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Sodium in PDB 6g2u: Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)

Enzymatic activity of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)

All present enzymatic activity of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2):
1.4.1.3;

Protein crystallography data

The structure of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2), PDB code: 6g2u was solved by V.F.Fadouloglou, C.Dimovasili, M.Providaki, D.Kotsifaki, I.Sarrou, A.Plaitakis, I.Zaganas, M.Kokkinidis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.65 / 2.93
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 121.795, 149.304, 433.315, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.9

Other elements in 6g2u:

The structure of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) also contains other interesting chemical elements:

Chlorine (Cl) 19 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) (pdb code 6g2u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 21 binding sites of Sodium where determined in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2), PDB code: 6g2u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 21 in 6g2u

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Sodium binding site 1 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


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 the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:58.4
occ:1.00
 N A:GLY478 3.1 42.0 1.0
CA A:GLY478 3.2 41.9 1.0
O A:HOH873 3.5 48.2 1.0
O A:ALA472 3.9 48.9 1.0
O A:HOH961 4.1 58.1 1.0
C A:ASN476 4.1 44.2 1.0
CA A:ASN476 4.1 46.4 1.0
O A:HOH874 4.2 64.7 1.0
N A:LEU477 4.2 43.9 1.0
C A:LEU477 4.3 47.3 1.0
C A:GLY478 4.4 42.2 1.0
O A:ASN476 4.5 49.6 1.0
O A:GLY478 4.6 46.4 1.0
ND2 A:ASN476 4.6 72.1 1.0
C A:ALA472 4.7 46.3 1.0
CA A:MET473 4.7 46.5 1.0
CA A:LEU477 4.9 48.7 1.0

Sodium binding site 2 out of 21 in 6g2u

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Sodium binding site 2 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:58.1
occ:1.00
 O A:HOH859 2.6 53.2 1.0
O A:HOH962 4.0 69.5 1.0
O A:HOH982 4.3 62.5 1.0
O A:HOH855 4.4 51.1 1.0
O A:HOH775 4.5 46.7 1.0
O A:LEU365 4.5 50.3 1.0
O A:HOH710 4.5 47.7 1.0
OD1 A:ASN368 4.6 47.6 1.0

Sodium binding site 3 out of 21 in 6g2u

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Sodium binding site 3 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:61.6
occ:1.00
 O C:HOH826 3.1 45.4 1.0
CD C:ARG423 3.2 53.9 1.0
O C:HOH879 3.4 64.2 1.0
O1 C:PO4604 3.4 91.6 1.0
O C:GLU419 3.8 53.2 1.0
CB C:ARG423 3.8 48.5 1.0
CG C:ARG423 3.9 54.5 1.0
NE C:ARG423 3.9 57.7 1.0
O C:HOH770 4.0 52.2 1.0
CA C:SER420 4.2 54.9 1.0
C C:GLU419 4.4 48.1 1.0
O C:HOH786 4.4 74.4 1.0
O2 C:PO4604 4.5 85.2 1.0
P C:PO4604 4.5 0.4 1.0
OG C:SER420 4.5 50.0 1.0
N C:SER420 4.6 49.3 1.0
CB C:SER420 4.9 44.9 1.0

Sodium binding site 4 out of 21 in 6g2u

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Sodium binding site 4 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na607

b:92.6
occ:1.00
 O C:HOH845 2.9 75.4 1.0
O C:HOH857 3.0 87.0 1.0
O C:HOH900 3.3 76.2 1.0
O2 C:PO4602 4.1 91.7 1.0
O C:HOH705 4.2 75.4 1.0
O C:HOH863 4.3 53.9 1.0
OD2 C:ASP442 4.7 84.5 1.0
O C:HOH706 4.7 67.6 1.0
O C:HOH711 4.8 65.4 1.0
OD1 C:ASP451 4.9 64.6 1.0
O C:HOH929 5.0 83.0 1.0

Sodium binding site 5 out of 21 in 6g2u

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Sodium binding site 5 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na603

b:36.9
occ:1.00
 O D:PRO58 2.7 40.3 1.0
O D:ILE55 2.8 39.6 1.0
OD1 D:ASN60 2.8 37.4 1.0
O D:HIS86 2.9 36.6 1.0
O D:ILE56 3.0 32.9 1.0
O D:HOH702 3.4 39.2 1.0
C D:ILE56 3.4 32.9 1.0
CA D:ILE56 3.5 34.0 1.0
CG D:ASN60 3.6 38.0 1.0
C D:ILE55 3.8 40.1 1.0
C D:PRO58 3.9 37.7 1.0
C D:HIS86 3.9 37.7 1.0
ND2 D:ASN60 4.0 37.1 1.0
NE2 D:HIS86 4.0 40.8 1.0
CE1 D:HIS86 4.1 38.6 1.0
N D:ILE56 4.1 39.6 1.0
CA D:SER87 4.2 32.0 1.0
CD2 D:HIS86 4.3 35.5 1.0
CB D:SER87 4.4 35.8 1.0
ND1 D:HIS86 4.4 33.9 1.0
N D:ASN60 4.4 34.3 1.0
N D:LYS57 4.5 35.7 1.0
N D:SER87 4.5 30.0 1.0
CG D:HIS86 4.5 34.8 1.0
N D:PRO58 4.6 36.8 1.0
CA D:CYS59 4.6 34.0 1.0
C D:CYS59 4.7 36.0 1.0
N D:CYS59 4.7 33.7 1.0
CD D:PRO58 4.7 33.1 1.0
CB D:ILE56 4.7 34.7 1.0
C D:LYS57 4.8 42.7 1.0
OH D:TYR497 4.8 70.7 1.0
CA D:PRO58 4.9 37.1 1.0
CG2 D:ILE56 4.9 40.2 1.0
CB D:ASN60 4.9 35.3 1.0
OG D:SER87 4.9 34.8 1.0

Sodium binding site 6 out of 21 in 6g2u

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Sodium binding site 6 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:63.2
occ:1.00
 O D:HOH838 2.7 44.1 1.0
O D:HOH796 3.6 51.5 1.0
O D:HOH1036 3.7 59.9 1.0
O D:HOH844 3.9 51.6 1.0
O D:HOH908 4.0 51.3 1.0
NE D:ARG150 4.3 43.8 1.0
CD D:ARG150 4.4 48.9 1.0
O D:HOH1031 4.6 64.9 1.0
CZ D:ARG150 4.7 41.8 1.0

Sodium binding site 7 out of 21 in 6g2u

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Sodium binding site 7 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:66.5
occ:1.00
 O D:LYS344 3.2 53.3 1.0
CG D:LYS346 4.3 47.9 1.0
C D:LYS344 4.4 48.0 1.0
O D:CYS323 4.6 48.3 1.0
CE D:LYS346 4.7 50.8 1.0
OD1 D:ASP322 4.7 64.3 1.0

Sodium binding site 8 out of 21 in 6g2u

Go back to Sodium Binding Sites List in 6g2u
Sodium binding site 8 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na606

b:80.3
occ:1.00
 CL D:CL618 3.5 93.6 1.0
O D:HOH927 4.3 63.8 1.0
NA D:NA608 4.8 83.2 1.0
O D:HOH1040 4.8 82.8 1.0

Sodium binding site 9 out of 21 in 6g2u

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Sodium binding site 9 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na607

b:72.9
occ:1.00
 O D:HOH851 3.7 75.8 1.0
O D:HOH1056 3.8 81.7 1.0
CE1 D:HIS470 3.9 52.5 1.0
O D:HOH927 4.1 63.8 1.0
O D:HOH754 4.1 68.2 1.0
NE2 D:HIS470 4.2 53.5 1.0
O D:HOH1040 4.2 82.8 1.0

Sodium binding site 10 out of 21 in 6g2u

Go back to Sodium Binding Sites List in 6g2u
Sodium binding site 10 out of 21 in the Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na608

b:83.2
occ:1.00
 O D:HOH925 3.2 69.9 1.0
O D:HOH1056 4.1 81.7 1.0
O D:HOH851 4.7 75.8 1.0
NA D:NA606 4.8 80.3 1.0

Reference:

V.F.Fadouloglou, C.Dimovasili, M.Providaki, D.Kotsifaki, I.Sarrou, A.Plaitakis, I.Zaganas, M.Kokkinidis. Crystal Structure of the Human Glutamate Dehydrogenase 2 (HGDH2) To Be Published.
Page generated: Tue Oct 8 08:53:43 2024

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