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Zinc in PDB 1my4: Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-Willardiine in the Zn Crystal Form

Protein crystallography data

The structure of Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-Willardiine in the Zn Crystal Form, PDB code: 1my4 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 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.840, 163.800, 48.010, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-Willardiine in the Zn Crystal Form (pdb code 1my4). 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 Iodo-Willardiine in the Zn Crystal Form, PDB code: 1my4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 1my4

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Zinc binding site 1 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-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 Iodo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:27.1
occ:1.00
OE2 B:GLU166 2.0 23.6 1.0
OE1 A:GLU42 2.0 26.4 1.0
O A:HOH718 2.1 28.5 1.0
NE2 A:HIS46 2.2 28.2 1.0
CD B:GLU166 2.7 22.3 1.0
OE1 B:GLU166 2.8 25.6 1.0
CD2 A:HIS46 3.0 26.1 1.0
CD A:GLU42 3.1 24.3 1.0
CE1 A:HIS46 3.2 27.7 1.0
OE2 A:GLU42 3.4 28.7 1.0
CD2 A:LEU241 4.2 25.6 1.0
CG B:GLU166 4.2 23.0 1.0
CG A:HIS46 4.2 25.8 1.0
ND1 A:HIS46 4.3 28.8 1.0
N B:SER168 4.3 19.8 1.0
CG A:GLU42 4.4 24.5 1.0
O B:ALA165 4.5 19.9 1.0
CB B:GLU166 4.8 22.1 1.0
CB A:GLU42 4.8 19.6 1.0
C B:PRO167 4.8 21.0 1.0
CA B:PRO167 4.8 21.4 1.0
CA B:GLU166 4.8 21.7 1.0
CB B:SER168 4.9 19.8 1.0
CA B:SER168 4.9 18.9 1.0
O A:GLU42 4.9 19.2 1.0

Zinc binding site 2 out of 5 in 1my4

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Zinc binding site 2 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-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 Iodo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:37.8
occ:1.00
NE2 B:HIS23 2.1 23.1 1.0
O B:HOH824 2.4 33.5 1.0
OE2 B:GLU30 2.6 36.4 1.0
OE1 B:GLU30 2.8 35.2 1.0
CD2 B:HIS23 3.1 23.2 1.0
CD B:GLU30 3.1 33.4 1.0
CE1 B:HIS23 3.1 19.7 1.0
CD B:LYS20 3.9 23.4 1.0
NZ B:LYS20 4.2 23.4 1.0
ND1 B:HIS23 4.2 22.4 1.0
CG B:HIS23 4.2 23.4 1.0
O B:GLU30 4.4 25.9 1.0
CG B:GLU30 4.6 32.9 1.0
CE B:LYS20 4.7 26.6 1.0
CD1 B:LEU26 5.0 38.7 1.0

Zinc binding site 3 out of 5 in 1my4

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Zinc binding site 3 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-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 Iodo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:30.3
occ:1.00
NE2 B:HIS46 2.0 21.6 1.0
OE1 B:GLU42 2.1 24.6 1.0
O B:HOH732 2.3 22.2 1.0
CE1 B:HIS46 2.8 23.4 1.0
CD2 B:HIS46 3.1 19.9 1.0
CD B:GLU42 3.1 21.5 1.0
OE2 B:GLU42 3.5 26.9 1.0
OE1 B:GLN244 3.7 39.6 1.0
CD2 B:LEU241 3.8 23.4 1.0
ND1 B:HIS46 4.0 24.4 1.0
CG B:HIS46 4.1 23.4 1.0
O B:HOH886 4.2 56.3 1.0
CG B:GLU42 4.4 22.2 1.0
CD B:GLN244 4.8 34.3 1.0
CB B:GLU42 4.8 17.4 1.0

Zinc binding site 4 out of 5 in 1my4

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Zinc binding site 4 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-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 Iodo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:31.9
occ:1.00
O C:HOH748 2.1 27.2 1.0
OD2 C:ASP65 2.1 30.1 1.0
O C:HOH766 2.2 50.1 1.0
CG C:ASP65 2.8 30.3 1.0
OD1 C:ASP65 2.8 30.4 1.0
OD2 C:ASP67 3.9 49.7 1.0
CB C:ASP65 4.3 28.6 1.0
CB C:ASP67 4.5 38.4 1.0
CG C:ASP67 4.7 43.5 1.0

Zinc binding site 5 out of 5 in 1my4

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Zinc binding site 5 out of 5 in the Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-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 Iodo-Willardiine in the Zn Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn705

b:73.7
occ:1.00
OE1 C:GLU42 3.0 47.4 1.0
CD2 C:HIS46 3.9 56.0 1.0
CD2 C:LEU241 3.9 25.6 1.0
CD C:GLU42 4.1 43.9 1.0
OE1 C:GLN244 4.1 47.9 1.0
NE2 C:HIS46 4.6 57.0 1.0
OE2 C:GLU42 4.7 48.9 1.0
CB C:GLU42 4.8 32.3 1.0
CG C:HIS46 5.0 53.2 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 22:39:57 2020
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