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Zinc in PDB 4n07: Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution

Protein crystallography data

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution, PDB code: 4n07 was solved by A.B.Noerholm, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.48 / 1.87
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.904, 164.034, 47.284, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.1

Other elements in 4n07:

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution (pdb code 4n07). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution, PDB code: 4n07:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4n07

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Zinc binding site 1 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:25.6
occ:1.00
 O A:ACT306 1.9 29.4 1.0
OE2 A:GLU30 2.0 25.1 1.0
NE2 A:HIS23 2.0 24.6 1.0
OXT A:ACT306 2.6 36.0 1.0
C A:ACT306 2.7 32.1 1.0
CD A:GLU30 2.8 21.6 1.0
OE1 A:GLU30 2.9 27.0 1.0
CD2 A:HIS23 2.9 25.2 1.0
CE1 A:HIS23 3.1 23.8 1.0
NZ A:LYS20 4.1 27.5 1.0
CD A:LYS20 4.1 20.8 1.0
CG A:HIS23 4.1 21.1 1.0
CH3 A:ACT306 4.2 38.0 1.0
ND1 A:HIS23 4.2 23.7 1.0
CG A:GLU30 4.2 26.3 1.0
O A:GLU30 4.4 21.7 1.0
CD2 A:LEU26 4.6 37.2 1.0
CE A:LYS20 4.7 22.6 1.0

Zinc binding site 2 out of 10 in 4n07

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Zinc binding site 2 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:62.8
occ:1.00
 OD1 A:ASP156 2.1 40.2 1.0
O A:HOH618 2.3 41.0 1.0
CG A:ASP156 3.1 34.6 1.0
OD2 A:ASP156 3.5 40.4 1.0
O A:HOH433 3.8 21.6 1.0
OG1 A:THR160 4.0 27.9 1.0
CB A:ASP156 4.3 24.2 1.0
O A:ASP156 4.5 25.5 1.0
NH1 A:ARG163 4.5 39.7 1.0
CD1 A:TRP159 4.7 21.0 1.0
CA A:ASP156 4.8 26.4 1.0
C A:ASP156 4.9 24.6 1.0

Zinc binding site 3 out of 10 in 4n07

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Zinc binding site 3 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:23.7
occ:0.54
 O A:HOH655 1.9 29.6 1.0
O2 A:CAC313 2.0 28.1 0.8
O A:ACT305 2.1 31.8 1.0
O A:HOH623 2.5 37.2 1.0
OXT A:ACT305 2.7 36.9 1.0
C A:ACT305 2.8 33.4 1.0
AS A:CAC313 3.3 24.6 0.8
C2 A:CAC313 3.5 22.8 0.8
NZ A:LYS144 3.9 24.8 1.0
CD2 A:PHE170 4.0 19.3 1.0
OG A:SER168 4.1 17.2 1.0
O A:HOH482 4.1 26.8 1.0
CH3 A:ACT305 4.3 31.0 1.0
CD B:LYS45 4.3 32.2 1.0
CG B:LYS45 4.4 30.2 1.0
OD1 A:ASP139 4.4 30.0 1.0
C1 A:CAC313 4.5 18.7 0.8
CE2 A:PHE170 4.6 16.8 1.0
O1 A:CAC313 4.6 18.6 0.8
CG A:PHE170 4.7 18.6 1.0
CB A:PHE170 4.8 18.9 1.0
CB A:SER168 5.0 17.9 1.0

Zinc binding site 4 out of 10 in 4n07

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Zinc binding site 4 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:29.8
occ:1.00
 NE2 A:HIS46 1.9 18.8 1.0
O A:HOH659 2.2 30.9 1.0
OE1 A:GLU42 2.2 26.3 1.0
CD2 A:HIS46 2.9 19.3 1.0
CE1 A:HIS46 2.9 29.0 1.0
CD A:GLU42 3.0 25.3 1.0
OE2 A:GLU42 3.3 30.6 1.0
CD2 A:LEU241 3.5 21.2 1.0
NZ A:LYS45 3.8 29.9 1.0
OE1 A:GLN244 3.8 29.4 1.0
CE A:LYS45 3.8 25.7 1.0
ND1 A:HIS46 4.0 29.9 1.0
CG A:HIS46 4.0 23.4 1.0
CG A:GLU42 4.3 23.9 1.0
CD A:GLN244 4.6 29.5 1.0
NE2 A:GLN244 4.7 31.3 1.0
CB A:GLU42 4.7 17.7 1.0
CG A:LEU241 5.0 17.1 1.0

