Atomistry » Potassium » PDB 5g17-5imu » 5gud
Atomistry »
  Potassium »
    PDB 5g17-5imu »
      5gud »

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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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

Go back to Potassium Binding Sites List in 5gud
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: Sun Dec 13 23:58:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy