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Sodium in PDB 4gdx: Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex

Enzymatic activity of Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex

All present enzymatic activity of Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex:
2.3.2.2; 3.4.19.13; 3.4.19.14;

Protein crystallography data

The structure of Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex, PDB code: 4gdx was solved by M.B.West, Y.Chen, S.Wickham, A.Heroux, K.Cahill, M.H.Hanigan, B.H.M.Mooers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 1.67
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.524, 125.247, 104.468, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.4

Other elements in 4gdx:

The structure of Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex (pdb code 4gdx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex, PDB code: 4gdx:

Sodium binding site 1 out of 1 in 4gdx

Go back to Sodium Binding Sites List in 4gdx
Sodium binding site 1 out of 1 in the Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Gamma-Glutamyl Transpeptidase--Glutamate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:31.4
occ:1.00
HD1 A:HIS36 2.0 27.3 1.0
O A:ASP34 2.3 44.7 1.0
HD3 B:LYS496 2.6 19.3 1.0
O B:HOH1212 2.7 11.0 1.0
ND1 A:HIS36 2.9 22.7 1.0
HA A:ASN35 2.9 43.0 1.0
O B:HOH1230 2.9 26.1 1.0
HA B:ALA557 3.1 13.5 1.0
O B:ALA556 3.2 14.3 1.0
HB2 B:LYS496 3.3 19.7 1.0
HB2 A:HIS36 3.3 22.5 1.0
C A:ASP34 3.4 37.0 1.0
H A:HIS36 3.4 33.2 1.0
CD B:LYS496 3.5 16.1 1.0
HE2 B:LYS496 3.5 20.9 1.0
HB2 B:ALA557 3.5 17.8 1.0
CA A:ASN35 3.6 35.8 1.0
N A:HIS36 3.6 27.7 1.0
HG2 B:LYS496 3.7 18.9 1.0
C A:ASN35 3.7 46.1 1.0
CE1 A:HIS36 3.8 28.1 1.0
CG A:HIS36 3.8 25.7 1.0
HZ3 B:LYS496 3.9 17.8 1.0
HE1 A:HIS36 3.9 33.7 1.0
N A:ASN35 3.9 42.3 1.0
CG B:LYS496 3.9 15.8 1.0
CA B:ALA557 3.9 11.2 1.0
CE B:LYS496 4.0 17.4 1.0
CB A:HIS36 4.0 18.8 1.0
HB1 B:ALA557 4.0 17.8 1.0
CB B:ALA557 4.0 14.8 1.0
CB B:LYS496 4.0 16.4 1.0
HG3 B:PRO566 4.1 22.7 1.0
HD2 B:LYS496 4.2 19.3 1.0
C B:ALA556 4.2 16.4 1.0
H B:SER558 4.3 13.0 1.0
CA A:HIS36 4.4 28.7 1.0
HD2 B:PRO566 4.4 13.6 1.0
NZ B:LYS496 4.4 14.8 1.0
CG A:ASP34 4.4 57.5 1.0
O A:ASN35 4.5 32.7 1.0
HD3 B:PRO566 4.5 13.6 1.0
OD1 A:ASP34 4.5 54.6 1.0
HB3 A:ASP34 4.6 61.9 1.0
N B:ALA557 4.6 11.4 1.0
HG2 B:PRO566 4.6 22.7 1.0
OE1 B:GLU565 4.6 19.6 1.0
OD2 A:ASP34 4.6 41.1 1.0
HA B:LYS496 4.6 12.9 1.0
CG B:PRO566 4.7 18.9 1.0
CA A:ASP34 4.7 59.8 1.0
HB3 B:LYS496 4.7 19.7 1.0
CD B:PRO566 4.7 11.4 1.0
H A:ASN35 4.8 50.7 1.0
CB A:ASP34 4.8 51.6 1.0
HB3 A:HIS36 4.8 22.5 1.0
HE3 B:LYS496 4.8 20.9 1.0
HG3 B:LYS496 4.9 18.9 1.0
CB A:ASN35 4.9 35.1 1.0
NE2 A:HIS36 4.9 39.7 1.0
CA B:LYS496 4.9 10.8 1.0
HB3 B:ALA557 4.9 17.8 1.0
N B:SER558 4.9 10.8 1.0
CD2 A:HIS36 5.0 44.9 1.0
HZ1 B:LYS496 5.0 17.8 1.0

Reference:

M.B.West, Y.Chen, S.Wickham, A.Heroux, K.Cahill, M.H.Hanigan, B.H.Mooers. Novel Insights Into Eukaryotic Gamma-Glutamyltranspeptidase 1 From the Crystal Structure of the Glutamate-Bound Human Enzyme. J.Biol.Chem. V. 288 31902 2013.
ISSN: ISSN 0021-9258
PubMed: 24047895
DOI: 10.1074/JBC.M113.498139
Page generated: Tue Dec 15 06:41:32 2020

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