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Zinc in PDB 3rtw: Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2

Protein crystallography data

The structure of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2, PDB code: 3rtw was solved by A.H.Ahmed, R.E.Oswald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.57 / 2.10
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.077, 114.102, 165.048, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 (pdb code 3rtw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2, PDB code: 3rtw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3rtw

Go back to Zinc Binding Sites List in 3rtw
Zinc binding site 1 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:35.2
occ:1.00
NE2 B:HIS23 2.4 33.5 1.0
CE1 B:HIS23 2.9 32.1 1.0
CD2 B:HIS23 3.6 31.7 1.0
ND1 B:HIS23 4.2 30.7 1.0
CG B:HIS23 4.5 31.0 1.0
CB B:MET19 4.9 28.0 1.0
CG B:MET19 4.9 27.6 1.0

Zinc binding site 2 out of 5 in 3rtw

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Zinc binding site 2 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:29.7
occ:1.00
NE2 B:HIS46 2.3 29.5 1.0
OE1 F:GLU166 2.3 28.3 1.0
OE1 B:GLU42 2.3 27.3 1.0
OE2 F:GLU166 2.7 29.3 1.0
CD F:GLU166 2.9 27.8 1.0
CD B:GLU42 3.0 26.1 1.0
OE2 B:GLU42 3.1 24.5 1.0
CD2 B:HIS46 3.1 26.4 1.0
CE1 B:HIS46 3.3 29.7 1.0
N F:SER168 4.0 22.5 1.0
CD B:LYS45 4.2 30.6 1.0
CE B:LYS45 4.3 35.0 1.0
CG B:HIS46 4.3 26.7 1.0
CB F:SER168 4.3 22.5 1.0
CG F:GLU166 4.3 25.7 1.0
ND1 B:HIS46 4.4 29.2 1.0
CA F:SER168 4.4 22.4 1.0
CG B:GLU42 4.5 23.6 1.0
O F:ALA165 4.5 24.7 1.0
CD2 B:LEU241 4.7 25.5 1.0
C F:PRO167 4.8 23.5 1.0
CB F:GLU166 5.0 26.1 1.0
CG B:LYS45 5.0 29.2 1.0
CA F:PRO167 5.0 23.0 1.0

Zinc binding site 3 out of 5 in 3rtw

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Zinc binding site 3 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:76.7
occ:1.00
OE1 D:GLU42 2.2 51.0 1.0
NE2 D:HIS46 2.3 53.6 1.0
CE1 D:HIS46 3.1 53.6 1.0
CD D:GLU42 3.2 49.1 1.0
OE2 D:GLU42 3.4 52.3 1.0
CD2 D:HIS46 3.5 48.3 1.0
O D:HOH376 3.7 49.5 1.0
O D:HOH422 4.1 54.1 1.0
ND1 D:HIS46 4.3 50.0 1.0
OE1 D:GLN244 4.4 45.7 1.0
CG D:HIS46 4.5 47.4 1.0
CG D:GLU42 4.6 42.8 1.0
CD2 D:LEU241 4.8 35.8 1.0

Zinc binding site 4 out of 5 in 3rtw

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Zinc binding site 4 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1

b:39.1
occ:1.00
NE2 F:HIS23 2.3 32.7 1.0
OE2 F:GLU30 2.3 47.0 1.0
CE1 F:HIS23 3.1 32.4 1.0
CD F:GLU30 3.3 45.1 1.0
CD2 F:HIS23 3.5 33.4 1.0
OE1 F:GLU30 3.5 45.8 1.0
CD F:LYS20 3.9 27.2 1.0
NZ F:LYS20 4.0 31.1 1.0
ND1 F:HIS23 4.3 31.1 1.0
CG F:HIS23 4.5 31.9 1.0
CE F:LYS20 4.6 28.5 1.0
CG F:GLU30 4.6 39.7 1.0
O F:HOH445 4.9 38.3 1.0
O F:GLU30 5.0 29.9 1.0

Zinc binding site 5 out of 5 in 3rtw

Go back to Zinc Binding Sites List in 3rtw
Zinc binding site 5 out of 5 in the Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Nitrowillardiine Bound to the Ligand Binding Domain of GLUA2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2

b:33.4
occ:1.00
NE2 F:HIS46 2.4 25.6 1.0
OE1 F:GLU42 2.4 24.5 1.0
CD F:GLU42 3.2 28.2 1.0
OE2 F:GLU42 3.4 33.6 1.0
CD2 F:HIS46 3.4 25.8 1.0
CE1 F:HIS46 3.4 30.6 1.0
OE1 F:GLN244 3.6 34.5 1.0
NZ F:LYS45 3.7 29.8 1.0
CE F:LYS45 3.9 29.8 1.0
CD2 F:LEU241 4.0 24.2 1.0
ND1 F:HIS46 4.5 30.4 1.0
CG F:HIS46 4.5 27.9 1.0
CG F:GLU42 4.6 26.1 1.0
CD F:GLN244 4.7 35.5 1.0

Reference:

K.Poon, A.H.Ahmed, L.M.Nowak, R.E.Oswald. Mechanisms of Modal Activation of GLUA3 Receptors. Mol.Pharmacol. V. 80 49 2011.
ISSN: ISSN 0026-895X
PubMed: 21464198
DOI: 10.1124/MOL.111.071688
Page generated: Wed Dec 16 04:48:01 2020

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