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Zinc in PDB 6hch: Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution.

Protein crystallography data

The structure of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution., PDB code: 6hch was solved by S.Laulumaa, K.V.Hansen, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.24 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.630, 163.580, 47.528, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 17.8

Other elements in 6hch:

The structure of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Zinc atom in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. (pdb code 6hch). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 23 binding sites of Zinc where determined in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution., PDB code: 6hch:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 23 in 6hch

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Zinc binding site 1 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.4
occ:0.92
O A:ACT313 1.8 39.2 0.9
NE2 A:HIS23 2.0 22.9 1.0
C A:ACT313 2.3 32.9 0.9
OXT A:ACT313 2.4 42.5 0.9
CE1 A:HIS23 2.9 27.3 1.0
CD2 A:HIS23 3.1 21.9 1.0
HE1 A:HIS23 3.1 32.8 1.0
HD2 A:HIS23 3.3 26.4 1.0
HE3 A:MET19 3.7 47.3 0.5
CH3 A:ACT313 3.8 39.3 0.9
HE1 A:MET19 3.8 47.3 0.5
ND1 A:HIS23 4.1 26.8 1.0
H2 A:ACT313 4.1 47.2 0.9
CE A:MET19 4.1 39.4 0.5
CG A:HIS23 4.2 23.8 1.0
H1 A:ACT313 4.2 47.2 0.9
HG3 A:GLU24 4.3 49.0 0.5
H3 A:ACT313 4.3 47.2 0.9
SD A:MET19 4.5 39.5 0.5
OE2 A:GLU24 4.6 41.5 0.5
HB3 A:MET19 4.7 28.8 0.5
HB3 A:MET19 4.8 28.1 0.5
HB2 A:MET19 4.8 28.1 0.5
HD1 A:HIS23 4.9 32.2 1.0
O A:HOH597 4.9 29.7 1.0
SD A:MET19 4.9 43.9 0.5
HB2 A:MET19 4.9 28.8 0.5
HG2 A:GLU24 4.9 50.4 0.5
HG2 A:GLU24 4.9 49.0 0.5
CG A:GLU24 5.0 40.8 0.5

Zinc binding site 2 out of 23 in 6hch

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Zinc binding site 2 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:50.7
occ:0.69
O A:HOH606 2.1 55.5 1.0
O A:HOH405 2.2 40.9 1.0
O A:HOH415 2.3 29.8 1.0
HE3 A:LYS210 3.6 50.3 1.0
HB3 A:LYS210 3.8 22.1 1.0
O A:LYS210 4.1 22.0 1.0
OE2 A:GLU201 4.2 27.3 1.0
OE1 A:GLU201 4.2 31.9 1.0
HZ1 A:LYS210 4.2 57.4 1.0
HZ2 A:LYS210 4.2 57.4 1.0
CE A:LYS210 4.5 41.9 1.0
NZ A:LYS210 4.5 47.8 1.0
CD A:GLU201 4.6 28.1 1.0
HG2 A:LYS210 4.6 26.1 1.0
CB A:LYS210 4.7 18.4 1.0
HE3 A:MET209 4.8 31.9 0.6
H A:LYS210 4.9 21.5 1.0

Zinc binding site 3 out of 23 in 6hch

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Zinc binding site 3 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:0.6
occ:0.85
O A:HOH444 2.4 44.9 1.0
HH11 A:ARG203 3.7 58.2 1.0
HB2 A:LYS204 4.0 31.7 1.0
O A:HOH619 4.3 46.6 1.0
NH1 A:ARG203 4.3 48.5 1.0
OE2 A:GLU260 4.3 33.1 1.0
O A:LYS204 4.4 26.7 1.0
HH12 A:ARG203 4.6 58.2 1.0
OE1 A:GLU260 4.6 40.4 1.0
HE A:ARG203 4.7 44.0 1.0
CB A:LYS204 4.9 26.4 1.0
CD A:GLU260 4.9 36.1 1.0

Zinc binding site 4 out of 23 in 6hch

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Zinc binding site 4 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:40.5
occ:0.31
OD1 A:ASP156 1.8 55.4 1.0
CG A:ASP156 2.5 44.7 1.0
OD2 A:ASP156 2.7 49.5 1.0
O A:HOH435 2.7 44.4 1.0
HH12 A:ARG163 3.5 75.5 1.0
HG1 A:THR160 3.6 35.4 1.0
OG1 A:THR160 3.8 29.5 1.0
CB A:ASP156 4.0 31.4 1.0
HD1 A:TRP159 4.1 28.0 1.0
NH1 A:ARG163 4.1 62.9 1.0
HH22 A:ARG163 4.1 83.9 1.0
O A:HOH441 4.2 24.0 1.0
HB2 A:ASP156 4.2 37.7 1.0
O A:ASP156 4.3 24.6 1.0
HA A:ASP156 4.4 28.1 1.0
HH11 A:ARG163 4.6 75.5 1.0
HB3 A:ASP156 4.6 37.7 1.0
CA A:ASP156 4.6 23.4 1.0
NH2 A:ARG163 4.7 69.9 1.0
C A:ASP156 4.8 21.5 1.0
CZ A:ARG163 4.8 63.8 1.0
CD1 A:TRP159 5.0 23.3 1.0
HB3 A:TRP159 5.0 24.3 1.0

