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Zinc in PDB 1my3: Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form

Protein crystallography data

The structure of Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form, PDB code: 1my3 was solved by R.Jin, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.061, 163.406, 47.848, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form (pdb code 1my3). 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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form, PDB code: 1my3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1my3

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Zinc binding site 1 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form


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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:20.6
occ:1.00
OE2 B:GLU166 1.9 20.8 1.0
OE1 A:GLU42 1.9 17.2 1.0
O B:HOH912 2.1 16.0 1.0
NE2 A:HIS46 2.1 21.8 1.0
CD B:GLU166 2.6 20.4 1.0
OE1 B:GLU166 2.8 20.1 1.0
CD A:GLU42 3.0 18.2 1.0
CE1 A:HIS46 3.1 23.7 1.0
CD2 A:HIS46 3.1 19.7 1.0
OE2 A:GLU42 3.3 16.7 1.0
CD2 A:LEU241 4.0 16.9 1.0
CG B:GLU166 4.1 18.9 1.0
ND1 A:HIS46 4.2 21.7 1.0
CG A:HIS46 4.2 18.7 1.0
CG A:GLU42 4.3 15.0 1.0
N B:SER168 4.3 14.4 1.0
O B:ALA165 4.6 17.3 1.0
CB B:GLU166 4.7 19.4 1.0
CB A:GLU42 4.7 14.5 1.0
CA B:GLU166 4.9 19.2 1.0
CB B:SER168 4.9 14.4 1.0
CA B:SER168 4.9 15.7 1.0
C B:PRO167 5.0 16.2 1.0
CA B:PRO167 5.0 16.2 1.0

Zinc binding site 2 out of 5 in 1my3

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Zinc binding site 2 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form


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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:29.9
occ:1.00
NE2 B:HIS23 2.1 19.8 1.0
OE2 B:GLU30 2.7 31.2 1.0
OE1 B:GLU30 2.8 28.8 1.0
CD2 B:HIS23 3.1 19.6 1.0
CD B:GLU30 3.1 29.2 1.0
CE1 B:HIS23 3.1 19.3 1.0
O B:HOH982 3.1 45.0 1.0
NZ B:LYS20 4.0 21.7 1.0
CD B:LYS20 4.1 18.8 1.0
ND1 B:HIS23 4.2 19.5 1.0
CG B:HIS23 4.2 20.5 1.0
O B:GLU30 4.3 21.8 1.0
CG B:GLU30 4.6 29.0 1.0
CE B:LYS20 4.7 20.6 1.0
CD1 B:LEU26 4.8 32.0 1.0

Zinc binding site 3 out of 5 in 1my3

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Zinc binding site 3 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form


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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:20.1
occ:1.00
OE1 B:GLU42 2.0 14.6 1.0
NE2 B:HIS46 2.0 15.4 1.0
O B:HOH869 2.1 22.7 1.0
CD B:GLU42 2.9 16.8 1.0
CD2 B:HIS46 2.9 17.5 1.0
CE1 B:HIS46 3.1 14.5 1.0
OE2 B:GLU42 3.2 16.9 1.0
CD2 B:LEU241 3.6 11.2 1.0
OE1 B:GLN244 3.9 29.6 1.0
CG B:HIS46 4.1 14.6 1.0
ND1 B:HIS46 4.1 18.4 1.0
CG B:GLU42 4.3 12.9 1.0
CB B:GLU42 4.7 12.2 1.0
CD B:GLN244 4.8 29.0 1.0
CD1 B:LEU246 4.8 23.7 1.0
NE2 B:GLN244 4.8 32.0 1.0
O B:GLU42 5.0 13.0 1.0

Zinc binding site 4 out of 5 in 1my3

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Zinc binding site 4 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form


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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:29.7
occ:1.00
O C:HOH913 2.3 32.8 1.0
OD2 C:ASP65 2.3 28.7 1.0
OD1 C:ASP65 2.8 32.1 1.0
CG C:ASP65 2.9 29.3 1.0
OD2 C:ASP67 3.9 38.0 1.0
CB C:ASP65 4.4 27.8 1.0
CB C:ASP67 4.5 34.2 1.0
CG C:ASP67 4.7 35.9 1.0

Zinc binding site 5 out of 5 in 1my3

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Zinc binding site 5 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form


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 Glutamate Receptor Ligand-Binding Core in Complex with Bromo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn705

b:55.2
occ:1.00
OE1 C:GLU42 2.5 33.6 1.0
NE2 C:HIS46 2.5 39.4 1.0
CD2 C:HIS46 3.1 35.5 1.0
CD C:GLU42 3.6 32.6 1.0
CE1 C:HIS46 3.7 38.0 1.0
OE1 C:GLN244 4.0 40.7 1.0
CD2 C:LEU241 4.0 17.2 1.0
OE2 C:GLU42 4.1 33.1 1.0
CG C:HIS46 4.4 35.1 1.0
NE2 C:GLN244 4.5 39.0 1.0
ND1 C:HIS46 4.7 37.2 1.0
CD C:GLN244 4.7 39.2 1.0
CD C:LYS45 4.8 37.6 1.0
O C:HOH948 4.8 57.9 1.0
CG C:GLU42 4.8 29.8 1.0
CB C:GLU42 4.9 27.8 1.0
O C:GLU42 4.9 22.7 1.0

Reference:

R.Jin, E.Gouaux. Probing the Function, Conformational Plasticity, and Dimer-Dimer Contacts of the GLUR2 Ligand-Binding Core: Studies of 5-Substituted Willardiines and GLUR2 S1S2 in the Crystal Biochemistry V. 42 5201 2003.
ISSN: ISSN 0006-2960
PubMed: 12731861
DOI: 10.1021/BI020632T
Page generated: Fri Sep 25 22:39:56 2020
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