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Potassium in PDB 5gud: Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)

Protein crystallography data

The structure of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex), PDB code: 5gud was solved by T.Tomita, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.83 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.587, 127.671, 126.627, 90.00, 106.70, 90.00
R / Rfree (%) 19.2 / 22.6

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Potassium atom in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) (pdb code 5gud). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 14 binding sites of Potassium where determined in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex), PDB code: 5gud:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 14 in 5gud

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Potassium binding site 1 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:30.3
occ:1.00
 O A:ALA295 2.6 25.6 1.0
O A:HOH943 2.6 34.5 1.0
O A:ALA301 2.7 24.8 1.0
O A:HOH630 2.7 39.9 1.0
O A:ILE298 2.8 27.3 1.0
C A:ALA295 3.7 24.5 1.0
C A:ILE298 3.8 28.2 1.0
C A:ALA301 3.8 24.9 1.0
N A:ALA301 4.0 26.4 1.0
N A:GLY300 4.1 29.1 1.0
CA A:ALA295 4.4 24.1 1.0
CA A:ALA301 4.4 25.4 1.0
CA A:GLU299 4.4 30.5 1.0
N A:GLU299 4.5 28.8 1.0
C A:GLU299 4.6 29.8 1.0
N A:ILE298 4.7 27.1 1.0
N A:ASP296 4.7 25.3 1.0
CB A:ALA301 4.8 25.6 1.0
CB A:ALA295 4.8 23.6 1.0
CA A:ILE298 4.8 27.3 1.0
C A:ASP296 4.8 26.5 1.0
O A:HOH835 4.8 31.2 1.0
O A:ASP296 4.8 25.4 1.0
C A:GLY300 4.9 28.0 1.0
CA A:ASP296 4.9 26.0 1.0
N A:THR302 4.9 24.0 1.0
CA A:GLY300 5.0 28.4 1.0

Potassium binding site 2 out of 14 in 5gud

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Potassium binding site 2 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:22.0
occ:1.00
 O A:HOH917 2.6 34.8 1.0
O A:ILE158 2.6 12.6 1.0
O A:HOH1017 2.8 25.3 1.0
O A:HIS155 2.9 13.8 1.0
OH A:TYR183 2.9 14.1 1.0
O A:HOH1047 2.9 31.8 1.0
CE1 A:TYR183 3.7 11.9 1.0
CZ A:TYR183 3.7 14.3 1.0
C A:ILE158 3.8 12.5 1.0
C A:HIS155 4.0 12.3 1.0
O A:HOH771 4.0 42.8 1.0
CA A:ARG156 4.5 15.3 1.0
N A:ILE158 4.5 13.3 1.0
C A:ARG156 4.6 15.6 1.0
O A:HOH1072 4.6 39.7 1.0
CA A:GLY159 4.6 11.9 1.0
O A:HOH1068 4.6 37.6 1.0
N A:GLY159 4.6 12.1 1.0
O A:ARG156 4.7 17.2 1.0
O A:HOH1080 4.7 29.8 1.0
N A:ARG156 4.7 13.3 1.0
O A:HOH1036 4.7 35.0 1.0
CA A:ILE158 4.8 12.3 1.0
CD2 A:HIS155 4.8 12.8 1.0
O A:HOH638 4.9 18.5 1.0
CA A:HIS155 5.0 12.3 1.0
CG1 A:ILE158 5.0 12.5 1.0

Potassium binding site 3 out of 14 in 5gud

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Potassium binding site 3 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:32.8
occ:1.00
 O A:SER232 2.6 21.2 1.0
O A:HOH1022 2.7 42.4 1.0
O A:HOH954 2.7 25.1 1.0
O A:SER230 2.9 21.7 1.0
OG A:SER230 3.0 25.3 1.0
C A:SER230 3.8 21.2 1.0
C A:SER232 3.8 20.9 1.0
NE2 A:GLN234 3.9 26.4 1.0
N A:SER230 4.1 22.6 1.0
CB A:SER230 4.1 22.7 1.0
CA A:SER230 4.2 22.2 1.0
N A:SER232 4.3 20.2 1.0
CD A:GLN234 4.4 24.3 1.0
O A:HOH608 4.5 34.5 1.0
CA A:SER232 4.6 20.9 1.0
CG A:GLN234 4.6 21.9 1.0
C A:ILE231 4.7 20.4 1.0
N A:GLY233 4.8 20.4 1.0
N A:ILE231 4.8 20.5 1.0
CA A:GLY233 4.8 20.9 1.0
CB A:SER232 4.9 20.8 1.0

Potassium binding site 4 out of 14 in 5gud

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Potassium binding site 4 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:25.4
occ:1.00
 O B:ILE158 2.7 16.5 1.0
O B:HOH908 2.7 22.3 1.0
O B:HOH922 2.8 33.0 1.0
O B:HIS155 2.8 14.4 1.0
OH B:TYR183 2.9 16.0 1.0
CZ B:TYR183 3.8 16.6 1.0
CE1 B:TYR183 3.8 15.2 1.0
C B:ILE158 3.8 15.6 1.0
C B:HIS155 4.0 15.2 1.0
CA B:ARG156 4.5 17.5 1.0
O B:HOH921 4.5 31.4 1.0
N B:ILE158 4.5 15.4 1.0
CA B:GLY159 4.5 15.5 1.0
C B:ARG156 4.6 17.6 1.0
N B:GLY159 4.6 15.3 1.0
O B:ARG156 4.7 18.6 1.0
O B:HOH927 4.7 33.1 1.0
N B:ARG156 4.7 16.8 1.0
CA B:ILE158 4.8 15.4 1.0
CD2 B:HIS155 4.8 13.5 1.0
O B:HOH708 4.8 19.0 1.0
O B:HOH939 4.9 28.8 1.0
CA B:HIS155 5.0 14.3 1.0
CG1 B:ILE158 5.0 15.9 1.0

Potassium binding site 5 out of 14 in 5gud

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Potassium binding site 5 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:23.8
occ:1.00
 O C:HOH895 2.5 38.2 1.0
O C:HOH946 2.7 23.0 1.0
O C:ILE158 2.8 13.9 1.0
O C:HIS155 2.8 14.0 1.0
OH C:TYR183 2.9 15.1 1.0
O C:HOH983 3.0 34.1 1.0
CE1 C:TYR183 3.7 14.1 1.0
CZ C:TYR183 3.8 14.0 1.0
C C:ILE158 3.9 13.3 1.0
C C:HIS155 4.0 14.6 1.0
O C:HOH941 4.5 34.6 1.0
CA C:ARG156 4.5 17.1 1.0
O C:HOH997 4.5 36.1 1.0
N C:ILE158 4.6 13.3 1.0
C C:ARG156 4.6 16.9 1.0
CA C:GLY159 4.6 12.2 1.0
O C:ARG156 4.7 17.9 1.0
N C:ARG156 4.7 15.8 1.0
N C:GLY159 4.7 12.1 1.0
O C:HOH639 4.8 20.4 1.0
CD2 C:HIS155 4.8 12.9 1.0
O C:HOH993 4.8 32.8 1.0
CA C:ILE158 4.8 12.4 1.0
CA C:HIS155 5.0 14.0 1.0
OE1 C:GLU191 5.0 18.7 1.0

Potassium binding site 6 out of 14 in 5gud

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Potassium binding site 6 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:43.2
occ:1.00
 O C:SER232 2.7 31.1 1.0
O C:HOH746 2.8 36.0 1.0
O C:SER230 2.9 32.0 1.0
OG C:SER230 3.1 35.5 1.0
NE2 C:GLN234 3.8 33.0 1.0
C C:SER230 3.8 32.2 1.0
C C:SER232 3.9 31.0 1.0
N C:SER230 4.1 32.2 1.0
CB C:SER230 4.2 32.7 1.0
CA C:SER230 4.2 32.5 1.0
O C:HOH677 4.4 48.1 1.0
N C:SER232 4.5 30.5 1.0
CD C:GLN234 4.5 33.9 1.0
CA C:SER232 4.7 30.9 1.0
CG C:GLN234 4.7 32.5 1.0
C C:ILE231 4.8 31.1 1.0
N C:ILE231 4.8 31.4 1.0
N C:GLY233 4.9 31.4 1.0
CB C:SER232 5.0 30.8 1.0

Potassium binding site 7 out of 14 in 5gud

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Potassium binding site 7 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:19.0
occ:1.00
 O D:ALA387 2.7 17.4 1.0
O B:ALA387 2.7 20.3 1.0
O B:HOH780 2.7 21.6 1.0
O F:HOH878 2.7 24.0 1.0
O D:HOH831 2.7 22.1 1.0
O F:ALA387 2.8 16.5 1.0
O D:HOH760 3.2 42.6 1.0
C B:ALA387 3.7 21.3 1.0
C D:ALA387 3.7 17.8 1.0
C F:ALA387 3.7 17.4 1.0
CA B:ALA387 4.0 20.8 1.0
CA F:ALA387 4.1 16.1 1.0
CA D:ALA387 4.1 17.2 1.0
CB B:ALA387 4.1 20.4 1.0
CB F:ALA387 4.2 16.9 1.0
CB D:ALA387 4.3 16.5 1.0
O B:HOH812 4.5 25.6 1.0
O F:HOH850 4.5 20.8 1.0
O D:HOH749 4.5 25.3 1.0
O B:HOH717 4.6 28.7 1.0
N D:SER388 4.8 18.8 1.0
O F:HOH716 4.8 22.5 1.0
N B:SER388 4.9 23.0 1.0
N F:SER388 4.9 18.2 1.0
OH D:TYR161 4.9 15.7 1.0
O D:HOH724 4.9 22.4 1.0
OH B:TYR161 4.9 14.0 1.0

