6 1.0
O B:HOH121 2.9 16.3 1.0
CE1 B:HIS77 3.0 33.5 1.0
CAE A:PXX151 3.1 28.6 1.0
CAF A:PXX151 3.1 28.6 1.0
CG B:HIS77 3.2 34.9 1.0
O A:HOH120 3.5 28.8 1.0
CB B:HIS77 3.6 36.2 1.0
NE2 B:HIS77 4.2 33.5 1.0
CAO A:PXX151 4.2 28.8 1.0
CAP A:PXX151 4.3 28.4 1.0
CD2 B:HIS77 4.3 34.3 1.0
CAC A:PXX151 4.4 28.5 1.0
O A:LYS42 4.4 40.3 1.0
CAD A:PXX151 4.4 29.1 1.0
CA B:HIS77 4.4 36.5 1.0
CAG A:PXX151 4.9 28.6 1.0
CAH A:PXX151 4.9 27.9 1.0

Nickel binding site 5 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 5 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni107

b:73.6
occ:1.00
N C:ALA1 2.1 46.0 1.0
OD2 C:ASP39 2.4 42.6 1.0
O C:ALA1 2.4 45.6 1.0
C C:ALA1 3.1 45.9 1.0
CA C:ALA1 3.1 45.9 1.0
CG C:ASP39 3.4 41.9 1.0
OD1 C:ASP39 3.7 43.4 1.0
CB C:ALA1 4.3 46.0 1.0
N C:ASP2 4.4 45.8 1.0
ND2 C:ASN6 4.6 41.7 1.0
CB C:ASP39 4.7 41.1 1.0
O C:ASP39 4.8 40.9 1.0

Nickel binding site 6 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 6 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni108

b:31.1
occ:1.00
O C:HOH123 2.0 27.6 1.0
NAJ B:PXX151 2.1 26.8 1.0
NAK B:PXX151 2.1 26.6 1.0
ND1 C:HIS77 2.1 33.2 1.0
O B:HOH122 2.2 27.8 1.0
CAQ B:PXX151 2.9 26.3 1.0
CAR B:PXX151 2.9 26.1 1.0
CE1 C:HIS77 3.0 33.0 1.0
CAE B:PXX151 3.1 26.0 1.0
CAF B:PXX151 3.1 26.2 1.0
CG C:HIS77 3.2 34.9 1.0
CB C:HIS77 3.6 35.9 1.0
NE2 C:HIS77 4.2 33.1 1.0
CAO B:PXX151 4.2 26.0 1.0
CAP B:PXX151 4.3 25.9 1.0
CD2 C:HIS77 4.3 34.4 1.0
CAC B:PXX151 4.3 26.4 1.0
O B:LYS42 4.4 39.9 1.0
CA C:HIS77 4.4 36.4 1.0
CAD B:PXX151 4.4 25.9 1.0
CAG B:PXX151 4.8 25.7 1.0
CAH B:PXX151 4.9 25.6 1.0

Nickel binding site 7 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 7 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni107

b:74.3
occ:1.00
N D:ALA1 2.2 45.9 1.0
O D:ALA1 2.3 45.8 1.0
OD2 D:ASP39 2.5 43.9 1.0
C D:ALA1 3.0 45.9 1.0
CA D:ALA1 3.2 45.9 1.0
CG D:ASP39 3.2 42.3 1.0
O D:HOH145 3.4 39.1 1.0
OD1 D:ASP39 3.4 43.4 1.0
N D:ASP2 4.3 45.7 1.0
CB D:ALA1 4.3 46.2 1.0
CB D:ASP39 4.6 41.2 1.0
ND2 D:ASN6 4.7 41.9 1.0
O D:ASP39 4.8 41.0 1.0
CA D:ASP2 4.9 45.6 1.0

Nickel binding site 8 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 8 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni108

b:32.5
occ:1.00
NAK F:PXX151 2.1 30.5 1.0
NAJ F:PXX151 2.1 30.6 1.0
ND1 D:HIS77 2.1 33.2 1.0
O F:HOH119 2.5 33.6 1.0
CAQ F:PXX151 2.9 30.5 1.0
CAR F:PXX151 2.9 30.7 1.0
O F:HOH118 3.0 14.5 1.0
CE1 D:HIS77 3.1 33.3 1.0
CAF F:PXX151 3.1 30.7 1.0
CAE F:PXX151 3.1 30.4 1.0
CG D:HIS77 3.2 35.2 1.0
CB D:HIS77 3.5 36.2 1.0
NE2 D:HIS77 4.2 33.8 1.0
CAO F:PXX151 4.2 30.7 1.0
CAP F:PXX151 4.3 30.9 1.0
CD2 D:HIS77 4.3 34.2 1.0
CA D:HIS77 4.3 36.6 1.0
CAD F:PXX151 4.4 30.7 1.0
CAC F:PXX151 4.4 30.5 1.0
O F:LYS42 4.5 40.1 1.0
O D:HOH148 4.7 32.5 1.0
CAG F:PXX151 4.9 30.4 1.0
CAH F:PXX151 4.9 30.0 1.0

Nickel binding site 9 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 9 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni107

b:60.0
occ:1.00
N E:ALA1 2.2 45.5 1.0
O E:ALA1 2.3 45.8 1.0
OD2 E:ASP39 2.3 44.3 1.0
O E:HOH149 2.5 27.5 1.0
C E:ALA1 3.0 45.8 1.0
CA E:ALA1 3.2 45.6 1.0
CG E:ASP39 3.3 42.8 1.0
OD1 E:ASP39 3.6 44.0 1.0
CB E:ALA1 4.1 45.7 1.0
N E:ASP2 4.3 45.5 1.0
CB E:ASP39 4.6 41.2 1.0
ND2 E:ASN6 4.6 42.9 1.0
O E:ASP39 4.7 41.3 1.0
CA E:ASP2 4.9 45.5 1.0

Nickel binding site 10 out of 24 in 3foo

Go back to Nickel Binding Sites List in 3foo
Nickel binding site 10 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni108

b:36.5
occ:1.00
NAK D:PXX151 2.1 31.8 1.0
NAJ D:PXX151 2.1 31.1 1.0
ND1 E:HIS77 2.1 34.3 1.0
O D:HOH113 2.5 24.0 1.0
O D:HOH114 2.6 23.4 1.0
CE1 E:HIS77 2.9 33.4 1.0
CAQ D:PXX151 2.9 30.4 1.0
CAR D:PXX151 2.9 31.0 1.0
CAF D:PXX151 3.1 30.7 1.0
CAE D:PXX151 3.1 31.1 1.0
CG E:HIS77 3.3 35.1 1.0
CB E:HIS77 3.8 36.2 1.0
NE2 E:HIS77 4.1 33.5 1.0
CAO D:PXX151 4.3 30.4 1.0
CAP D:PXX151 4.3 31.0 1.0
CD2 E:HIS77 4.3 33.8 1.0
CAD D:PXX151 4.4 30.4 1.0
CAC D:PXX151 4.4 30.8 1.0
O D:LYS42 4.4 40.1 1.0
CA E:HIS77 4.5 36.7 1.0
CAH D:PXX151 4.9 30.2 1.0
CAG D:PXX151 4.9 30.8 1.0

Reference:

R.J.Radford, F.A.Tezcan. A Superprotein Triangle Driven By Nickel(II) Coordination: Exploiting Non-Natural Metal Ligands in Protein Self-Assembly J.Am.Chem.Soc. V. 131 9136 2009.
ISSN: ISSN 0002-7863
PubMed: 19527025
DOI: 10.1021/JA9000695
Page generated: Wed Dec 16 01:23:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy