Atomistry » Iodine » PDB 1lkr-1pvh » 1my4
Atomistry »
  Iodine »
    PDB 1lkr-1pvh »
      1my4 »

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 Aug 11 12:29:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy