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

Protein crystallography data

The structure of Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmk 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) 86.14 / 2.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 99.467, 99.467, 109.544, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 23.3

Other elements in 3nmk:

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

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 (pdb code 3nmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nmk

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn152

b:31.5
occ:1.00
NAJ D:PXX151 2.1 36.1 1.0
NAK B:PXX151 2.1 27.0 1.0
NAJ B:PXX151 2.1 26.7 1.0
NAK D:PXX151 2.1 37.9 1.0
O B:HOH113 2.6 18.2 1.0
CAQ D:PXX151 2.9 35.1 1.0
CAR D:PXX151 2.9 38.9 1.0
CAR B:PXX151 2.9 26.7 1.0
CAQ B:PXX151 2.9 25.5 1.0
CAE B:PXX151 3.1 26.9 1.0
CAF B:PXX151 3.1 29.9 1.0
CAE D:PXX151 3.1 39.0 1.0
CAF D:PXX151 3.2 44.7 1.0
CAO D:PXX151 4.2 33.1 1.0
CAP D:PXX151 4.2 38.0 1.0
CAO B:PXX151 4.3 27.8 1.0
CAP B:PXX151 4.3 27.2 1.0
CAC B:PXX151 4.4 31.1 1.0
CAD B:PXX151 4.4 23.1 1.0
CAC D:PXX151 4.4 33.2 1.0
CAD D:PXX151 4.5 35.1 1.0
O B:HOH112 4.7 17.5 1.0
O B:LYS42 4.8 36.6 1.0
CAG D:PXX151 4.9 34.3 1.0
CAH B:PXX151 4.9 23.8 1.0
CAG B:PXX151 4.9 26.9 1.0
CAH D:PXX151 4.9 28.2 1.0
O C:HOH107 4.9 16.0 1.0

Zinc binding site 2 out of 2 in 3nmk

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn152

b:30.4
occ:1.00
NAJ A:PXX151 2.1 31.9 1.0
NAK C:PXX151 2.1 28.1 1.0
NAJ C:PXX151 2.1 30.2 1.0
NAK A:PXX151 2.1 39.2 1.0
O C:HOH107 2.6 16.0 1.0
CAQ A:PXX151 2.9 33.8 1.0
CAR A:PXX151 2.9 37.6 1.0
CAR C:PXX151 2.9 26.2 1.0
CAQ C:PXX151 2.9 26.3 1.0
CAE C:PXX151 3.1 28.8 1.0
CAF C:PXX151 3.1 26.9 1.0
CAE A:PXX151 3.1 36.4 1.0
CAF A:PXX151 3.2 43.1 1.0
CAO A:PXX151 4.2 33.8 1.0
CAP A:PXX151 4.2 35.9 1.0
CAO C:PXX151 4.3 29.9 1.0
CAP C:PXX151 4.3 27.8 1.0
CAC C:PXX151 4.4 32.0 1.0
CAD C:PXX151 4.4 22.6 1.0
CAC A:PXX151 4.4 32.5 1.0
CAD A:PXX151 4.5 34.4 1.0
O C:LYS42 4.8 36.6 1.0
O B:HOH113 4.8 18.2 1.0
CAG A:PXX151 4.9 33.7 1.0
CAG C:PXX151 4.9 30.3 1.0
CAH C:PXX151 4.9 23.5 1.0
CAH A:PXX151 4.9 26.6 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: Wed Dec 16 04:39:01 2020

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