Potassium in PDB 6pi1: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.71 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.624, 163.013, 65.624, 90.00, 94.51, 90.00
R / Rfree (%) 16.3 / 19.9

Other elements in 6pi1:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide (pdb code 6pi1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6pi1

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Potassium binding site 1 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:7.6
occ:0.54
 O A:LEU217 2.4 7.7 1.0
O A:ASP195 2.4 8.9 1.0
OD1 A:ASP193 2.5 8.1 1.0
O A:HIS197 2.6 6.1 1.0
OG A:SER216 2.7 8.6 1.0
O A:ASP193 2.9 9.7 1.0
CG A:ASP193 3.3 8.7 1.0
C A:ASP195 3.4 8.6 1.0
C A:LEU217 3.5 6.7 1.0
C A:ASP193 3.5 8.8 1.0
C A:HIS197 3.6 8.2 1.0
N A:ASP195 3.7 8.5 1.0
CB A:ASP193 3.8 9.4 1.0
CB A:HIS218 3.9 4.7 1.0
N A:LEU217 3.9 7.9 1.0
CB A:SER216 3.9 7.6 1.0
CA A:ASP195 4.0 9.2 1.0
C A:VAL194 4.1 6.6 1.0
OD2 A:ASP193 4.2 10.4 1.0
N A:VAL194 4.2 7.6 1.0
CB A:ASP195 4.2 10.9 1.0
ND1 A:HIS218 4.2 5.9 1.0
CA A:HIS198 4.3 7.5 1.0
CA A:ASP193 4.3 8.6 1.0
N A:HIS198 4.3 7.5 1.0
N A:HIS197 4.3 7.9 1.0
CA A:LEU217 4.3 10.9 1.0
CA A:HIS218 4.3 6.3 1.0
CA A:VAL194 4.3 6.6 1.0
CA A:SER216 4.3 8.2 1.0
N A:GLY199 4.4 7.3 1.0
N A:HIS218 4.4 7.9 1.0
O A:HOH640 4.4 9.6 1.0
C A:PHE196 4.4 6.3 1.0
C A:SER216 4.4 7.9 1.0
CG A:HIS218 4.5 5.4 1.0
CA A:HIS197 4.6 8.0 1.0
N A:PHE196 4.6 6.9 1.0
C A:HIS198 4.6 8.3 1.0
O A:PHE196 4.7 7.6 1.0
O A:VAL194 4.8 9.4 1.0
CE1 A:HIS158 4.8 7.6 1.0
OD1 A:ASP195 4.9 9.3 1.0
CA A:PHE196 4.9 9.4 1.0
ND1 A:HIS158 5.0 7.3 1.0

Potassium binding site 2 out of 8 in 6pi1

Go back to Potassium Binding Sites List in 6pi1
Potassium binding site 2 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:11.5
occ:0.74
 O A:VAL212 2.7 14.0 1.0
O A:HOH596 2.8 11.1 1.0
O A:PHE206 2.8 10.6 1.0
O A:HOH545 2.8 12.9 1.0
O A:TYR243 2.9 12.2 1.0
O A:ARG209 2.9 13.4 1.0
C A:PHE206 3.7 10.5 1.0
C A:TYR243 3.7 10.5 1.0
CB A:PHE206 3.8 8.1 1.0
CB A:TYR243 3.9 13.3 1.0
OG1 A:THR214 3.9 10.5 1.0
C A:VAL212 3.9 10.6 1.0
C A:ARG209 4.1 13.4 1.0
N A:THR214 4.3 9.2 1.0
CA A:TYR243 4.4 10.8 1.0
CA A:PHE206 4.4 13.3 1.0
CA A:TYR207 4.5 11.1 1.0
N A:TYR207 4.5 12.7 1.0
CA A:LEU213 4.5 12.0 1.0
N A:ARG209 4.5 12.0 1.0
N A:ASN244 4.5 11.2 1.0
O A:TYR207 4.6 14.2 1.0
CG2 A:THR214 4.6 15.5 1.0
C A:TYR207 4.6 11.4 1.0
N A:LEU213 4.7 9.4 1.0
CA A:ARG209 4.7 12.0 1.0
CB A:THR214 4.7 12.7 1.0
O A:GLY240 4.7 11.9 1.0
C A:LEU213 4.8 12.9 1.0
CB A:ASN244 4.8 10.5 1.0
CB A:ARG209 4.9 11.4 1.0
CA A:ASN244 4.9 10.6 1.0
CA A:VAL212 5.0 11.8 1.0

