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Potassium in PDB 4xg1: Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp

Enzymatic activity of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp

All present enzymatic activity of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp:
4.1.1.20;

Protein crystallography data

The structure of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp, PDB code: 4xg1 was solved by M.G.Peverelli, J.M.Wubben, S.Panjikar, M.A.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.960, 103.130, 93.590, 90.00, 94.77, 90.00
R / Rfree (%) 21.1 / 24.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp (pdb code 4xg1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp, PDB code: 4xg1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 4xg1

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Potassium binding site 1 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:45.5
occ:1.00
 O A:LEU192 2.7 45.7 1.0
O A:LEU189 2.7 49.0 1.0
O A:HOH647 2.8 9.1 1.0
O A:SER187 3.1 40.7 1.0
O A:HOH677 3.2 27.9 1.0
O A:ALA186 3.3 50.8 1.0
C A:LEU192 3.6 39.3 1.0
CA A:SER187 3.8 51.5 1.0
C A:SER187 3.8 46.9 1.0
C A:LEU189 3.9 50.4 1.0
C A:ALA186 4.2 51.8 1.0
CA A:GLU193 4.3 38.9 1.0
N A:GLU193 4.3 38.3 1.0
N A:SER187 4.4 52.6 1.0
CB A:LEU192 4.6 38.0 1.0
N A:LEU189 4.6 59.5 1.0
CA A:LEU192 4.6 38.3 1.0
N A:ILE194 4.7 37.7 1.0
O A:HOH691 4.7 26.3 1.0
N A:LEU192 4.8 39.9 1.0
CA A:LEU189 4.8 53.9 1.0
N A:GLU190 4.9 46.2 1.0
O A:GLU190 4.9 46.1 1.0
CA A:GLU190 4.9 43.5 1.0
N A:ASP188 4.9 48.7 1.0
CB A:SER187 5.0 49.9 1.0

Potassium binding site 2 out of 6 in 4xg1

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Potassium binding site 2 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:24.0
occ:1.00
 N D:ILE418 3.3 16.5 1.0
N A:ILE418 3.3 16.3 1.0
CA D:HIS417 3.7 15.8 1.0
CA A:HIS417 3.7 14.2 1.0
C D:HIS417 3.9 16.0 1.0
C A:HIS417 4.0 15.0 1.0
CG1 D:ILE418 4.1 19.2 1.0
ND1 A:HIS417 4.1 16.1 1.0
CB A:HIS417 4.1 15.0 1.0
CG1 A:ILE418 4.2 22.8 1.0
CB D:HIS417 4.2 16.4 1.0
ND1 D:HIS417 4.2 18.1 1.0
CA D:ILE418 4.3 18.7 1.0
CG2 D:ILE418 4.3 17.6 1.0
CA A:ILE418 4.4 17.9 1.0
O A:ILE418 4.4 14.4 1.0
CB D:ILE418 4.4 18.5 1.0
O D:ILE418 4.4 22.2 1.0
O D:GLU416 4.5 12.7 1.0
O A:GLU416 4.5 12.0 1.0
CG2 A:ILE418 4.6 18.6 1.0
CB A:ILE418 4.6 19.9 1.0
CG A:HIS417 4.6 16.1 1.0
CG D:HIS417 4.7 17.6 1.0
N D:HIS417 4.8 14.2 1.0
C D:ILE418 4.8 20.8 1.0
N A:HIS417 4.9 13.0 1.0
C A:ILE418 4.9 17.6 1.0
CD1 D:ILE418 4.9 19.5 1.0

Potassium binding site 3 out of 6 in 4xg1

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Potassium binding site 3 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:33.7
occ:1.00
 O B:HOH649 2.6 10.1 1.0
O B:LEU192 3.0 40.5 1.0
O B:SER187 3.1 37.3 1.0
O B:LEU189 3.1 24.0 1.0
O B:ALA186 3.5 32.1 1.0
CA B:SER187 3.6 38.5 1.0
C B:SER187 3.7 37.0 1.0
C B:LEU192 3.9 33.3 1.0
CA B:GLU193 4.2 36.1 1.0
C B:ALA186 4.2 35.7 1.0
N B:SER187 4.3 38.8 1.0
C B:LEU189 4.4 33.1 1.0
N B:GLU193 4.4 33.6 1.0
N B:ILE194 4.5 33.5 1.0
CB B:SER187 4.7 39.6 1.0
CD1 B:ILE194 4.8 35.7 1.0
CG1 B:ILE194 4.8 33.1 1.0
N B:LEU189 4.8 38.5 1.0
CA B:LEU192 4.9 32.8 1.0
CB B:LEU192 4.9 31.2 1.0
N B:ASP188 4.9 38.1 1.0
C B:GLU193 4.9 36.4 1.0