Potassium binding site 8 out of 14 in 5gud

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Potassium binding site 8 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:22.2
occ:1.00
 O D:HOH906 2.6 36.7 1.0
O D:ILE158 2.7 15.2 1.0
O D:HOH940 2.7 24.6 1.0
OH D:TYR183 2.8 16.0 1.0
O D:HIS155 2.8 15.5 1.0
O D:HOH932 3.0 33.7 1.0
CZ D:TYR183 3.7 15.1 1.0
CE1 D:TYR183 3.7 14.7 1.0
C D:ILE158 3.8 15.3 1.0
C D:HIS155 4.0 15.1 1.0
NH1 D:ARG162 4.3 28.8 1.0
O D:HOH949 4.4 38.6 1.0
CA D:ARG156 4.4 17.7 1.0
N D:ILE158 4.5 14.7 1.0
C D:ARG156 4.5 17.8 1.0
CA D:GLY159 4.6 14.8 1.0
N D:GLY159 4.6 15.6 1.0
O D:ARG156 4.7 19.3 1.0
N D:ARG156 4.7 16.5 1.0
O D:HOH962 4.7 36.8 1.0
CA D:ILE158 4.8 15.7 1.0
CD2 D:HIS155 4.8 13.1 1.0
O D:HOH969 4.8 31.8 1.0
O D:HOH638 4.9 19.6 1.0
CA D:HIS155 5.0 14.7 1.0
OE1 D:GLU191 5.0 24.3 1.0
CE2 D:TYR183 5.0 13.9 1.0

Potassium binding site 9 out of 14 in 5gud

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Potassium binding site 9 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:13.3
occ:1.00
 O A:HOH886 2.6 15.6 1.0
O E:ALA387 2.7 14.0 1.0
O C:ALA387 2.7 12.7 1.0
O E:HOH886 2.7 16.4 1.0
O C:HOH785 2.7 15.5 1.0
O A:ALA387 2.7 12.4 1.0
C E:ALA387 3.7 12.8 1.0
C A:ALA387 3.7 13.5 1.0
C C:ALA387 3.7 13.2 1.0
CA A:ALA387 4.0 13.0 1.0
CA C:ALA387 4.0 13.1 1.0
CA E:ALA387 4.1 12.9 1.0
CB A:ALA387 4.1 13.1 1.0
CB C:ALA387 4.2 13.4 1.0
CB E:ALA387 4.2 11.6 1.0
O A:HOH813 4.5 18.1 1.0
O E:HOH851 4.5 19.3 1.0
O C:HOH820 4.5 18.6 1.0
O A:HOH758 4.7 19.1 1.0
O C:HOH736 4.7 19.3 1.0
O E:HOH764 4.8 18.9 1.0
N E:SER388 4.8 13.5 1.0
OH A:TYR161 4.8 13.9 1.0
OH E:TYR161 4.8 11.5 1.0
N A:SER388 4.9 15.1 1.0
N C:SER388 4.9 14.4 1.0
OH C:TYR161 4.9 15.0 1.0

Potassium binding site 10 out of 14 in 5gud

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Potassium binding site 10 out of 14 in the Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Glutamate Dehydrogenase From Corynebacterium Glutamicum (Alpha- Iminoglutarate/Nadp+ Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K504

b:28.1
occ:1.00
 O E:SER232 2.5 21.7 1.0
O E:HOH941 2.7 28.6 1.0
O E:HOH1055 2.7 38.8 1.0
OG E:SER230 2.9 25.1 1.0
O E:SER230 2.9 21.8 1.0
C E:SER230 3.7 21.6 1.0
C E:SER232 3.8 21.5 1.0
O E:HOH970 3.8 43.5 1.0
NE2 E:GLN234 3.9 25.5 1.0
CB E:SER230 4.0 23.2 1.0
N E:SER230 4.1 22.9 1.0
CA E:SER230 4.1 22.4 1.0
N E:SER232 4.3 20.5 1.0
CD E:GLN234 4.5 22.5 1.0
CA E:SER232 4.6 21.2 1.0
O E:HOH650 4.6 33.3 1.0
CG E:GLN234 4.6 21.3 1.0
C E:ILE231 4.6 20.9 1.0
N E:ILE231 4.7 21.0 1.0
N E:GLY233 4.7 21.4 1.0
CA E:GLY233 4.8 21.6 1.0
CB E:SER232 5.0 21.9 1.0

Reference:

T.Tomita, L.Yin, S.Nakamura, S.Kosono, T.Kuzuyama, M.Nishiyama. Crystal Structure of the 2-Iminoglutarate-Bound Complex of Glutamate Dehydrogenase From Corynebacterium Glutamicum Febs Lett. V. 591 1611 2017.
ISSN: ISSN 1873-3468
PubMed: 28486765
DOI: 10.1002/1873-3468.12667
Page generated: Mon Aug 12 13:46:10 2024

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