Zinc binding site 5 out of 10 in 4n07

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Zinc binding site 5 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:17.7
occ:1.00
 O1 A:CAC313 1.9 18.6 0.8
OE1 A:GLU166 1.9 20.3 1.0
OE1 B:GLU42 2.0 17.0 1.0
NE2 B:HIS46 2.0 17.3 1.0
OE2 A:GLU166 2.6 21.1 1.0
CD A:GLU166 2.6 21.5 1.0
CD B:GLU42 3.0 20.1 1.0
CD2 B:HIS46 3.0 17.4 1.0
CE1 B:HIS46 3.0 25.0 1.0
AS A:CAC313 3.3 24.6 0.8
OE2 B:GLU42 3.3 18.1 1.0
CD2 B:LEU241 4.0 21.2 1.0
C2 A:CAC313 4.0 22.8 0.8
C1 A:CAC313 4.0 18.7 0.8
CG A:GLU166 4.1 19.2 1.0
ND1 B:HIS46 4.1 20.9 1.0
CG B:HIS46 4.1 17.0 1.0
N A:SER168 4.2 15.7 1.0
CG B:GLU42 4.3 16.4 1.0
CB A:SER168 4.6 17.9 1.0
O2 A:CAC313 4.7 28.1 0.8
CB B:GLU42 4.7 13.9 1.0
O A:ALA165 4.7 15.6 1.0
CA A:SER168 4.7 16.3 1.0
CB A:GLU166 4.8 19.6 1.0
CA A:PRO167 5.0 18.7 1.0
C A:PRO167 5.0 17.2 1.0
CA A:GLU166 5.0 21.6 1.0

Zinc binding site 6 out of 10 in 4n07

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Zinc binding site 6 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:31.9
occ:1.00
 NE2 B:HIS23 2.0 32.0 1.0
O B:HOH540 2.2 37.1 1.0
OXT B:ACT303 2.3 37.6 1.0
O B:ACT303 2.3 43.1 1.0
C B:ACT303 2.7 37.9 1.0
CD2 B:HIS23 3.0 32.8 1.0
CE1 B:HIS23 3.0 30.8 1.0
ND1 B:HIS23 4.1 29.8 1.0
CG B:HIS23 4.2 31.5 1.0
CH3 B:ACT303 4.2 37.7 1.0
CB B:MET19 4.7 30.0 1.0
CG B:MET19 4.9 29.2 1.0
O B:HOH563 5.0 37.8 1.0

Zinc binding site 7 out of 10 in 4n07

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Zinc binding site 7 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:78.3
occ:1.00
 OD1 B:ASP156 2.4 46.7 1.0
NH1 B:ARG163 3.1 49.0 1.0
O B:HOH550 3.3 42.8 1.0
CG B:ASP156 3.6 41.7 1.0
O B:HOH503 3.8 34.4 1.0
OG1 B:THR160 3.8 35.8 1.0
CD1 B:TRP159 3.8 32.1 1.0
O B:ASP156 4.3 32.8 1.0
OD2 B:ASP156 4.4 42.6 1.0
CZ B:ARG163 4.4 50.4 1.0
CB B:ASP156 4.6 36.8 1.0
NE1 B:TRP159 4.7 30.8 1.0
CA B:ASP156 4.8 34.7 1.0
CG B:TRP159 4.8 28.2 1.0
C B:ASP156 4.9 29.9 1.0
N B:THR160 5.0 30.8 1.0

Zinc binding site 8 out of 10 in 4n07

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Zinc binding site 8 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


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 GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn308

b:47.6
occ:1.00
 O C:HOH603 2.0 41.2 1.0
NE2 C:HIS46 2.1 37.9 1.0
OXT C:ACT305 2.3 47.3 1.0
OE1 C:GLU42 2.3 35.4 1.0
O C:ACT305 2.5 50.8 1.0
C C:ACT305 2.7 43.6 1.0
CE1 C:HIS46 3.0 42.7 1.0
CD2 C:HIS46 3.2 33.0 1.0
CD C:GLU42 3.3 34.0 1.0
OE2 C:GLU42 3.6 38.0 1.0
CE C:LYS45 3.9 42.1 1.0
NZ C:LYS45 3.9 44.2 1.0
O C:HOH586 4.0 46.5 1.0
CD2 C:LEU241 4.0 24.1 1.0
CH3 C:ACT305 4.0 38.3 1.0
ND1 C:HIS46 4.1 44.8 1.0
CG C:HIS46 4.3 40.0 1.0
CG C:GLU42 4.6 20.5 1.0
OE1 C:GLN244 4.7 36.1 1.0
CB C:GLU42 4.9 23.5 1.0

Zinc binding site 9 out of 10 in 4n07

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Zinc binding site 9 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn309

b:67.3
occ:1.00
 O C:HOH556 2.0 38.5 1.0
OD2 C:ASP156 2.2 37.2 1.0
O C:HOH544 2.8 41.7 1.0
CG C:ASP156 3.2 33.1 1.0
OD1 C:ASP156 3.7 39.8 1.0
O C:HOH440 3.8 25.9 1.0
OG1 C:THR160 4.0 32.6 1.0
O C:ASP156 4.3 26.8 1.0
CB C:ASP156 4.4 31.6 1.0
CD1 C:TRP159 4.5 23.4 1.0
O C:HOH527 4.5 36.3 1.0
NH2 C:ARG163 4.7 48.5 1.0
CA C:ASP156 4.8 26.6 1.0
C C:ASP156 4.9 25.6 1.0

Zinc binding site 10 out of 10 in 4n07

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Zinc binding site 10 out of 10 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L483Y- N754S) in Complex with Glutamate and Bpam-344 at 1.87 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn310

b:35.0
occ:0.41
 OD2 C:ASP139 2.1 31.1 0.5
O C:HOH574 2.4 38.8 1.0
OXT C:ACT307 2.6 47.1 1.0
OD1 C:ASP139 2.6 28.1 0.5
CG C:ASP139 2.6 27.4 0.5
C C:ACT307 3.3 40.2 1.0
O C:ACT307 3.5 34.2 1.0
OG C:SER140 3.6 32.8 1.0
CB C:ASP139 4.1 27.7 0.5
CG C:ASP139 4.2 28.6 0.5
CB C:ASP139 4.2 27.6 0.5
NZ C:LYS144 4.3 29.1 1.0
OD1 C:ASP139 4.3 27.9 0.5
N C:SER140 4.5 22.6 1.0
CH3 C:ACT307 4.5 35.5 1.0
OD2 C:ASP139 4.5 27.6 0.5
NZ C:LYS60 4.5 32.8 1.0
CB C:SER140 4.8 24.7 1.0
CA C:ASP139 5.0 24.8 0.5

Reference:

A.B.Nrholm, P.Francotte, L.Olsen, C.Krintel, K.Frydenvang, E.Goffin, S.Challal, L.Danober, I.Botez-Pop, P.Lestage, B.Pirotte, J.S.Kastrup. Synthesis, Pharmacological and Structural Characterization, and Thermodynamic Aspects of GLUA2-Positive Allosteric Modulators with A 3,4-Dihydro-2H-1,2,4-Benzothiadiazine 1,1-Dioxide Scaffold. J.Med.Chem. V. 56 8736 2013.
ISSN: ISSN 0022-2623
PubMed: 24131202
DOI: 10.1021/JM4012092
Page generated: Wed Dec 16 05:36:16 2020

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