Atomistry » Zinc » PDB 3u6l-3udr » 3u92
Atomistry »
  Zinc »
    PDB 3u6l-3udr »
      3u92 »

Zinc in PDB 3u92: Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form

Protein crystallography data

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form, PDB code: 3u92 was solved by J.Kumar, M.L.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.53 / 1.90
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 129.537, 55.654, 90.052, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 3u92:

The structure of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form (pdb code 3u92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form, PDB code: 3u92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 1 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn259

b:32.9
occ:1.00
HE3 A:LYS246 1.9 68.9 1.0
OE2 A:GLU194 2.0 32.7 1.0
HE2 A:LYS246 2.3 68.9 1.0
OE1 A:GLU194 2.3 31.9 1.0
CE A:LYS246 2.5 57.5 1.0
CD A:GLU194 2.5 21.7 1.0
HZ1 A:LYS246 3.4 80.4 1.0
HD3 A:LYS246 3.5 35.6 1.0
NZ A:LYS246 3.5 67.0 1.0
CD A:LYS246 3.6 29.7 1.0
HG2 A:LYS246 3.8 31.6 1.0
HZ2 A:LYS246 4.0 80.4 1.0
O A:HOH350 4.0 46.4 1.0
CG A:GLU194 4.0 35.8 1.0
HD1 A:TRP250 4.1 39.4 1.0
HZ3 A:LYS246 4.1 80.4 1.0
CG A:LYS246 4.2 26.3 1.0
CD1 A:TRP250 4.2 32.8 1.0
HB3 A:TRP250 4.3 30.6 1.0
HD2 A:LYS246 4.3 35.6 1.0
HG2 A:GLU194 4.4 43.0 1.0
HG22 A:THR191 4.4 36.0 1.0
HG3 A:GLU194 4.4 43.0 1.0
CG A:TRP250 4.4 28.8 1.0
HB2 A:TRP250 4.5 30.6 1.0
O A:HOH461 4.5 55.2 1.0
HG3 A:LYS246 4.6 31.6 1.0
CB A:TRP250 4.6 25.5 1.0
NE1 A:TRP250 4.8 29.8 1.0
HB3 A:GLU194 4.8 27.4 1.0
O A:HOH404 4.9 34.8 1.0
O A:HOH368 4.9 31.7 1.0
CB A:GLU194 5.0 22.9 1.0

Zinc binding site 2 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 2 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn260

b:53.0
occ:0.75
ND1 A:HIS80 2.0 44.1 1.0
O A:HOH356 2.1 61.2 1.0
HB3 A:HIS80 2.8 58.2 1.0
CE1 A:HIS80 2.9 53.1 1.0
CG A:HIS80 3.0 56.2 1.0
HE1 A:HIS80 3.1 63.8 1.0
CB A:HIS80 3.4 48.5 1.0
HB2 A:HIS80 4.0 58.2 1.0
NE2 A:HIS80 4.1 56.2 1.0
CD2 A:HIS80 4.1 62.6 1.0
HG2 A:PRO220 4.3 42.5 1.0
HA A:HIS80 4.3 59.1 1.0
O A:HOH316 4.3 44.1 1.0
CA A:HIS80 4.5 49.3 1.0
HB2 A:PRO220 4.8 40.0 1.0
O A:HIS80 4.9 42.7 1.0
HB3 A:PRO220 5.0 40.0 1.0
HD2 A:HIS80 5.0 75.2 1.0

Zinc binding site 3 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 3 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn261

b:60.1
occ:0.79
O A:HOH460 2.1 53.1 1.0
NE2 A:HIS45 2.1 94.3 1.0
O A:HOH451 2.2 57.2 1.0
CD2 A:HIS45 2.9 78.0 1.0
HD2 A:HIS45 3.0 93.5 1.0
CE1 A:HIS45 3.2 90.4 1.0
HE1 A:HIS45 3.5 0.5 1.0
CG A:HIS45 4.1 57.0 1.0
ND1 A:HIS45 4.2 69.4 1.0
O A:HOH351 4.4 55.4 1.0
O A:HOH439 4.4 49.3 1.0
O A:HOH440 4.4 43.0 1.0
HZ1 A:LYS241 4.9 64.7 1.0

