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Iodine 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

Other elements in 1my4:

The structure of Crystal Structure of Glutamate Receptor Ligand-Binding Core in Complex with Iodo-Willardiine in the Zn Crystal Form also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 1my4

Go back to Iodine Binding Sites List in 1my4
Iodine binding site 1 out of 3 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 Iodine with other atoms in the I 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:I601

b:50.4
occ:1.00
I5 A:IWD601 0.0 50.4 1.0
C5 A:IWD601 2.1 29.6 1.0
O A:HOH711 2.7 35.8 1.0
C6 A:IWD601 3.0 26.4 1.0
C4 A:IWD601 3.2 27.0 1.0
O4 A:IWD601 3.5 23.3 1.0
OG1 A:THR174 3.7 22.0 1.0
O A:HOH715 3.7 24.6 1.0
CB A:MET196 3.9 19.4 1.0
CE A:MET196 3.9 22.4 1.0
O A:HOH754 4.0 31.0 1.0
CG A:MET196 4.0 17.4 1.0
OE1 A:GLU13 4.1 28.4 1.0
CD A:GLU13 4.1 29.2 1.0
OE1 A:GLU193 4.3 19.1 1.0
OE2 A:GLU13 4.3 32.1 1.0
N1 A:IWD601 4.3 22.6 1.0
N3 A:IWD601 4.5 24.5 1.0
OH A:TYR61 4.6 26.0 1.0
CG A:GLU13 4.6 24.6 1.0
CB A:GLU193 4.6 18.4 1.0
OH A:TYR220 4.6 18.7 1.0
SD A:MET196 4.8 25.0 1.0
CB A:THR174 4.8 17.0 1.0
CG2 A:THR174 4.9 17.5 1.0
CG A:GLU193 5.0 16.5 1.0

Iodine binding site 2 out of 3 in 1my4

Go back to Iodine Binding Sites List in 1my4
Iodine binding site 2 out of 3 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 Iodine with other atoms in the I 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:I602

b:47.9
occ:1.00
I5 B:IWD602 0.0 47.9 1.0
C5 B:IWD602 2.1 25.4 1.0
O B:HOH725 2.7 34.0 1.0
C6 B:IWD602 3.0 16.4 1.0
C4 B:IWD602 3.2 21.0 1.0
O4 B:IWD602 3.4 19.1 1.0
OG1 B:THR174 3.6 18.1 1.0
O B:HOH707 3.8 22.6 1.0
CB B:MET196 3.8 17.0 1.0
CE B:MET196 3.9 21.3 1.0
CG B:MET196 4.0 15.7 1.0
OE1 B:GLU193 4.2 16.6 1.0
O B:HOH764 4.2 32.9 1.0
N1 B:IWD602 4.3 16.2 1.0
CD B:GLU13 4.4 32.8 1.0
N3 B:IWD602 4.4 20.1 1.0
OE2 B:GLU13 4.4 32.2 1.0
OH B:TYR61 4.5 22.1 1.0
CG2 B:THR174 4.6 17.6 1.0
OE1 B:GLU13 4.6 35.6 1.0
OH B:TYR220 4.6 14.9 1.0
CB B:GLU193 4.6 11.0 1.0
CB B:THR174 4.7 19.1 1.0
CG B:GLU13 4.7 27.7 1.0
SD B:MET196 4.8 23.9 1.0
N B:GLU193 4.9 13.2 1.0
C2 B:IWD602 4.9 17.9 1.0
CD B:GLU193 5.0 13.2 1.0

Iodine binding site 3 out of 3 in 1my4

Go back to Iodine Binding Sites List in 1my4
Iodine binding site 3 out of 3 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 Iodine with other atoms in the I 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
C:I603

b:63.8
occ:1.00
I5 C:IWD603 0.0 63.8 1.0
C5 C:IWD603 2.1 36.6 1.0
O C:HOH708 2.6 34.8 1.0
C6 C:IWD603 3.0 32.5 1.0
C4 C:IWD603 3.2 33.1 1.0
O4 C:IWD603 3.4 30.2 1.0
OG1 C:THR174 3.7 27.5 1.0
CB C:MET196 3.8 28.3 1.0
CG C:MET196 3.8 31.1 1.0
CE C:MET196 3.9 33.7 1.0
O C:HOH738 4.0 34.6 1.0
O C:HOH714 4.0 27.6 1.0
OE1 C:GLU193 4.1 24.4 1.0
N1 C:IWD603 4.2 27.8 1.0
OE2 C:GLU13 4.3 34.9 1.0
CD C:GLU13 4.3 33.5 1.0
OH C:TYR61 4.4 23.9 1.0
N3 C:IWD603 4.4 28.1 1.0
CG C:GLU13 4.5 32.9 1.0
CB C:GLU193 4.6 18.2 1.0
CG2 C:THR174 4.7 24.7 1.0
SD C:MET196 4.7 36.7 1.0
OH C:TYR220 4.7 22.7 1.0
OE1 C:GLU13 4.8 34.9 1.0
CB C:THR174 4.8 28.4 1.0
CD C:GLU193 4.8 22.9 1.0
CG C:GLU193 4.9 20.1 1.0
C2 C:IWD603 4.9 28.1 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: Sun Dec 13 19:20:25 2020

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