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Zinc in PDB 6dhm: Bovine Glutamate Dehydrogenase Complexed with Zinc

Enzymatic activity of Bovine Glutamate Dehydrogenase Complexed with Zinc

All present enzymatic activity of Bovine Glutamate Dehydrogenase Complexed with Zinc:
1.4.1.2;

Protein crystallography data

The structure of Bovine Glutamate Dehydrogenase Complexed with Zinc, PDB code: 6dhm was solved by T.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.88 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.110, 98.760, 165.640, 90.00, 101.55, 90.00
R / Rfree (%) 19.7 / 27

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Bovine Glutamate Dehydrogenase Complexed with Zinc (pdb code 6dhm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Bovine Glutamate Dehydrogenase Complexed with Zinc, PDB code: 6dhm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6dhm

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Zinc binding site 1 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:57.3
occ:1.00
OE1 A:GLU151 2.0 32.7 1.0
NE2 D:HIS57 2.2 24.8 1.0
CE1 D:HIS57 2.7 24.9 1.0
CD A:GLU151 2.8 32.8 1.0
OE2 A:GLU151 3.3 36.4 1.0
CD2 D:HIS57 3.5 25.9 1.0
OE1 D:GLN84 3.9 25.6 1.0
ND1 D:HIS57 4.0 21.3 1.0
CG A:GLU151 4.0 24.9 1.0
CG D:HIS57 4.4 26.5 1.0
CE A:LYS154 4.6 24.8 1.0
CD D:GLN84 4.7 26.1 1.0
NZ A:LYS154 4.8 28.6 1.0
CB A:GLU151 4.9 22.8 1.0
CB D:ASN56 4.9 24.5 1.0

Zinc binding site 2 out of 12 in 6dhm

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Zinc binding site 2 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:28.1
occ:1.00
NE2 A:HIS450 1.9 18.2 1.0
NE2 A:HIS209 2.1 27.9 1.0
O1B A:GTP603 2.3 22.3 1.0
CD2 A:HIS450 2.8 20.0 1.0
CE1 A:HIS450 2.9 22.0 1.0
CD2 A:HIS209 3.0 25.5 1.0
CE1 A:HIS209 3.1 23.7 1.0
PB A:GTP603 3.4 35.2 1.0
O3B A:GTP603 3.4 25.1 1.0
NH2 A:ARG217 3.9 17.2 1.0
ND1 A:HIS450 4.0 24.1 1.0
CG A:HIS450 4.0 19.1 1.0
NE A:ARG217 4.1 24.1 1.0
O3' A:GTP603 4.1 38.1 1.0
O3A A:GTP603 4.1 34.4 1.0
C3' A:GTP603 4.1 32.9 1.0
CG A:HIS209 4.1 20.9 1.0
ND1 A:HIS209 4.2 22.9 1.0
PG A:GTP603 4.2 34.6 1.0
CZ A:ARG217 4.3 25.7 1.0
O2G A:GTP603 4.3 25.6 1.0
O1G A:GTP603 4.3 32.6 1.0
OH A:TYR262 4.4 27.9 1.0
CA A:GLY210 4.5 24.3 1.0
OG A:SER213 4.7 31.2 1.0
O2B A:GTP603 4.7 31.6 1.0
CE A:LYS446 4.8 25.7 1.0
N A:GLY210 4.9 24.9 1.0
O2' A:GTP603 4.9 28.7 1.0
C2' A:GTP603 5.0 31.9 1.0

Zinc binding site 3 out of 12 in 6dhm

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Zinc binding site 3 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:71.3
occ:1.00
OE1 B:GLU151 2.0 42.0 1.0
NE2 E:HIS57 2.2 36.2 1.0
OE2 B:GLU151 2.5 43.3 1.0
CE1 E:HIS57 2.6 31.3 1.0
CD B:GLU151 2.6 33.3 1.0
CD2 E:HIS57 3.5 25.4 1.0
OE1 E:GLN84 3.8 31.2 1.0
ND1 E:HIS57 3.9 30.1 1.0
CG B:GLU151 4.1 20.1 1.0
CE B:LYS154 4.1 23.8 1.0
NZ B:LYS154 4.3 25.8 1.0
CD E:GLN84 4.3 25.1 1.0
CG E:HIS57 4.4 27.9 1.0
NE2 E:GLN84 4.8 32.6 1.0
CB B:GLU151 4.8 20.4 1.0
CB E:ASN56 5.0 23.9 1.0
CA B:GLU151 5.0 20.6 1.0

Zinc binding site 4 out of 12 in 6dhm

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Zinc binding site 4 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:38.5
occ:1.00
NE2 B:HIS450 2.0 27.1 1.0
NE2 B:HIS209 2.1 19.2 1.0
O1B B:GTP603 2.4 27.7 1.0
CD2 B:HIS450 3.0 26.5 1.0
CD2 B:HIS209 3.1 22.7 1.0
CE1 B:HIS450 3.1 21.1 1.0
CE1 B:HIS209 3.1 21.3 1.0
O3B B:GTP603 3.2 37.5 1.0
PB B:GTP603 3.4 36.5 1.0
C3' B:GTP603 3.9 32.3 1.0
NE B:ARG217 4.0 22.8 1.0
O1G B:GTP603 4.0 40.5 1.0
PG B:GTP603 4.0 47.9 1.0
CG B:HIS450 4.1 22.5 1.0
ND1 B:HIS450 4.1 20.8 1.0
CA B:GLY210 4.2 20.9 1.0
O3' B:GTP603 4.2 35.8 1.0
ND1 B:HIS209 4.2 19.5 1.0
O2G B:GTP603 4.2 39.0 1.0
CG B:HIS209 4.2 19.6 1.0
OH B:TYR262 4.4 33.8 1.0
NH2 B:ARG217 4.4 35.0 1.0
OG B:SER213 4.5 39.0 1.0
O2B B:GTP603 4.5 37.0 1.0
O3A B:GTP603 4.5 43.6 1.0
CZ B:ARG217 4.5 33.9 1.0
N B:GLY210 4.7 22.6 1.0
C2' B:GTP603 4.7 32.2 1.0
CD B:ARG217 4.7 29.5 1.0
O2' B:GTP603 4.8 36.5 1.0
C4' B:GTP603 5.0 34.1 1.0

Zinc binding site 5 out of 12 in 6dhm

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Zinc binding site 5 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn604

b:62.0
occ:1.00
OE2 C:GLU151 2.0 32.1 1.0
NE2 F:HIS57 2.1 20.9 1.0
OE1 C:GLU151 2.4 26.3 1.0
CD C:GLU151 2.5 26.8 1.0
CE1 F:HIS57 2.8 22.4 1.0
CD2 F:HIS57 3.3 17.7 1.0
NZ C:LYS154 3.6 25.1 1.0
CE C:LYS154 3.9 25.5 1.0
CG C:GLU151 3.9 24.9 1.0
ND1 F:HIS57 4.0 19.9 1.0
CG F:HIS57 4.3 19.1 1.0
OE1 F:GLN84 4.6 25.6 1.0
CB C:GLU151 4.7 21.1 1.0
NH2 C:ARG147 4.7 30.2 1.0
CD F:GLN84 4.8 25.7 1.0
CB F:ASN56 4.8 14.6 1.0
CA C:GLU151 4.9 19.2 1.0
NE2 F:GLN84 4.9 32.7 1.0

Zinc binding site 6 out of 12 in 6dhm

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Zinc binding site 6 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn605

b:37.4
occ:1.00
NE2 C:HIS450 2.0 25.5 1.0
NE2 C:HIS209 2.1 32.1 1.0
O2B C:GTP603 2.2 28.8 1.0
CD2 C:HIS209 2.9 31.6 1.0
CD2 C:HIS450 3.0 28.0 1.0
CE1 C:HIS450 3.0 21.8 1.0
CE1 C:HIS209 3.1 35.3 1.0
PB C:GTP603 3.5 36.9 1.0
O2G C:GTP603 3.5 41.2 1.0
O3' C:GTP603 3.8 35.7 1.0
NH2 C:ARG217 4.0 30.2 1.0
O3A C:GTP603 4.0 46.4 1.0
O3B C:GTP603 4.1 35.9 1.0
C3' C:GTP603 4.1 41.4 1.0
ND1 C:HIS450 4.1 23.2 1.0
CG C:HIS209 4.1 30.2 1.0
CG C:HIS450 4.1 21.9 1.0
ND1 C:HIS209 4.2 33.6 1.0
PG C:GTP603 4.2 44.1 1.0
O3G C:GTP603 4.2 37.7 1.0
CA C:GLY210 4.3 26.4 1.0
OH C:TYR262 4.3 35.6 1.0
O2' C:GTP603 4.4 41.7 1.0
NE C:ARG217 4.4 29.7 1.0
CZ C:ARG217 4.4 35.3 1.0
O1B C:GTP603 4.7 41.7 1.0
C2' C:GTP603 4.7 40.0 1.0
OG C:SER213 4.8 29.3 1.0
N C:GLY210 4.8 29.2 1.0
CG C:LYS446 5.0 42.7 1.0

Zinc binding site 7 out of 12 in 6dhm

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Zinc binding site 7 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn604

b:70.5
occ:1.00
OE1 D:GLU151 2.0 37.6 1.0
OE2 D:GLU151 2.1 37.1 1.0
NE2 A:HIS57 2.2 37.8 1.0
CD D:GLU151 2.4 30.5 1.0
CE1 A:HIS57 2.7 35.0 1.0
CD2 A:HIS57 3.5 29.7 1.0
OE1 A:GLN84 3.7 27.8 1.0
NZ D:LYS154 3.8 29.0 1.0
CG D:GLU151 3.9 19.3 1.0
ND1 A:HIS57 3.9 24.1 1.0
CE D:LYS154 4.0 31.4 1.0
CG A:HIS57 4.3 24.9 1.0
CD A:GLN84 4.6 26.4 1.0
CB D:GLU151 4.6 24.8 1.0
CA D:GLU151 4.9 20.6 1.0

Zinc binding site 8 out of 12 in 6dhm

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Zinc binding site 8 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn605

b:34.5
occ:1.00
NE2 D:HIS450 2.0 24.6 1.0
NE2 D:HIS209 2.0 19.1 1.0
O2B D:GTP603 2.2 19.8 1.0
CD2 D:HIS450 2.9 23.6 1.0
CD2 D:HIS209 3.0 23.9 1.0
CE1 D:HIS450 3.0 24.1 1.0
CE1 D:HIS209 3.0 23.8 1.0
O2G D:GTP603 3.5 35.7 1.0
PB D:GTP603 3.5 21.9 1.0
NH1 D:ARG217 3.6 27.9 1.0
O3B D:GTP603 4.1 33.3 1.0
ND1 D:HIS209 4.1 22.1 1.0
CG D:HIS209 4.1 22.5 1.0
C3' D:GTP603 4.1 32.8 1.0
ND1 D:HIS450 4.1 23.6 1.0
CG D:HIS450 4.1 21.5 1.0
O3A D:GTP603 4.1 36.8 1.0
CZ D:ARG217 4.3 23.9 1.0
PG D:GTP603 4.3 37.6 1.0
CA D:GLY210 4.3 24.5 1.0
O3' D:GTP603 4.4 27.0 1.0
O3G D:GTP603 4.5 25.3 1.0
N D:GLY210 4.7 25.9 1.0
O1B D:GTP603 4.7 25.5 1.0
CG D:LYS446 4.7 26.0 1.0
C2' D:GTP603 4.8 28.0 1.0
O2' D:GTP603 4.8 28.8 1.0
NH2 D:ARG217 4.8 29.7 1.0
OH D:TYR262 4.8 24.1 1.0
OG D:SER213 4.8 26.0 1.0
NE D:ARG217 4.9 25.6 1.0

Zinc binding site 9 out of 12 in 6dhm

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Zinc binding site 9 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn604

b:58.4
occ:1.00
OE1 E:GLU151 2.0 31.2 1.0
OE2 E:GLU151 2.0 32.0 1.0
NE2 B:HIS57 2.1 24.8 1.0
CD E:GLU151 2.3 27.7 1.0
CE1 B:HIS57 2.5 24.9 1.0
CD2 B:HIS57 3.4 24.6 1.0
NZ E:LYS154 3.5 27.5 1.0
ND1 B:HIS57 3.8 23.9 1.0
CG E:GLU151 3.8 25.0 1.0
CE E:LYS154 4.0 29.7 1.0
OE1 B:GLN84 4.1 22.4 1.0
CG B:HIS57 4.3 24.5 1.0
CB E:GLU151 4.6 25.6 1.0
CD B:GLN84 4.9 27.2 1.0
CA E:GLU151 4.9 23.6 1.0

Zinc binding site 10 out of 12 in 6dhm

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Zinc binding site 10 out of 12 in the Bovine Glutamate Dehydrogenase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Bovine Glutamate Dehydrogenase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn605

b:27.4
occ:1.00
NE2 E:HIS450 2.1 26.8 1.0
NE2 E:HIS209 2.1 25.4 1.0
O2B E:GTP603 2.4 15.5 1.0
CE1 E:HIS209 3.0 22.5 1.0
CD2 E:HIS450 3.0 20.7 1.0
CD2 E:HIS209 3.0 22.9 1.0
CE1 E:HIS450 3.1 24.1 1.0
O3B E:GTP603 3.2 24.8 1.0
PB E:GTP603 3.3 24.8 1.0
O2G E:GTP603 3.9 20.7 1.0
C3' E:GTP603 3.9 21.1 1.0
PG E:GTP603 3.9 29.4 1.0
NH2 E:ARG217 4.0 26.0 1.0
O3G E:GTP603 4.1 17.6 1.0
ND1 E:HIS209 4.1 17.9 1.0
CG E:HIS209 4.1 19.6 1.0
ND1 E:HIS450 4.2 23.6 1.0
CG E:HIS450 4.2 17.6 1.0
OH E:TYR262 4.2 27.4 1.0
NE E:ARG217 4.4 26.3 1.0
O3A E:GTP603 4.4 31.3 1.0
O3' E:GTP603 4.5 19.0 1.0
C2' E:GTP603 4.5 19.4 1.0
O1B E:GTP603 4.5 23.5 1.0
CA E:GLY210 4.6 17.3 1.0
CZ E:ARG217 4.6 27.6 1.0
O2' E:GTP603 4.7 17.0 1.0
N E:GLY210 4.7 14.6 1.0
OG E:SER213 4.7 23.0 1.0
C5' E:GTP603 4.8 22.8 1.0
C4' E:GTP603 4.9 20.0 1.0

Reference:

J.Bailey, L.Powell, L.Sinanan, J.Neal, M.Li, T.Smith, E.Bell. A Novel Mechanism of V-Type Zinc Inhibition of Glutamate Dehydrogenase Results From Disruption of Subunit Interactions Necessary For Efficient Catalysis. Febs J. V. 278 3140 2011.
ISSN: ISSN 1742-4658
PubMed: 21749647
DOI: 10.1111/J.1742-4658.2011.08240.X
Page generated: Wed Dec 16 11:40:07 2020

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