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Zinc in PDB 3jpy: Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B

Protein crystallography data

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy was solved by E.Karakas, N.Simorowski, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 3.21
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.368, 143.368, 88.467, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 23.3

Other elements in 3jpy:

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb code 3jpy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3jpy

Go back to Zinc Binding Sites List in 3jpy
Zinc binding site 1 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.8
occ:0.46
OE2 A:GLU284 2.0 0.2 1.0
NE2 A:HIS127 2.1 0.1 1.0
CD A:GLU284 2.1 0.3 1.0
CG A:GLU284 2.4 0.5 1.0
CD2 A:HIS127 2.9 0.6 1.0
CE1 A:HIS127 2.9 0.6 1.0
OE1 A:GLU284 3.1 0.0 1.0
ND1 A:HIS127 3.9 99.5 1.0
CG A:HIS127 3.9 0.3 1.0
CB A:GLU284 4.0 0.5 1.0
CA A:GLU284 4.9 0.3 1.0

Zinc binding site 2 out of 5 in 3jpy

Go back to Zinc Binding Sites List in 3jpy
Zinc binding site 2 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:0.1
occ:0.31
ND1 A:HIS359 2.0 0.4 1.0
OD2 A:ASP381 2.1 0.3 1.0
OD1 A:ASP381 2.2 0.8 1.0
CG A:ASP381 2.3 0.3 1.0
CE1 A:HIS359 2.6 0.4 1.0
CG A:HIS359 3.2 0.0 1.0
CB A:ASP381 3.6 0.6 1.0
CB A:HIS359 3.8 0.3 1.0
NE2 A:HIS359 3.8 0.2 1.0
CD2 A:HIS359 4.1 0.8 1.0
CA A:HIS359 4.4 0.6 1.0
CA A:ASP381 4.5 0.2 1.0
O A:MET358 4.5 0.2 1.0

Zinc binding site 3 out of 5 in 3jpy

Go back to Zinc Binding Sites List in 3jpy
Zinc binding site 3 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:0.5
occ:1.00
ND1 A:HIS60 2.0 0.1 1.0
OE1 A:GLU345 2.2 0.4 1.0
CE1 A:HIS60 2.5 1.0 1.0
CG A:HIS60 3.2 0.8 1.0
CD A:GLU345 3.2 0.8 1.0
OE2 A:GLU345 3.6 1.0 1.0
NE2 A:HIS60 3.7 0.2 1.0
CB A:HIS60 3.9 1.0 1.0
CD2 A:HIS60 4.0 0.3 1.0
CA A:HIS60 4.5 0.4 1.0
CG A:GLU345 4.6 0.7 1.0

Zinc binding site 4 out of 5 in 3jpy

Go back to Zinc Binding Sites List in 3jpy
Zinc binding site 4 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:0.2
occ:1.00
OE1 A:GLU162 1.8 0.7 1.0
OE2 A:GLU163 2.2 0.0 1.0
CD A:GLU162 3.0 0.7 1.0
CD A:GLU163 3.3 0.4 1.0
OE2 A:GLU162 3.5 0.7 1.0
CA A:GLU163 3.6 0.0 1.0
N A:GLU163 3.8 0.8 1.0
CG A:GLU163 4.0 0.4 1.0
C A:GLU162 4.1 0.5 1.0
O A:GLU162 4.2 0.1 1.0
CG A:GLU162 4.2 1.0 1.0
OE1 A:GLU163 4.3 1.0 1.0
CB A:GLU163 4.4 1.0 1.0
CB A:GLU162 4.5 0.1 1.0
C A:GLU163 4.6 0.9 1.0
O A:GLU163 4.9 0.4 1.0
CA A:GLU162 4.9 0.6 1.0

Zinc binding site 5 out of 5 in 3jpy

Go back to Zinc Binding Sites List in 3jpy
Zinc binding site 5 out of 5 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:0.8
occ:0.23
ND1 A:HIS311 2.0 1.0 1.0
CE1 A:HIS311 2.8 0.9 1.0
CG A:HIS311 3.2 0.2 1.0
CB A:HIS311 3.8 0.2 1.0
NE2 A:HIS311 4.0 0.2 1.0
CD2 A:HIS311 4.2 0.9 1.0
CA A:HIS311 4.7 0.1 1.0
O A:GLU310 4.7 0.7 1.0

Reference:

E.Karakas, N.Simorowski, H.Furukawa. Structure of the Zinc-Bound Amino-Terminal Domain of the Nmda Receptor NR2B Subunit. Embo J. V. 28 3910 2009.
ISSN: ISSN 0261-4189
PubMed: 19910922
DOI: 10.1038/EMBOJ.2009.338
Page generated: Wed Dec 16 04:28:26 2020

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