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Nickel in PDB 3bix: Crystal Structure of the Extracellular Esterase Domain of Neuroligin-1

Protein crystallography data

The structure of Crystal Structure of the Extracellular Esterase Domain of Neuroligin-1, PDB code: 3bix was solved by D.Arac, A.A.Boucard, E.Ozkan, P.Strop, E.Newell, T.C.Sudhof, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.88 / 1.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 173.744, 173.744, 108.045, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 20.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Extracellular Esterase Domain of Neuroligin-1 (pdb code 3bix). 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 the Extracellular Esterase Domain of Neuroligin-1, PDB code: 3bix:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3bix

Go back to Nickel Binding Sites List in 3bix
Nickel binding site 1 out of 2 in the Crystal Structure of the Extracellular Esterase Domain of Neuroligin-1


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 the Extracellular Esterase Domain of Neuroligin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2

b:28.7
occ:1.00
NE2 A:HIS642 2.0 34.4 1.0
NE2 D:HIS642 2.1 35.5 1.0
NE2 D:HIS640 2.2 32.1 1.0
NE2 A:HIS640 2.2 33.5 1.0
CE1 A:HIS642 2.6 34.5 1.0
CE1 D:HIS642 2.6 35.7 1.0
CD2 A:HIS640 3.0 32.4 1.0
CD2 D:HIS640 3.1 30.9 1.0
CE1 D:HIS640 3.2 33.3 1.0
CD2 A:HIS642 3.3 35.5 1.0
CE1 A:HIS640 3.3 34.5 1.0
CD2 D:HIS642 3.3 36.9 1.0
ND1 A:HIS642 3.9 36.3 1.0
ND1 D:HIS642 3.9 37.2 1.0
CG A:HIS642 4.2 36.2 1.0
CG A:HIS640 4.2 32.1 1.0
CG D:HIS642 4.2 37.2 1.0
CG D:HIS640 4.2 31.8 1.0
ND1 D:HIS640 4.3 32.4 1.0
ND1 A:HIS640 4.3 33.3 1.0
CD1 A:TYR445 4.8 33.7 1.0
CB A:TYR445 4.8 29.5 1.0
CD1 D:TYR445 4.8 33.3 1.0
CB D:TYR445 4.9 29.4 1.0
CG A:TYR445 4.9 32.8 1.0
CG D:TYR445 4.9 32.0 1.0

Nickel binding site 2 out of 2 in 3bix

Go back to Nickel Binding Sites List in 3bix
Nickel binding site 2 out of 2 in the Crystal Structure of the Extracellular Esterase Domain of Neuroligin-1


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 the Extracellular Esterase Domain of Neuroligin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1

b:28.7
occ:1.00
NE2 C:HIS642 2.1 36.5 1.0
NE2 B:HIS642 2.1 35.4 1.0
NE2 C:HIS640 2.2 33.5 1.0
NE2 B:HIS640 2.2 31.9 1.0
CE1 B:HIS642 2.6 35.1 1.0
CE1 C:HIS642 2.7 36.4 1.0
CD2 C:HIS640 3.0 32.2 1.0
CD2 B:HIS640 3.0 31.2 1.0
CE1 C:HIS640 3.2 34.1 1.0
CD2 C:HIS642 3.3 37.2 1.0
CE1 B:HIS640 3.3 33.4 1.0
CD2 B:HIS642 3.3 36.0 1.0
ND1 B:HIS642 3.9 36.8 1.0
ND1 C:HIS642 3.9 37.5 1.0
CG C:HIS640 4.2 32.3 1.0
CG C:HIS642 4.2 37.2 1.0
CG B:HIS642 4.2 36.8 1.0
CG B:HIS640 4.2 31.6 1.0
ND1 C:HIS640 4.3 32.8 1.0
ND1 B:HIS640 4.3 33.0 1.0
CD1 C:TYR445 4.8 35.0 1.0
CB C:TYR445 4.8 30.5 1.0
CB B:TYR445 4.9 29.2 1.0
CD1 B:TYR445 4.9 33.5 1.0
CG C:TYR445 4.9 33.7 1.0
CG B:TYR445 4.9 32.0 1.0

Reference:

D.Arac, A.A.Boucard, E.Ozkan, P.Strop, E.Newell, T.C.Sudhof, A.T.Brunger. Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1BETA Complex Reveal Specific Protein-Protein and Protein-Ca(2+) Interactions. Neuron V. 56 992 2007.
ISSN: ISSN 0896-6273
PubMed: 18093522
DOI: 10.1016/J.NEURON.2007.12.002
Page generated: Thu Oct 29 06:19:16 2020
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