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Nickel in PDB 3nmj: Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2

Protein crystallography data

The structure of Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmj 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) 85.99 / 3.10
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 99.291, 99.291, 109.317, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 23.8

Other elements in 3nmj:

The structure of Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 (pdb code 3nmj). 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 Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmj:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3nmj

Go back to Nickel Binding Sites List in 3nmj
Nickel binding site 1 out of 2 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni152

b:44.4
occ:1.00
NAK D:PXX151 2.1 63.8 1.0
NAJ D:PXX151 2.1 49.3 1.0
NAK B:PXX151 2.1 35.2 1.0
NAJ B:PXX151 2.1 38.1 1.0
O D:HOH107 2.6 22.7 1.0
CAR D:PXX151 2.8 61.7 1.0
CAQ D:PXX151 2.8 57.0 1.0
CAR B:PXX151 2.9 33.5 1.0
CAQ B:PXX151 2.9 34.4 1.0
CAF B:PXX151 3.1 35.6 1.0
CAE D:PXX151 3.1 54.7 1.0
CAF D:PXX151 3.1 73.2 1.0
CAE B:PXX151 3.1 39.7 1.0
CAP D:PXX151 4.2 61.5 1.0
CAO D:PXX151 4.2 56.3 1.0
CAP B:PXX151 4.2 33.8 1.0
CAO B:PXX151 4.2 33.9 1.0
CAD B:PXX151 4.4 36.2 1.0
CAC D:PXX151 4.4 56.5 1.0
CAD D:PXX151 4.4 67.1 1.0
CAC B:PXX151 4.4 38.9 1.0
O B:LYS42 4.7 53.1 1.0
O A:HOH107 4.8 19.9 1.0
CAH B:PXX151 4.8 33.9 1.0
CAG D:PXX151 4.8 56.1 1.0
CAH D:PXX151 4.8 62.3 1.0
CAG B:PXX151 4.9 35.5 1.0

Nickel binding site 2 out of 2 in 3nmj

Go back to Nickel Binding Sites List in 3nmj
Nickel binding site 2 out of 2 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni152

b:44.5
occ:1.00
NAJ A:PXX151 2.1 46.4 1.0
NAK A:PXX151 2.1 63.1 1.0
NAK C:PXX151 2.1 38.6 1.0
NAJ C:PXX151 2.1 38.8 1.0
O A:HOH107 2.6 19.9 1.0
CAQ A:PXX151 2.8 55.4 1.0
CAR A:PXX151 2.8 61.3 1.0
CAR C:PXX151 2.9 36.4 1.0
CAQ C:PXX151 2.9 36.0 1.0
CAF C:PXX151 3.1 39.8 1.0
CAE A:PXX151 3.1 51.6 1.0
CAF A:PXX151 3.1 73.0 1.0
CAE C:PXX151 3.1 39.7 1.0
CAO A:PXX151 4.2 54.4 1.0
CAP A:PXX151 4.2 61.5 1.0
CAP C:PXX151 4.2 39.1 1.0
CAO C:PXX151 4.2 36.0 1.0
CAD C:PXX151 4.4 39.3 1.0
CAC A:PXX151 4.4 53.9 1.0
CAD A:PXX151 4.4 66.4 1.0
CAC C:PXX151 4.4 39.1 1.0
O D:HOH107 4.8 22.7 1.0
CAG A:PXX151 4.8 52.4 1.0
CAH C:PXX151 4.8 39.1 1.0
CAH A:PXX151 4.8 60.4 1.0
O C:LYS42 4.9 53.1 1.0
CAG C:PXX151 4.9 35.1 1.0
CB C:PRO53 5.0 52.6 1.0

Reference:

R.J.Radford, M.Lawrenz, P.C.Nguyen, J.A.Mccammon, F.A.Tezcan. Porous Protein Frameworks with Unsaturated Metal Centers in Sterically Encumbered Coordination Sites. Chem.Commun.(Camb.) V. 47 313 2011.
ISSN: ISSN 1359-7345
PubMed: 20740227
DOI: 10.1039/C0CC02168G
Page generated: Thu Oct 29 06:21:16 2020
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