Potassium binding site 4 out of 6 in 4xg1

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Potassium binding site 4 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:56.5
occ:1.00
 S A:SCN501 3.4 65.9 1.0
C A:SCN501 3.8 53.3 1.0
O B:SER378 3.9 6.5 1.0
O A:HOH644 3.9 16.3 1.0
NH1 B:ARG404 4.2 7.8 1.0
NH2 B:ARG89 4.4 13.7 1.0
O B:HOH671 4.4 19.3 1.0
N A:SCN501 4.4 42.0 1.0
OE2 A:GLU416 4.4 11.1 1.0
CZ B:ARG404 4.5 8.0 1.0
C B:SER378 4.5 6.6 1.0
NE B:ARG404 4.7 8.5 1.0
NH2 B:ARG389 4.8 21.9 1.0
CA B:THR379 4.8 5.8 1.0
OG B:SER381 4.8 6.5 1.0
CD B:ARG404 4.9 8.9 1.0
OE1 B:GLU392 4.9 19.1 1.0
O A:LEU412 4.9 12.6 1.0
CB B:SER378 4.9 7.5 1.0
N B:THR379 5.0 6.1 1.0

Potassium binding site 5 out of 6 in 4xg1

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Potassium binding site 5 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:50.5
occ:1.00
 O C:LEU189 2.6 44.7 1.0
O C:HOH656 2.7 16.9 1.0
O C:LEU192 2.7 34.8 1.0
O C:ALA186 2.9 37.9 1.0
O C:SER187 3.0 37.4 1.0
C C:SER187 3.6 40.9 1.0
CA C:SER187 3.6 44.4 1.0
C C:LEU192 3.6 34.2 1.0
C C:LEU189 3.8 43.8 1.0
C C:ALA186 3.8 39.9 1.0
N C:SER187 4.1 43.6 1.0
N C:LEU189 4.3 49.3 1.0
N C:GLU193 4.3 37.7 1.0
CB C:LEU192 4.4 33.8 1.0
CA C:GLU193 4.4 39.1 1.0
CA C:LEU192 4.5 35.4 1.0
CA C:LEU189 4.6 45.3 1.0
N C:LEU192 4.7 37.2 1.0
N C:ASP188 4.7 42.1 1.0
N C:ILE194 4.8 34.6 1.0
O C:HOH705 4.8 31.6 1.0
CB C:SER187 4.8 47.4 1.0
N C:GLU190 4.8 43.2 1.0
OG C:SER187 4.9 48.2 1.0

Potassium binding site 6 out of 6 in 4xg1

Go back to Potassium Binding Sites List in 4xg1
Potassium binding site 6 out of 6 in the Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Psychromonas Ingrahamii Diaminopimelate Decarboxylase with Llp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:40.9
occ:1.00
 O D:HOH642 2.4 18.3 1.0
O D:LEU189 2.8 45.1 1.0
O D:LEU192 2.9 52.8 1.0
O D:SER187 2.9 65.2 1.0
O D:ALA186 3.2 72.2 1.0
C D:SER187 3.5 66.0 1.0
CA D:SER187 3.6 66.5 1.0
C D:LEU192 3.8 47.5 1.0
C D:LEU189 4.0 53.1 1.0
C D:ALA186 4.1 67.3 1.0
N D:SER187 4.2 69.0 1.0
CA D:GLU193 4.4 51.5 1.0
N D:GLU193 4.5 47.7 1.0
N D:LEU189 4.5 60.2 1.0
CB D:LEU192 4.7 51.7 1.0
N D:ASP188 4.7 67.3 1.0
CB D:SER187 4.7 67.4 1.0
CA D:LEU192 4.8 49.6 1.0
N D:ILE194 4.8 52.3 1.0
CA D:LEU189 4.8 58.6 1.0
N D:LEU192 4.9 51.5 1.0
CD1 D:ILE194 5.0 56.6 1.0

Reference:

M.G.Peverelli, J.Newman, S.Panjikar, M.A.Perugini. Expression to Crystallization of Diaminopimelate Decarboxylase From the Psychrophile Psychromonas Ingrahamii To Be Published.
Page generated: Sun Dec 13 23:51:56 2020

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