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Zinc in PDB 5nf6: Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 A Resolution

Protein crystallography data

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 A Resolution, PDB code: 5nf6 was solved by K.Frydenvang, R.Venskutonyte, T.S.Thorsen, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.48 / 2.55
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 130.138, 56.071, 87.516, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.6

Other elements in 5nf6:

The structure of Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 A Resolution (pdb code 5nf6). 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 Cip-As at 2.55 A Resolution, PDB code: 5nf6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5nf6

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Zinc binding site 1 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:29.1
occ:0.91
OE1 A:GLU96 1.9 38.6 1.0
ND1 A:HIS93 1.9 33.6 1.0
OD1 B:ASP240 2.0 35.4 1.0
ND1 B:HIS243 2.0 34.2 1.0
CG B:ASP240 2.7 35.5 1.0
CE1 A:HIS93 2.7 28.5 1.0
OD2 B:ASP240 2.8 35.2 1.0
CD A:GLU96 2.9 24.6 1.0
CG B:HIS243 3.0 30.1 1.0
CE1 B:HIS243 3.0 33.7 1.0
CG A:HIS93 3.1 34.0 1.0
CB B:HIS243 3.3 29.1 1.0
OE2 A:GLU96 3.3 22.4 1.0
CB A:HIS93 3.6 32.7 1.0
CA A:HIS93 3.8 27.5 1.0
NE2 A:HIS93 3.9 32.6 1.0
O B:HOH440 4.0 50.8 1.0
NE2 B:HIS243 4.1 35.3 1.0
CD2 B:HIS243 4.1 29.5 1.0
CD2 A:HIS93 4.1 28.0 1.0
CB B:ASP240 4.1 36.6 1.0
O A:HOH409 4.2 32.5 1.0
CG A:GLU96 4.2 27.4 1.0
CB A:GLU96 4.5 26.1 1.0
N A:HIS93 4.6 31.4 1.0
CA B:HIS243 4.8 26.6 1.0
O B:ASP240 4.8 30.8 1.0
CA B:ASP240 4.8 35.2 1.0
C A:HIS93 4.9 30.6 1.0
O A:HIS93 4.9 29.9 1.0

Zinc binding site 2 out of 6 in 5nf6

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Zinc binding site 2 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:43.6
occ:0.58
NE2 B:HIS45 2.6 47.0 1.0
CD2 B:HIS45 3.3 45.0 1.0
CE1 B:HIS45 3.4 44.4 1.0
ND1 B:HIS45 4.3 42.5 1.0
CG B:HIS45 4.3 41.4 1.0
O B:HIS45 4.6 46.7 1.0

Zinc binding site 3 out of 6 in 5nf6

Go back to Zinc Binding Sites List in 5nf6
Zinc binding site 3 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:0.1
occ:0.50
ND1 B:HIS80 2.4 64.5 1.0
OXT B:ACT305 2.5 63.8 1.0
O B:ACT305 2.6 58.2 1.0
C B:ACT305 3.0 60.3 1.0
CG B:HIS80 3.1 60.1 1.0
CB B:HIS80 3.2 58.4 1.0
CE1 B:HIS80 3.5 62.9 1.0
CD2 B:HIS80 4.4 57.2 1.0
CH3 B:ACT305 4.4 57.0 1.0
NE2 B:HIS80 4.5 58.7 1.0
CA B:HIS80 4.7 55.0 1.0
O B:HIS80 4.9 47.6 1.0

Zinc binding site 4 out of 6 in 5nf6

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Zinc binding site 4 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:39.6
occ:0.87
OE2 A:GLU247 1.8 48.7 1.0
NE2 A:HIS243 1.9 59.5 1.0
CE1 A:HIS243 2.4 55.1 1.0
CD A:GLU247 2.8 53.1 1.0
OE1 A:GLU247 3.2 64.2 1.0
CD2 A:HIS243 3.2 52.9 1.0
ND1 A:HIS243 3.6 51.0 1.0
CG A:HIS243 4.1 53.8 1.0
CG A:GLU247 4.1 47.7 1.0

Zinc binding site 5 out of 6 in 5nf6

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Zinc binding site 5 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:97.8
occ:0.66
O A:HOH431 1.9 87.2 1.0
NE2 A:HIS45 2.3 63.4 1.0
CD2 A:HIS45 3.1 57.7 1.0
CE1 A:HIS45 3.5 62.2 1.0
CG A:HIS45 4.3 55.5 1.0
ND1 A:HIS45 4.4 58.8 1.0
O A:HOH423 4.6 49.4 1.0

Zinc binding site 6 out of 6 in 5nf6

Go back to Zinc Binding Sites List in 5nf6
Zinc binding site 6 out of 6 in the Structure of GLUK3 Ligand-Binding Domain (S1S2) in Complex with Cip-As at 2.55 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 Cip-As at 2.55 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:82.2
occ:0.88
ND1 A:HIS80 2.1 63.6 1.0
CG A:HIS80 2.8 68.1 1.0
CB A:HIS80 3.0 65.6 1.0
CE1 A:HIS80 3.2 66.4 1.0
O A:HOH436 3.5 56.0 1.0
CD2 A:HIS80 4.0 70.9 1.0
CA A:HIS80 4.1 60.6 1.0
NE2 A:HIS80 4.2 70.4 1.0
O A:HIS80 4.4 60.9 1.0
C A:HIS80 4.7 60.5 1.0
CG A:PRO220 4.8 40.6 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 22:47:46 2024

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