Zinc binding site 5 out of 23 in 6hch

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Zinc binding site 5 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:55.9
occ:0.53
O A:HOH625 2.2 57.0 1.0
OE1 A:GLU24 2.4 39.0 0.5
OE2 A:GLU24 2.7 41.7 0.5
CD A:GLU24 2.9 41.8 0.5
CG A:GLU24 4.4 42.0 0.5
O A:HOH418 4.5 33.8 1.0
O A:HOH645 4.5 46.1 1.0
HA A:GLU24 4.6 40.5 0.5
HA A:GLU24 4.6 40.0 0.5
HG2 A:GLU24 4.7 49.0 0.5
HG2 A:GLU24 4.7 50.4 0.5
O A:HOH481 4.7 32.0 1.0
HG3 A:GLU24 4.8 50.4 0.5
HB3 A:GLU24 4.8 44.5 0.5

Zinc binding site 6 out of 23 in 6hch

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Zinc binding site 6 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 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 GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:64.3
occ:0.57
OE1 A:GLU77 2.3 21.8 0.6
OG1 A:THR54 2.7 23.7 1.0
O A:HOH457 2.8 34.5 1.0
CD A:GLU77 3.0 24.8 0.6
HA A:VAL56 3.1 18.4 1.0
OE2 A:GLU77 3.1 27.8 0.6
HG1 A:THR54 3.2 28.5 1.0
OG1 A:THR9 3.3 17.8 1.0
O A:HOH574 3.3 46.7 1.0
HB A:THR9 3.3 18.0 1.0
HG1 A:THR9 3.5 21.4 1.0
HB A:THR54 3.5 25.0 1.0
HA A:THR9 3.5 17.8 1.0
CD A:GLU77 3.6 30.2 0.4
OE1 A:GLU77 3.6 25.9 0.4
OE2 A:GLU77 3.6 27.5 0.4
CB A:THR54 3.7 20.8 1.0
CB A:THR9 3.7 15.0 1.0
O A:ILE55 3.9 19.4 1.0
CA A:VAL56 3.9 15.3 1.0
HB2 A:ALA83 4.0 21.9 1.0
C A:ILE55 4.0 17.4 1.0
N A:VAL56 4.1 16.7 1.0
O A:THR54 4.1 23.7 1.0
HG3 A:GLU77 4.1 27.7 0.4
CA A:THR9 4.2 14.8 1.0
C A:THR54 4.2 21.2 1.0
H A:GLY57 4.2 25.5 1.0
HB3 A:GLU77 4.3 22.3 0.4
HB3 A:GLU77 4.4 23.2 0.6
CG A:GLU77 4.4 23.1 0.4
CG A:GLU77 4.4 19.8 0.6
H A:VAL56 4.5 20.1 1.0
N A:ILE55 4.5 16.8 1.0
CA A:THR54 4.6 17.1 1.0
HG21 A:THR54 4.6 25.1 1.0
HB A:VAL56 4.6 18.8 1.0
HG23 A:VAL56 4.6 25.6 1.0
H A:THR10 4.7 17.1 1.0
N A:GLY57 4.7 21.2 1.0
CG2 A:THR54 4.8 20.9 1.0
HG2 A:GLU77 4.8 23.8 0.6
C A:VAL56 4.8 16.8 1.0
O A:HOH629 4.8 52.0 1.0
CB A:GLU77 4.8 18.5 0.4
CB A:GLU77 4.8 19.4 0.6
CB A:VAL56 4.8 15.7 1.0
HG12 A:VAL7 4.9 21.2 1.0
CA A:ILE55 4.9 16.3 1.0
O A:VAL8 4.9 20.6 1.0
CB A:ALA83 4.9 18.2 1.0
H A:ILE55 4.9 20.2 1.0
HB2 A:GLU77 5.0 23.2 0.6

Zinc binding site 7 out of 23 in 6hch

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Zinc binding site 7 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:57.0
occ:0.72
O A:HOH628 2.2 25.0 0.5
O A:HOH666 2.3 25.8 0.5
O A:HOH660 2.5 44.5 1.0
O A:HOH666 3.7 30.7 0.5
O A:HOH628 3.9 23.5 0.6
HZ2 A:LYS116 4.5 37.4 0.6
HG2 A:LYS185 4.7 43.5 1.0
HB3 A:LYS185 4.7 35.3 1.0
HA A:LYS185 5.0 28.7 1.0

Zinc binding site 8 out of 23 in 6hch

Go back to Zinc Binding Sites List in 6hch
Zinc binding site 8 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:68.9
occ:0.44
OE2 A:GLU132 2.0 73.6 1.0
O A:HOH595 2.6 57.5 1.0
CD A:GLU132 3.0 68.8 1.0
HE3 A:LYS187 3.4 54.3 1.0
HZ2 A:LYS187 3.4 58.9 1.0
OE1 A:GLU132 3.4 72.6 1.0
NZ A:LYS187 4.0 49.0 1.0
HZ1 A:LYS187 4.0 58.9 1.0
CE A:LYS187 4.1 45.2 1.0
CG A:GLU132 4.3 52.8 1.0
HG2 A:GLU132 4.4 63.4 1.0
HG3 A:GLU132 4.5 63.4 1.0
HD2 A:LYS187 4.6 41.0 1.0
HZ3 A:LYS187 4.8 58.9 1.0
HE2 A:LYS187 4.8 54.3 1.0
CD A:LYS187 5.0 34.1 1.0

Zinc binding site 9 out of 23 in 6hch

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Zinc binding site 9 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:73.6
occ:0.63
OD1 A:ASP126 2.2 33.1 1.0
O A:HOH414 2.5 46.6 1.0
CG A:ASP126 3.0 38.0 1.0
OD2 A:ASP126 3.2 32.0 1.0
O A:HOH462 3.2 47.3 1.0
HG A:SER123 3.8 29.2 1.0
OG A:SER123 4.2 24.4 1.0
HB2 A:GLU122 4.3 43.3 1.0
CB A:ASP126 4.5 23.3 1.0
HA A:ASP126 4.6 27.5 1.0
H A:ASP126 4.7 25.8 1.0
HB2 A:ASP126 4.9 28.0 1.0
CA A:ASP126 4.9 22.9 1.0
HB3 A:GLU125 5.0 34.8 1.0
HB3 A:ASP126 5.0 28.0 1.0

Zinc binding site 10 out of 23 in 6hch

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Zinc binding site 10 out of 23 in the Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of GLUA2 Ligand-Binding Domain (S1S2J-L504Y-N775S) in Complex with Glutamate and TDPAM01 at 1.6 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn315

b:21.2
occ:0.98
OE2 C:GLU166 1.7 20.2 1.0
OE1 A:GLU42 2.0 18.8 1.0
NE2 A:HIS46 2.0 19.3 1.0
O A:ACT316 2.2 25.5 1.0
CD C:GLU166 2.5 25.9 1.0
OE1 C:GLU166 2.6 23.1 1.0
CD A:GLU42 2.9 24.6 1.0
CD2 A:HIS46 3.0 18.3 1.0
CE1 A:HIS46 3.0 26.6 1.0
H1 A:ACT316 3.1 50.9 1.0
HD2 A:HIS46 3.2 22.0 1.0
HE1 A:HIS46 3.2 32.0 1.0
OE2 A:GLU42 3.3 21.8 1.0
C A:ACT316 3.3 44.7 1.0
HD21 A:LEU241 3.3 31.2 1.0
CH3 A:ACT316 3.7 42.4 1.0
H C:SER168 3.8 21.2 1.0
HD3 A:LYS45 3.9 69.1 1.0
CG C:GLU166 4.0 22.9 1.0
HB2 C:SER168 4.0 23.9 1.0
CD2 A:LEU241 4.0 26.0 1.0
HB3 A:GLU42 4.1 19.5 1.0
HD23 A:LEU241 4.1 31.2 1.0
ND1 A:HIS46 4.1 27.1 1.0
CG A:HIS46 4.1 19.0 1.0
H2 A:ACT316 4.1 50.9 1.0
HA C:GLU166 4.2 22.1 1.0
HD22 A:LEU241 4.2 31.2 1.0
HA C:PRO167 4.2 21.5 1.0
HD22 A:LEU246 4.2 27.7 0.5
CG A:GLU42 4.3 17.0 1.0
N C:SER168 4.3 17.6 1.0
HG3 C:GLU166 4.4 27.4 1.0
HB3 C:GLU166 4.4 25.6 1.0
H3 A:ACT316 4.5 50.9 1.0
HG2 C:GLU166 4.5 27.4 1.0
OXT A:ACT316 4.5 38.4 1.0
HA A:GLU42 4.5 17.7 1.0
O C:ALA165 4.6 19.0 1.0
HG3 A:GLU42 4.6 20.4 1.0
CB A:GLU42 4.6 16.2 1.0
HA C:SER168 4.6 18.6 1.0
CB C:GLU166 4.7 21.3 1.0
HB3 A:LYS45 4.8 29.3 1.0
CA C:SER168 4.9 15.5 1.0
CB C:SER168 4.9 19.9 1.0
CD A:LYS45 4.9 57.5 1.0
HD1 A:HIS46 4.9 32.5 1.0
CA C:GLU166 4.9 18.4 1.0
HG2 A:GLU42 4.9 20.4 1.0
HG A:LEU246 4.9 34.4 0.5
C C:PRO167 5.0 19.7 1.0
CA C:PRO167 5.0 17.9 1.0

Reference:

S.Laulumaa, K.V.Hansen, M.Masternak, T.Drapier, P.Francotte, B.Pirotte, K.Frydenvang, J.S.Kastrup. Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GLUA2 Receptor. Acs Med.Chem.Lett. V. 10 243 2019.
ISSN: ISSN 1948-5875
PubMed: 30891120
DOI: 10.1021/ACSMEDCHEMLETT.8B00369
Page generated: Wed Dec 16 11:56:30 2020

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