Zinc binding site 4 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 4 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn259

b:24.4
occ:0.85
OD1 B:ASP240 2.0 30.8 1.0
ND1 A:HIS93 2.0 29.8 1.0
ND1 B:HIS243 2.0 27.9 1.0
OE1 A:GLU96 2.0 27.3 1.0
OD2 B:ASP240 2.2 44.1 1.0
CG B:ASP240 2.4 32.2 1.0
CE1 A:HIS93 2.8 37.6 1.0
HE1 A:HIS93 2.8 45.1 1.0
CD A:GLU96 2.9 29.8 1.0
CE1 B:HIS243 3.0 34.1 1.0
CG B:HIS243 3.0 28.0 1.0
HE1 B:HIS243 3.2 41.0 1.0
HB3 B:HIS243 3.2 33.4 1.0
OE2 A:GLU96 3.2 30.9 1.0
HA A:HIS93 3.2 38.6 1.0
CG A:HIS93 3.2 28.9 1.0
HB2 B:HIS243 3.3 33.4 1.0
CB B:HIS243 3.4 27.9 1.0
HB3 A:HIS93 3.5 40.8 1.0
CB A:HIS93 3.7 34.0 1.0
CA A:HIS93 3.9 32.2 1.0
CB B:ASP240 3.9 34.9 1.0
NE2 A:HIS93 4.0 39.5 1.0
O B:HOH337 4.1 47.5 1.0
NE2 B:HIS243 4.1 34.8 1.0
HB2 A:GLU96 4.1 30.6 1.0
CD2 B:HIS243 4.1 32.6 1.0
O A:HOH385 4.2 39.1 1.0
CD2 A:HIS93 4.2 37.9 1.0
HB2 B:ASP240 4.3 41.9 1.0
CG A:GLU96 4.3 25.8 1.0
HA B:ASP240 4.3 31.4 1.0
HB3 B:ASP240 4.4 41.9 1.0
HB3 A:GLU96 4.5 30.6 1.0
CB A:GLU96 4.6 25.5 1.0
HB2 A:HIS93 4.6 40.8 1.0
CA B:ASP240 4.7 26.2 1.0
N A:HIS93 4.7 26.9 1.0
HG3 A:GLU96 4.8 30.9 1.0
O B:ASP240 4.8 28.6 1.0
HG2 A:GLU96 4.8 30.9 1.0
CA B:HIS243 4.9 27.5 1.0
O A:HIS93 5.0 29.5 1.0
C A:HIS93 5.0 30.2 1.0
H A:HIS93 5.0 32.3 1.0
HD2 B:HIS243 5.0 39.1 1.0

Zinc binding site 5 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 5 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn260

b:40.4
occ:0.37
O B:HOH336 2.1 45.8 1.0
O B:HOH361 2.2 42.6 1.0
O B:HOH335 2.8 68.0 1.0
HE2 B:MET221 3.2 0.2 1.0
O B:GLU96 3.9 50.8 1.0
OD1 B:ASP100 3.9 40.7 1.0
CE B:MET221 4.1 0.7 1.0
HB3 B:GLU96 4.2 48.4 1.0
HE1 B:MET221 4.3 0.2 1.0
HE3 B:MET221 4.3 0.2 1.0
O B:HOH283 4.4 32.0 1.0
HH22 B:ARG226 4.6 81.3 1.0
HH12 B:ARG226 4.8 60.0 1.0
C B:GLU96 4.9 48.2 1.0
HG2 B:MET221 4.9 74.2 1.0
HA B:ASP100 5.0 45.4 1.0