Potassium binding site 3 out of 8 in 6pi1

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Potassium binding site 3 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:8.5
occ:0.52
 O B:LEU217 2.4 9.1 1.0
O B:ASP195 2.4 11.4 1.0
OD1 B:ASP193 2.5 8.3 1.0
O B:HIS197 2.5 8.8 1.0
OG B:SER216 2.7 10.0 1.0
O B:ASP193 3.0 12.9 1.0
CG B:ASP193 3.2 11.6 1.0
C B:ASP195 3.4 8.1 1.0
C B:LEU217 3.5 8.2 1.0
C B:HIS197 3.5 9.6 1.0
C B:ASP193 3.6 10.3 1.0
N B:ASP195 3.7 7.5 1.0
CB B:ASP193 3.8 11.1 1.0
CB B:HIS218 3.9 5.4 1.0
N B:LEU217 3.9 8.5 1.0
CB B:SER216 3.9 9.7 1.0
CA B:ASP195 4.0 9.1 1.0
C B:VAL194 4.1 9.6 1.0
OD2 B:ASP193 4.1 10.3 1.0
N B:VAL194 4.1 9.0 1.0
ND1 B:HIS218 4.2 8.2 1.0
N B:HIS197 4.2 7.6 1.0
CB B:ASP195 4.2 10.3 1.0
CA B:HIS198 4.2 8.7 1.0
N B:HIS198 4.3 11.0 1.0
CA B:ASP193 4.3 8.5 1.0
O B:HOH628 4.3 10.5 1.0
CA B:VAL194 4.3 9.1 1.0
CA B:LEU217 4.3 10.2 1.0
CA B:SER216 4.4 9.5 1.0
CA B:HIS218 4.4 6.5 1.0
N B:GLY199 4.4 7.9 1.0
N B:HIS218 4.4 10.7 1.0
C B:PHE196 4.4 11.6 1.0
C B:SER216 4.4 10.0 1.0
CA B:HIS197 4.5 9.2 1.0
CG B:HIS218 4.5 8.7 1.0
N B:PHE196 4.5 6.5 1.0
C B:HIS198 4.6 6.1 1.0
O B:PHE196 4.7 7.3 1.0
O B:VAL194 4.7 8.3 1.0
CE1 B:HIS158 4.8 12.3 1.0
OD1 B:ASP195 4.9 8.7 1.0
CA B:PHE196 4.9 8.9 1.0

Potassium binding site 4 out of 8 in 6pi1

Go back to Potassium Binding Sites List in 6pi1
Potassium binding site 4 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:11.1
occ:0.66
 O B:VAL212 2.7 15.3 1.0
O B:PHE206 2.7 12.5 1.0
O B:HOH558 2.7 17.7 1.0
O B:ARG209 2.8 14.4 1.0
O B:HOH512 2.9 15.4 1.0
O B:TYR243 3.1 15.0 1.0
C B:PHE206 3.6 13.3 1.0
CB B:TYR243 3.8 15.9 1.0
C B:TYR243 3.8 13.2 1.0
CB B:PHE206 3.8 8.9 1.0
C B:VAL212 3.9 13.9 1.0
OG1 B:THR214 3.9 12.1 1.0
C B:ARG209 4.0 15.9 1.0
N B:THR214 4.4 13.5 1.0
CA B:PHE206 4.4 12.8 1.0
N B:ARG209 4.4 12.7 1.0
CA B:TYR243 4.5 14.8 1.0
CA B:TYR207 4.5 10.7 1.0
CA B:LEU213 4.5 14.5 1.0
N B:TYR207 4.5 11.4 1.0
O B:TYR207 4.5 14.7 1.0
C B:TYR207 4.6 11.7 1.0
N B:ASN244 4.6 10.1 1.0
CA B:ARG209 4.6 12.8 1.0
N B:LEU213 4.7 12.2 1.0
CG2 B:THR214 4.7 13.4 1.0
O B:GLY240 4.8 16.7 1.0
CB B:ARG209 4.8 12.9 1.0
C B:LEU213 4.8 11.8 1.0
CB B:THR214 4.8 9.3 1.0
CA B:VAL212 4.9 13.1 1.0
CB B:ASN244 5.0 14.7 1.0
CA B:ASN244 5.0 15.6 1.0
CA B:GLY240 5.0 16.4 1.0

Potassium binding site 5 out of 8 in 6pi1

Go back to Potassium Binding Sites List in 6pi1
Potassium binding site 5 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:10.8
occ:0.57
 O C:ASP195 2.4 7.8 1.0
OD1 C:ASP193 2.4 9.8 1.0
O C:LEU217 2.4 8.0 1.0
O C:HIS197 2.6 9.3 1.0
OG C:SER216 2.7 9.1 1.0
O C:ASP193 2.9 8.5 1.0
CG C:ASP193 3.2 10.8 1.0
C C:ASP195 3.5 7.3 1.0
C C:ASP193 3.5 7.5 1.0
C C:LEU217 3.5 8.0 1.0
C C:HIS197 3.6 7.2 1.0
N C:ASP195 3.7 6.7 1.0
CB C:ASP193 3.8 7.8 1.0
CB C:HIS218 3.9 6.5 1.0
N C:LEU217 3.9 8.0 1.0
CB C:SER216 3.9 8.5 1.0
CA C:ASP195 4.0 9.0 1.0
C C:VAL194 4.1 9.6 1.0
OD2 C:ASP193 4.1 8.8 1.0
N C:VAL194 4.1 5.8 1.0
ND1 C:HIS218 4.2 7.7 1.0
N C:HIS197 4.2 6.8 1.0
CA C:ASP193 4.3 9.0 1.0
CB C:ASP195 4.3 8.0 1.0
CA C:HIS198 4.3 7.7 1.0
N C:HIS198 4.3 7.5 1.0
CA C:VAL194 4.3 8.4 1.0
CA C:SER216 4.3 7.2 1.0
N C:GLY199 4.3 7.2 1.0
O C:HOH632 4.3 9.6 1.0
CA C:LEU217 4.4 7.1 1.0
CA C:HIS218 4.4 5.6 1.0
C C:SER216 4.4 9.1 1.0
N C:HIS218 4.4 7.0 1.0
C C:PHE196 4.5 7.6 1.0
CG C:HIS218 4.5 7.3 1.0
CA C:HIS197 4.5 8.2 1.0
N C:PHE196 4.6 5.7 1.0
C C:HIS198 4.6 5.3 1.0
O C:PHE196 4.8 5.5 1.0
CE1 C:HIS158 4.8 13.9 1.0
O C:VAL194 4.8 9.2 1.0
CA C:PHE196 4.9 6.6 1.0
ND1 C:HIS158 5.0 9.5 1.0
OD1 C:ASP195 5.0 9.5 1.0

Potassium binding site 6 out of 8 in 6pi1

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Potassium binding site 6 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:10.5
occ:0.67
 O C:VAL212 2.7 13.1 1.0
O C:PHE206 2.7 12.4 1.0
O C:HOH554 2.8 13.9 1.0
O C:HOH546 2.9 14.9 1.0
O C:ARG209 2.9 15.5 1.0
O C:TYR243 3.0 10.1 1.0
C C:PHE206 3.6 12.3 1.0
C C:TYR243 3.7 14.6 1.0
CB C:TYR243 3.8 11.1 1.0
OG1 C:THR214 3.8 12.4 1.0
CB C:PHE206 3.9 10.3 1.0
C C:VAL212 4.0 11.5 1.0
C C:ARG209 4.0 17.1 1.0
N C:THR214 4.4 10.0 1.0
CA C:TYR243 4.4 12.0 1.0
CA C:PHE206 4.4 10.1 1.0
CA C:TYR207 4.4 11.2 1.0
O C:TYR207 4.5 13.1 1.0
N C:ARG209 4.5 13.7 1.0
N C:TYR207 4.5 12.0 1.0
N C:ASN244 4.5 12.1 1.0
C C:TYR207 4.5 13.2 1.0
CA C:LEU213 4.6 13.2 1.0
CA C:ARG209 4.7 13.2 1.0
CG2 C:THR214 4.7 12.8 1.0
N C:LEU213 4.7 11.8 1.0
CB C:THR214 4.8 11.2 1.0
CB C:ARG209 4.8 16.3 1.0
O C:GLY240 4.8 13.3 1.0
C C:LEU213 4.9 11.2 1.0
CB C:ASN244 4.9 12.0 1.0
CA C:ASN244 5.0 13.7 1.0
CA C:VAL212 5.0 12.5 1.0

Potassium binding site 7 out of 8 in 6pi1

Go back to Potassium Binding Sites List in 6pi1
Potassium binding site 7 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K402

b:8.0
occ:0.51
 O D:LEU217 2.4 10.2 1.0
OD1 D:ASP193 2.4 9.9 1.0
O D:ASP195 2.5 9.9 1.0
O D:HIS197 2.5 9.4 1.0
OG D:SER216 2.6 10.9 1.0
O D:ASP193 3.0 10.8 1.0
CG D:ASP193 3.2 15.1 1.0
C D:ASP195 3.5 6.9 1.0
C D:LEU217 3.5 9.9 1.0
C D:HIS197 3.5 9.9 1.0
C D:ASP193 3.5 8.8 1.0
N D:ASP195 3.7 8.8 1.0
CB D:ASP193 3.7 9.4 1.0
N D:LEU217 3.8 9.2 1.0
CB D:SER216 3.9 9.8 1.0
CB D:HIS218 3.9 8.2 1.0
CA D:ASP195 4.0 9.7 1.0
OD2 D:ASP193 4.1 12.0 1.0
C D:VAL194 4.1 9.8 1.0
N D:VAL194 4.2 9.1 1.0
CB D:ASP195 4.2 10.9 1.0
ND1 D:HIS218 4.2 9.6 1.0
N D:HIS197 4.3 9.4 1.0
CA D:ASP193 4.3 11.2 1.0
CA D:HIS198 4.3 8.2 1.0
N D:HIS198 4.3 7.9 1.0
CA D:SER216 4.3 9.6 1.0
CA D:VAL194 4.3 10.4 1.0
CA D:LEU217 4.3 11.0 1.0
O D:HOH638 4.3 9.8 1.0
N D:GLY199 4.4 12.8 1.0
CA D:HIS218 4.4 8.8 1.0
C D:PHE196 4.4 12.3 1.0
C D:SER216 4.4 9.8 1.0
N D:HIS218 4.4 9.6 1.0
CA D:HIS197 4.5 8.5 1.0
CG D:HIS218 4.5 10.0 1.0
N D:PHE196 4.6 8.6 1.0
C D:HIS198 4.6 10.5 1.0
O D:PHE196 4.7 10.9 1.0
O D:VAL194 4.8 12.8 1.0
CE1 D:HIS158 4.8 13.1 1.0
OD1 D:ASP195 4.9 10.9 1.0
CA D:PHE196 5.0 10.7 1.0
ND1 D:HIS158 5.0 10.1 1.0

Potassium binding site 8 out of 8 in 6pi1

Go back to Potassium Binding Sites List in 6pi1
Potassium binding site 8 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K403

b:13.1
occ:0.77
 O D:PHE206 2.6 14.7 1.0
O D:HOH603 2.7 15.5 1.0
O D:VAL212 2.7 17.7 1.0
O D:ARG209 2.8 16.6 1.0
O D:HOH526 3.0 14.1 1.0
O D:TYR243 3.0 12.9 1.0
C D:PHE206 3.6 15.7 1.0
C D:TYR243 3.8 15.2 1.0
CB D:PHE206 3.8 13.1 1.0
CB D:TYR243 3.8 12.9 1.0
OG1 D:THR214 3.8 14.1 1.0
C D:VAL212 3.9 12.7 1.0
C D:ARG209 3.9 17.4 1.0
CA D:PHE206 4.4 9.9 1.0
N D:ARG209 4.4 16.2 1.0
N D:THR214 4.4 11.3 1.0
CA D:TYR243 4.4 15.1 1.0
N D:TYR207 4.5 12.2 1.0
CA D:TYR207 4.5 10.2 1.0
O D:TYR207 4.5 16.0 1.0
C D:TYR207 4.6 14.7 1.0
CA D:LEU213 4.6 13.8 1.0
N D:ASN244 4.6 11.3 1.0
CA D:ARG209 4.6 17.4 1.0
CG2 D:THR214 4.7 9.5 1.0
N D:LEU213 4.7 11.3 1.0
CB D:ARG209 4.8 21.1 1.0
O D:GLY240 4.8 16.5 1.0
CB D:THR214 4.8 13.4 1.0
C D:LEU213 4.9 12.4 1.0
CB D:ASN244 4.9 14.9 1.0
CA D:VAL212 5.0 15.0 1.0
CA D:ASN244 5.0 11.9 1.0
N D:SER210 5.0 17.0 1.0

Reference:

J.D.Osko, B.W.Roose, S.A.Shinsky, D.W.Christianson. Structure and Function of the Acetylpolyamine Amidohydrolase From the Deep Earth Halophilemarinobacter Subterrani. Biochemistry V. 58 3755 2019.
ISSN: ISSN 0006-2960
PubMed: 31436969
DOI: 10.1021/ACS.BIOCHEM.9B00582
Page generated: Mon Dec 14 01:05:13 2020

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