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Zinc in PDB 5o4f: Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution

Protein crystallography data

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution, PDB code: 5o4f was solved by S.Moellerud, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 2.10
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.392, 56.205, 87.462, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.5

Other elements in 5o4f:

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution (pdb code 5o4f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution, PDB code: 5o4f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5o4f

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Zinc binding site 1 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:31.7
occ:1.00
OE1 A:GLU96 1.9 40.6 1.0
OD1 B:ASP240 1.9 38.0 1.0
ND1 A:HIS93 2.0 35.2 1.0
ND1 B:HIS243 2.0 41.2 1.0
CG B:ASP240 2.6 30.8 1.0
OD2 B:ASP240 2.6 31.5 1.0
CE1 A:HIS93 2.7 32.5 1.0
CD A:GLU96 2.9 34.6 1.0
CG B:HIS243 3.0 37.9 1.0
CE1 B:HIS243 3.0 40.6 1.0
CG A:HIS93 3.2 33.6 1.0
OE2 A:GLU96 3.3 33.4 1.0
CB B:HIS243 3.3 33.6 1.0
CB A:HIS93 3.7 34.0 1.0
CA A:HIS93 3.9 32.1 1.0
NE2 A:HIS93 3.9 31.6 1.0
CB B:ASP240 4.1 30.1 1.0
NE2 B:HIS243 4.1 42.3 1.0
CD2 B:HIS243 4.1 39.5 1.0
O A:HOH440 4.1 44.2 1.0
CD2 A:HIS93 4.1 31.6 1.0
CG A:GLU96 4.2 32.4 1.0
CB A:GLU96 4.5 30.4 1.0
N A:HIS93 4.7 29.9 1.0
CA B:ASP240 4.7 28.3 1.0
O B:ASP240 4.8 32.6 1.0
CA B:HIS243 4.8 33.0 1.0
O A:HIS93 4.9 39.1 1.0
C A:HIS93 4.9 34.4 1.0

Zinc binding site 2 out of 6 in 5o4f

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Zinc binding site 2 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:89.1
occ:0.50
O B:HOH413 1.9 54.5 1.0
ND1 B:HIS80 2.5 73.1 1.0
CG B:HIS80 2.9 69.0 1.0
CB B:HIS80 3.1 62.6 1.0
CE1 B:HIS80 3.4 74.5 1.0
CD2 B:HIS80 4.0 71.8 1.0
NE2 B:HIS80 4.1 73.8 1.0
CA B:HIS80 4.6 57.1 1.0

Zinc binding site 3 out of 6 in 5o4f

Go back to Zinc Binding Sites List in 5o4f
Zinc binding site 3 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:95.0
occ:1.00
OE1 B:GLU42 2.1 42.3 1.0
NZ B:LYS241 2.3 65.3 1.0
CD B:GLU42 2.9 46.1 1.0
OE2 B:GLU42 3.0 51.4 1.0
CE B:LYS241 3.2 59.6 1.0
CD B:LYS241 3.4 51.0 1.0
OE1 B:GLU239 4.2 64.2 1.0
CG B:GLU42 4.3 39.3 1.0
CD2 B:LEU236 4.4 30.8 1.0
CB B:GLU42 4.8 33.7 1.0
CG B:LYS241 4.8 42.9 1.0

Zinc binding site 4 out of 6 in 5o4f

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Zinc binding site 4 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:32.7
occ:1.00
OE2 A:GLU194 1.9 45.6 1.0
NZ A:LYS246 2.0 46.2 1.0
CD A:GLU194 2.6 35.8 1.0
OE1 A:GLU194 2.7 37.3 1.0
CE A:LYS246 3.1 43.8 1.0
CG A:GLU194 4.0 36.5 1.0
CD A:LYS246 4.4 39.9 1.0
NE2 A:GLN198 4.6 47.9 1.0
O A:HOH405 4.7 40.3 1.0

Zinc binding site 5 out of 6 in 5o4f

Go back to Zinc Binding Sites List in 5o4f
Zinc binding site 5 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:97.2
occ:1.00
ND1 A:HIS80 2.2 90.3 1.0
CG A:HIS80 2.5 86.2 1.0
CB A:HIS80 2.6 77.3 1.0
ZN A:ZN305 2.9 96.5 1.0
CE1 A:HIS80 3.2 92.8 1.0
CD2 A:HIS80 3.6 90.6 1.0
NE2 A:HIS80 3.9 93.1 1.0
CA A:HIS80 3.9 68.4 1.0
O A:HIS80 4.4 66.7 1.0
O A:ACT308 4.5 65.6 1.0
C A:HIS80 4.7 65.7 1.0
N A:HIS80 5.0 63.3 1.0

Zinc binding site 6 out of 6 in 5o4f

Go back to Zinc Binding Sites List in 5o4f
Zinc binding site 6 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with the Agonist Lm-12B at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:96.5
occ:1.00
ZN A:ZN304 2.9 97.2 1.0
OXT A:ACT308 3.0 65.3 1.0
O A:HIS80 3.1 66.7 1.0
O A:ACT308 3.1 65.6 1.0
CB A:HIS80 3.5 77.3 1.0
C A:ACT308 3.5 64.7 1.0
C A:HIS80 4.1 65.7 1.0
CA A:HIS80 4.3 68.4 1.0
CG A:HIS80 4.5 86.2 1.0
ND1 A:HIS80 4.7 90.3 1.0
NH2 A:ARG4 4.9 82.9 1.0

Reference:

S.Mllerud, A.Pinto, L.Marconi, K.Frydenvang, T.S.Thorsen, S.Laulumaa, R.Venskutonyte, S.Winther, A.M.C.Moral, L.Tamborini, P.Conti, D.S.Pickering, J.S.Kastrup. Structure and Affinity of Two Bicyclic Glutamate Analogues at Ampa and Kainate Receptors. Acs Chem Neurosci V. 8 2056 2017.
ISSN: ESSN 1948-7193
PubMed: 28691798
DOI: 10.1021/ACSCHEMNEURO.7B00201
Page generated: Sun Oct 27 23:12:48 2024

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