Zinc binding site 6 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 6 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn261

b:36.7
occ:0.52
HZ2 B:LYS241 1.4 78.3 1.0
OE1 B:GLU42 2.0 37.2 1.0
O B:HOH393 2.1 58.7 1.0
OE2 B:GLU42 2.1 47.8 1.0
NZ B:LYS241 2.2 65.3 1.0
CD B:GLU42 2.3 38.3 1.0
HE3 B:LYS241 2.6 76.8 1.0
HZ3 B:LYS241 2.6 78.3 1.0
CE B:LYS241 2.7 64.0 1.0
HE2 B:LYS241 2.8 76.8 1.0
HZ1 B:LYS241 2.8 78.3 1.0
CG B:GLU42 3.8 34.4 1.0
HD21 B:LEU236 3.8 32.1 1.0
HG3 B:GLU42 4.2 41.3 1.0
CD B:LYS241 4.2 59.6 1.0
HG2 B:GLU42 4.3 41.3 1.0
O B:HOH422 4.3 58.4 1.0
HD23 B:LEU236 4.3 32.1 1.0
HB3 B:GLU42 4.3 34.2 1.0
HA B:GLU42 4.4 35.8 1.0
CD2 B:LEU236 4.4 26.7 1.0
HD22 B:LEU236 4.4 32.1 1.0
HD2 B:LYS241 4.5 71.5 1.0
HD11 B:ILE46 4.5 44.8 1.0
HD3 B:LYS241 4.6 71.5 1.0
CB B:GLU42 4.6 28.5 1.0
HG3 B:LYS241 4.8 50.9 1.0
HG13 B:ILE46 4.9 43.2 1.0

Zinc binding site 7 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 7 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn262

b:39.7
occ:0.47
OE2 B:GLU238 2.0 98.0 1.0
OE1 B:GLU238 2.1 72.3 1.0
O B:HOH321 2.1 54.3 1.0
O B:HOH396 2.1 45.2 1.0
CD B:GLU238 2.3 84.6 1.0
O A:HOH437 3.3 43.4 1.0
CG B:GLU238 3.9 73.5 1.0
O A:HOH345 4.1 47.3 1.0
HG3 B:GLU238 4.3 88.2 1.0
HG2 B:GLU238 4.3 88.2 1.0
O B:HOH415 4.3 35.5 1.0
HA B:GLU238 4.4 53.5 1.0
HG A:SER212 4.4 44.6 1.0
OG A:SER212 4.7 37.1 1.0
HB2 B:GLU238 4.7 60.0 1.0
CB B:GLU238 4.8 50.0 1.0
HB3 A:SER212 4.9 42.6 1.0

Zinc binding site 8 out of 8 in 3u92

Go back to Zinc Binding Sites List in 3u92
Zinc binding site 8 out of 8 in the Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the GLUK3 Ligand Binding Domain Complex with Kainate and Zinc: P2221 Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn263

b:53.0
occ:0.53
ND1 B:HIS80 2.0 0.6 1.0
CE1 B:HIS80 2.9 0.5 1.0
CG B:HIS80 3.0 89.8 1.0
HE1 B:HIS80 3.0 0.8 1.0
HB2 B:HIS80 3.2 94.2 1.0
CB B:HIS80 3.4 78.5 1.0
HB3 B:HIS80 3.5 94.2 1.0
NE2 B:HIS80 4.0 86.7 1.0
CD2 B:HIS80 4.0 83.4 1.0
HD2 B:HIS80 4.9 0.1 1.0
CA B:HIS80 4.9 51.3 1.0

Reference:

J.Veran, J.Kumar, P.S.Pinheiro, A.Athane, M.L.Mayer, D.Perrais, C.Mulle. Zinc Potentiates GLUK3 Glutamate Receptor Function By Stabilizing the Ligand Binding Domain Dimer Interface. Neuron V. 76 565 2012.
ISSN: ISSN 0896-6273
PubMed: 23141068
DOI: 10.1016/J.NEURON.2012.08.027
Page generated: Wed Dec 16 04:53:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy