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Zinc in PDB 6zyu: Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549

Protein crystallography data

The structure of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549, PDB code: 6zyu was solved by J.Dorosz, K.M.Christensen, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.324, 163.084, 47.449, 90, 90, 90
R / Rfree (%) 16.2 / 18.7

Other elements in 6zyu:

The structure of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Fluorine (F) 6 atoms
Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 (pdb code 6zyu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549, PDB code: 6zyu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6zyu

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Zinc binding site 1 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:56.2
occ:0.47
OD1 A:ASP156 2.1 50.8 1.0
CG A:ASP156 3.2 41.3 1.0
O A:HOH482 3.3 31.7 1.0
OD2 A:ASP156 3.9 43.3 1.0
CD1 A:TRP159 4.1 25.3 1.0
NH2 A:ARG163 4.1 94.2 1.0
OG1 A:THR160 4.2 27.5 1.0
CB A:ASP156 4.2 33.8 1.0
O A:ASP156 4.4 27.7 1.0
CA A:ASP156 4.5 28.7 1.0
CZ A:ARG163 4.6 88.5 1.0
NH1 A:ARG163 4.7 89.7 1.0
O A:SER150 4.8 29.5 1.0
C A:ASP156 4.8 25.6 1.0
NE1 A:TRP159 5.0 23.2 1.0

Zinc binding site 2 out of 8 in 6zyu

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Zinc binding site 2 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:64.5
occ:0.71
O A:HOH404 2.4 40.4 1.0
O A:HOH477 4.0 47.8 1.0
OE2 A:GLU201 4.1 33.7 1.0
OE1 A:GLU201 4.2 41.1 1.0
O A:LYS210 4.2 26.7 1.0
CB A:LYS210 4.6 20.7 1.0
CD A:GLU201 4.6 36.4 1.0
CE A:LYS210 4.8 44.7 1.0
CG A:LYS210 4.8 26.1 1.0
CD A:LYS210 4.8 34.1 1.0

Zinc binding site 3 out of 8 in 6zyu

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Zinc binding site 3 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:21.5
occ:1.00
OE2 A:GLU166 1.9 26.4 1.0
O1 A:CAC303 1.9 21.7 0.8
OE2 B:GLU42 2.0 27.8 1.0
NE2 B:HIS46 2.1 26.0 1.0
CD A:GLU166 2.6 27.0 1.0
OE1 A:GLU166 2.6 26.6 1.0
CD B:GLU42 2.9 27.0 1.0
CD2 B:HIS46 2.9 23.3 1.0
CE1 B:HIS46 3.1 28.6 1.0
OE1 B:GLU42 3.2 25.2 1.0
AS A:CAC303 3.3 27.2 0.8
C2 A:CAC303 4.0 31.8 0.8
C1 A:CAC303 4.0 21.2 0.8
CG A:GLU166 4.1 24.2 1.0
CD2 B:LEU241 4.1 29.6 1.0
CG B:HIS46 4.1 24.6 1.0
ND1 B:HIS46 4.2 26.2 1.0
CG B:GLU42 4.3 24.0 1.0
N A:SER168 4.3 19.4 1.0
CB A:SER168 4.6 22.4 1.0
O2 A:CAC303 4.7 29.2 0.8
CB B:GLU42 4.7 18.3 1.0
O A:ALA165 4.7 21.9 1.0
CB A:GLU166 4.7 20.4 1.0
CA A:SER168 4.7 17.9 1.0
CA A:GLU166 4.9 21.4 1.0
C A:PRO167 5.0 24.7 1.0

Zinc binding site 4 out of 8 in 6zyu

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Zinc binding site 4 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:24.7
occ:0.65
OXT B:ACT306 1.8 37.4 1.0
NE2 B:HIS23 2.0 44.2 1.0
C B:ACT306 2.3 49.0 1.0
O B:ACT306 2.4 58.6 1.0
CE1 B:HIS23 3.0 39.5 1.0
CD2 B:HIS23 3.1 35.3 1.0
CH3 B:ACT306 3.8 48.2 1.0
ND1 B:HIS23 4.1 37.0 1.0
CG B:HIS23 4.2 33.9 1.0
OE2 B:GLU24 4.7 85.8 1.0
CB B:MET19 4.9 36.8 1.0

Zinc binding site 5 out of 8 in 6zyu

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Zinc binding site 5 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:65.7
occ:0.58
O B:HOH407 2.5 45.8 1.0
OE1 B:GLU201 3.9 52.9 1.0
OE2 B:GLU201 4.1 44.5 1.0
O B:LYS210 4.3 33.4 1.0
CD B:GLU201 4.4 45.1 1.0
CB B:LYS210 4.7 32.1 1.0

Zinc binding site 6 out of 8 in 6zyu

Go back to Zinc Binding Sites List in 6zyu
Zinc binding site 6 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:18.3
occ:0.70
OE2 B:GLU166 1.9 35.7 1.0
CD B:GLU166 2.7 33.8 1.0
OE1 B:GLU166 2.8 35.4 1.0
O B:HOH554 3.7 47.1 1.0
CG B:GLU166 4.1 32.2 1.0
CB B:GLU166 4.9 32.6 1.0

Zinc binding site 7 out of 8 in 6zyu

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Zinc binding site 7 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:26.5
occ:1.00
OXT C:ACT303 1.9 31.1 0.7
OE2 C:GLU24 2.0 67.6 0.3
NE2 C:HIS23 2.1 38.4 1.0
C C:ACT303 2.7 38.5 0.7
O C:ACT303 2.9 47.6 0.7
CD C:GLU24 3.0 60.6 0.3
CE1 C:HIS23 3.0 33.2 1.0
CD2 C:HIS23 3.1 33.5 1.0
CG C:GLU24 3.4 43.6 0.3
CH3 C:ACT303 4.1 39.7 0.7
OE1 C:GLU24 4.1 60.7 0.3
ND1 C:HIS23 4.1 32.9 1.0
CG C:HIS23 4.2 33.3 1.0
SD C:MET19 4.7 37.0 1.0
CG C:GLU24 4.7 48.7 0.7
CB C:GLU24 4.8 42.5 0.3
CB C:GLU24 4.9 42.5 0.7

Zinc binding site 8 out of 8 in 6zyu

Go back to Zinc Binding Sites List in 6zyu
Zinc binding site 8 out of 8 in the Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:38.7
occ:0.55
O C:HOH524 1.8 39.3 1.0
OE2 C:GLU42 2.1 49.8 1.0
NE2 C:HIS46 2.1 57.0 1.0
CD2 C:HIS46 3.0 52.1 1.0
CD C:GLU42 3.1 43.3 1.0
CE1 C:HIS46 3.2 58.7 1.0
NZ C:LYS45 3.3 68.2 1.0
CE C:LYS45 3.3 61.6 1.0
OE1 C:GLU42 3.5 49.8 1.0
CD2 C:LEU241 4.0 37.8 1.0
CG C:HIS46 4.2 50.3 1.0
ND1 C:HIS46 4.3 57.1 1.0
CG C:GLU42 4.5 34.5 1.0
OE1 C:GLN244 4.5 52.1 1.0
CB C:GLU42 4.7 30.7 1.0
CD C:LYS45 4.8 53.5 1.0
O C:GLU42 5.0 28.0 1.0

Reference:

J.Dorosz, K.M.Christensen, J.S.Kastrup. Structure of the GLUA2 Ligand-Binding Domain (L483Y-N754S) in Complex with Glutamate and BPAM549 To Be Published.
Page generated: Sat Aug 21 17:58:48 2021

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