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Zinc in PDB 5h8s: Structure of the Human GLUA2 Lbd in Complex with GNE3419

Protein crystallography data

The structure of Structure of the Human GLUA2 Lbd in Complex with GNE3419, PDB code: 5h8s was solved by H.J.A.Wallweber, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.81 / 1.70
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.232, 114.461, 162.744, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.6

Other elements in 5h8s:

The structure of Structure of the Human GLUA2 Lbd in Complex with GNE3419 also contains other interesting chemical elements:

Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Human GLUA2 Lbd in Complex with GNE3419 (pdb code 5h8s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Human GLUA2 Lbd in Complex with GNE3419, PDB code: 5h8s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5h8s

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Zinc binding site 1 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:24.3
occ:1.00
OE2 C:GLU166 1.8 22.7 1.0
O2 A:CAC305 1.9 23.2 1.0
OE1 A:GLU42 2.0 23.5 1.0
NE2 A:HIS46 2.1 23.7 1.0
CD C:GLU166 2.6 23.0 1.0
OE1 C:GLU166 2.7 26.9 1.0
CD A:GLU42 2.9 25.2 1.0
CD2 A:HIS46 3.1 23.9 1.0
CE1 A:HIS46 3.2 29.8 1.0
OE2 A:GLU42 3.2 24.6 1.0
AS A:CAC305 3.3 33.8 1.0
C2 A:CAC305 4.0 28.6 1.0
C1 A:CAC305 4.0 27.7 1.0
CD2 A:LEU241 4.0 24.3 1.0
CG C:GLU166 4.0 22.9 1.0
N C:SER168 4.2 21.4 1.0
CG A:HIS46 4.2 23.3 1.0
ND1 A:HIS46 4.2 25.6 1.0
CG A:GLU42 4.3 19.8 1.0
CB A:GLU42 4.7 18.5 1.0
O C:ALA165 4.7 23.0 1.0
CB C:GLU166 4.7 25.8 1.0
CB C:SER168 4.7 22.1 1.0
O1 A:CAC305 4.7 33.8 1.0
CA C:SER168 4.7 22.6 1.0
C C:PRO167 4.9 22.4 1.0
CA C:GLU166 4.9 22.7 1.0
CA C:PRO167 5.0 23.8 1.0

Zinc binding site 2 out of 6 in 5h8s

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Zinc binding site 2 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:32.7
occ:1.00
O A:HOH579 1.9 36.6 1.0
NE2 A:HIS23 2.1 27.2 1.0
CD2 A:HIS23 3.1 26.2 1.0
CE1 A:HIS23 3.1 31.6 1.0
ND1 A:HIS23 4.2 29.3 1.0
CG A:HIS23 4.2 30.7 1.0
CB A:MET19 4.9 25.9 1.0

Zinc binding site 3 out of 6 in 5h8s

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Zinc binding site 3 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:25.5
occ:1.00
OE2 C:GLU30 1.9 27.6 1.0
NE2 C:HIS23 2.0 23.5 1.0
O C:HOH618 2.0 32.4 1.0
CD C:GLU30 2.8 25.7 1.0
OE1 C:GLU30 3.0 26.4 1.0
CD2 C:HIS23 3.0 22.8 1.0
CE1 C:HIS23 3.0 21.9 1.0
NZ C:LYS20 4.0 27.0 1.0
CD C:LYS20 4.1 23.5 1.0
ND1 C:HIS23 4.1 25.8 1.0
CG C:HIS23 4.1 24.9 1.0
CG C:GLU30 4.2 28.4 1.0
O C:GLU30 4.4 23.4 1.0
CD2 C:LEU26 4.7 35.9 1.0
CE C:LYS20 4.7 26.7 1.0

Zinc binding site 4 out of 6 in 5h8s

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Zinc binding site 4 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn304

b:23.7
occ:1.00
NE2 C:HIS46 2.0 20.6 1.0
OE2 C:GLU42 2.0 20.7 1.0
O C:HOH607 2.2 20.5 1.0
CD C:GLU42 3.0 23.8 1.0
CE1 C:HIS46 3.0 23.2 1.0
CD2 C:HIS46 3.0 23.0 1.0
OE1 C:GLU42 3.2 26.1 1.0
CD2 C:LEU241 3.7 24.5 1.0
O C:HOH557 3.9 37.4 1.0
CE C:LYS45 4.0 25.3 1.0
NZ C:LYS45 4.0 23.4 1.0
ND1 C:HIS46 4.1 26.0 1.0
OE1 C:GLN244 4.2 32.1 1.0
CG C:HIS46 4.2 20.6 1.0
CG C:GLU42 4.3 22.1 1.0
CB C:GLU42 4.7 18.2 1.0

Zinc binding site 5 out of 6 in 5h8s

Go back to Zinc Binding Sites List in 5h8s
Zinc binding site 5 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:60.4
occ:1.00
NE2 B:HIS46 2.3 35.0 1.0
OE1 B:GLU42 2.6 35.2 1.0
O B:HOH488 2.8 42.6 1.0
CE1 B:HIS46 3.2 39.4 1.0
CD2 B:HIS46 3.3 31.4 1.0
NZ B:LYS45 3.3 52.8 1.0
CD B:GLU42 3.6 33.4 1.0
CE B:LYS45 3.7 42.6 1.0
OE1 B:GLN244 3.7 44.2 1.0
CD2 B:LEU241 3.8 28.4 1.0
O B:HOH402 3.8 36.2 1.0
OE2 B:GLU42 4.1 43.3 1.0
ND1 B:HIS46 4.3 38.5 1.0
CG B:HIS46 4.4 31.2 1.0
NE2 B:GLN244 4.5 41.5 1.0
CD B:GLN244 4.5 44.5 1.0
CG B:GLU42 4.8 28.3 1.0
CB B:GLU42 4.9 24.1 1.0

Zinc binding site 6 out of 6 in 5h8s

Go back to Zinc Binding Sites List in 5h8s
Zinc binding site 6 out of 6 in the Structure of the Human GLUA2 Lbd in Complex with GNE3419


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 Human GLUA2 Lbd in Complex with GNE3419 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:93.6
occ:1.00
OD2 B:ASP156 2.6 63.4 1.0
CG B:ASP156 3.1 52.2 1.0
OD1 B:ASP156 3.1 56.1 1.0
O B:HOH473 3.7 43.6 1.0
OG1 B:THR160 3.9 52.8 1.0
NH1 B:ARG163 4.1 69.2 1.0
O B:ASP156 4.2 43.4 1.0
NH2 B:ARG163 4.2 66.9 1.0
CB B:ASP156 4.4 49.1 1.0
CZ B:ARG163 4.4 66.7 1.0
CD1 B:TRP159 4.5 47.6 1.0
CA B:ASP156 4.7 44.3 1.0
C B:ASP156 4.7 41.6 1.0

Reference:

D.H.Hackos, P.J.Lupardus, T.Grand, Y.Chen, T.M.Wang, P.Reynen, A.Gustafson, H.J.Wallweber, M.Volgraf, B.D.Sellers, J.B.Schwarz, P.Paoletti, M.Sheng, Q.Zhou, J.E.Hanson. Positive Allosteric Modulators of GLUN2A-Containing Nmdars with Distinct Modes of Action and Impacts on Circuit Function. Neuron V. 89 983 2016.
ISSN: ISSN 1097-4199
PubMed: 26875626
DOI: 10.1016/J.NEURON.2016.01.016
Page generated: Wed Dec 16 06:20:09 2020

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