Atomistry » Zinc » PDB 1mkm-1mxz » 1ms7
Atomistry »
  Zinc »
    PDB 1mkm-1mxz »
      1ms7 »

Zinc in PDB 1ms7: X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate

Protein crystallography data

The structure of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate, PDB code: 1ms7 was solved by C.Kasper, M.-L.Lunn, T.Liljefors, E.Gouaux, J.Egebjerg, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.56 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.723, 162.863, 47.133, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.3

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate (pdb code 1ms7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate, PDB code: 1ms7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 1 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:53.1
occ:1.00
O A:HOH3184 2.2 54.7 1.0
OE1 A:GLU39 2.2 35.5 1.0
O A:HOH3223 2.2 39.3 1.0
NE2 A:HIS43 2.5 36.1 1.0
O A:HOH3333 3.0 51.8 1.0
CD A:GLU39 3.2 33.9 1.0
NZ A:LYS42 3.3 40.3 1.0
CE1 A:HIS43 3.4 35.6 1.0
CD2 A:HIS43 3.5 33.9 1.0
OE2 A:GLU39 3.6 38.9 1.0
CE A:LYS42 3.6 38.7 1.0
CD2 A:LEU238 4.1 22.6 1.0
O A:HOH3314 4.3 47.7 1.0
OE1 A:GLN241 4.4 45.6 1.0
CG A:GLU39 4.4 31.1 1.0
ND1 A:HIS43 4.6 36.1 1.0
CG A:HIS43 4.7 33.9 1.0
CB A:GLU39 4.9 27.6 1.0

Zinc binding site 2 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 2 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:35.4
occ:1.00
OD2 A:ASP62 2.1 26.4 1.0
O A:HOH3326 2.3 33.4 1.0
O A:HOH3076 2.5 41.2 1.0
CG A:ASP62 2.8 26.1 1.0
OD1 A:ASP62 2.8 27.8 1.0
OD2 A:ASP64 4.1 41.1 1.0
CB A:ASP62 4.2 25.4 1.0
CB A:ASP64 4.5 36.7 1.0
CG A:ASP64 4.8 38.9 1.0
CG2 A:THR65 4.9 30.7 1.0
O A:HOH3189 5.0 39.2 1.0

Zinc binding site 3 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 3 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:28.2
occ:1.00
NE2 B:HIS20 2.1 24.1 1.0
OE2 B:GLU27 2.1 23.2 1.0
O B:HOH3424 2.1 33.7 1.0
NE2 A:HIS20 2.2 26.4 1.0
CD B:GLU27 2.9 22.9 1.0
OE1 B:GLU27 3.0 21.7 1.0
CD2 B:HIS20 3.0 23.9 1.0
CD2 A:HIS20 3.0 25.2 1.0
CE1 B:HIS20 3.1 24.0 1.0
CE1 A:HIS20 3.2 25.5 1.0
CG A:GLU21 3.6 38.9 1.0
CD B:LYS17 4.0 21.4 1.0
NZ B:LYS17 4.0 23.4 1.0
CG B:HIS20 4.2 23.6 1.0
ND1 B:HIS20 4.2 25.4 1.0
CG A:HIS20 4.2 27.1 1.0
ND1 A:HIS20 4.3 23.8 1.0
O B:GLU27 4.3 20.3 1.0
CD A:GLU21 4.3 40.9 1.0
CG B:GLU27 4.3 21.2 1.0
CE B:LYS17 4.7 20.1 1.0
CD1 B:LEU23 4.7 41.6 1.0
SD A:MET16 4.7 32.5 1.0
CB A:GLU21 4.8 35.5 1.0
OE1 A:GLU21 4.8 39.5 1.0
OE2 A:GLU21 4.9 41.5 1.0
O A:HOH3188 4.9 44.6 1.0

Zinc binding site 4 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 4 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:24.1
occ:1.00
NE2 B:HIS43 1.9 17.6 1.0
O B:HOH3453 2.1 25.5 1.0
OE1 B:GLU39 2.2 20.9 1.0
CE1 B:HIS43 2.8 21.7 1.0
CD2 B:HIS43 2.9 19.1 1.0
CD B:GLU39 3.0 21.1 1.0
OE2 B:GLU39 3.3 21.7 1.0
CD2 B:LEU238 3.6 17.1 1.0
OE1 B:GLN241 3.6 31.4 1.0
NZ B:LYS42 3.7 19.9 1.0
CE B:LYS42 3.7 21.7 1.0
ND1 B:HIS43 4.0 20.4 1.0
CG B:HIS43 4.0 19.9 1.0
O B:HOH3388 4.2 44.2 1.0
CG B:GLU39 4.4 18.8 1.0
CD B:GLN241 4.5 28.9 1.0
NE2 B:GLN241 4.6 31.8 1.0
CB B:GLU39 4.8 14.6 1.0
CG B:LEU243 4.9 18.2 1.0

Zinc binding site 5 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 5 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:27.4
occ:1.00
O B:HOH3438 2.0 30.0 1.0
O B:HOH3439 2.1 39.1 1.0
ZN B:ZN3006 3.2 22.1 1.0
OG B:SER165 3.8 18.8 1.0
OE2 B:GLU163 3.8 20.0 1.0
CB B:SER165 3.8 13.5 1.0
O B:HOH3013 4.2 16.3 1.0
O B:HOH3129 4.2 33.0 1.0
CA B:SER165 4.3 14.5 1.0
OE1 B:GLU163 4.3 17.8 1.0
CD B:GLU163 4.4 17.4 1.0
O B:ALA162 4.5 17.1 1.0
O B:ARG160 4.7 21.9 1.0
N B:SER165 4.8 15.6 1.0
O B:HOH3284 4.9 46.0 1.0

Zinc binding site 6 out of 6 in 1ms7

Go back to Zinc Binding Sites List in 1ms7
Zinc binding site 6 out of 6 in the X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of the GLUR2 Ligand-Binding Core (S1S2J) in Complex with (S)-Des-Me-Ampa at 1.97 A Resolution, Crystallization in the Presence of Zinc Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3006

b:22.1
occ:1.00
OE1 B:GLU163 1.8 17.8 1.0
CD B:GLU163 2.4 17.4 1.0
OE2 B:GLU163 2.5 20.0 1.0
ZN B:ZN3005 3.2 27.4 1.0
CG B:GLU163 3.8 20.7 1.0
O B:HOH3438 4.0 30.0 1.0
N B:SER165 4.2 15.6 1.0
CB B:GLU163 4.5 21.3 1.0
CB B:SER165 4.6 13.5 1.0
CA B:SER165 4.7 14.5 1.0
O B:ALA162 4.7 17.1 1.0
CA B:GLU163 4.7 19.7 1.0
C B:PRO164 4.9 17.4 1.0
CA B:PRO164 5.0 18.9 1.0

Reference:

C.Kasper, M.-L.Lunn, T.Liljefors, E.Gouaux, J.Egebjerg, J.S.Kastrup. GLUR2 Ligand-Binding Core Complexes: Importance of the Isoxazolol Moiety and 5-Substituent For the Binding Mode of Ampa-Type Agonists Febs Lett. V. 531 173 2002.
ISSN: ISSN 0014-5793
PubMed: 12417307
DOI: 10.1016/S0014-5793(02)03496-8
Page generated: Wed Dec 16 02:57:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy