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Potassium in PDB 5bke: Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine

Protein crystallography data

The structure of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 5bke was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 266.432, 55.494, 183.663, 90.00, 118.97, 90.00
R / Rfree (%) 18.8 / 23.3

Other elements in 5bke:

The structure of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine also contains other interesting chemical elements:

Manganese (Mn) 7 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine (pdb code 5bke). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 5bke:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 1 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:38.6
occ:1.00
O A:HOH708 2.5 44.8 1.0
O A:HOH790 3.0 59.0 1.0
O A:HOH557 3.5 24.6 1.0
NE2 A:HIS215 3.6 21.9 1.0
N A:SER118 3.7 18.2 1.0
OD1 A:ASP117 3.8 17.4 1.0
O A:HOH677 3.8 32.2 1.0
CE2 A:PHE120 3.9 22.3 1.0
CA A:ASP117 4.0 17.9 1.0
CD2 A:HIS115 4.2 15.9 1.0
CE1 A:HIS215 4.2 21.8 1.0
C A:ASP117 4.4 17.6 1.0
CB A:ASP117 4.4 17.8 1.0
CG A:ASP117 4.5 18.2 1.0
NH1 A:ARG279 4.6 22.5 1.0
CA A:SER118 4.6 20.3 1.0
NE2 A:HIS115 4.6 16.0 1.0
CD2 A:HIS215 4.6 21.7 1.0
CZ A:PHE120 4.7 22.9 1.0
CD2 A:PHE120 4.8 22.6 1.0
MN A:MN401 4.8 16.0 1.0
O A:SER116 4.9 16.4 1.0
OD1 A:ASN111 4.9 24.1 1.0
O A:HOH742 4.9 48.5 1.0
N A:ASP117 5.0 17.2 1.0

Potassium binding site 2 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 2 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:48.3
occ:1.00
O B:HOH688 2.6 29.9 1.0
O B:HOH743 3.0 46.6 1.0
NE2 B:HIS215 3.6 19.9 1.0
O B:HOH559 3.6 20.2 1.0
N B:SER118 3.7 18.3 1.0
O B:HOH675 3.7 28.3 1.0
CE2 B:PHE120 3.8 25.2 1.0
OD1 B:ASP117 3.9 18.4 1.0
CA B:ASP117 4.1 18.5 1.0
CE1 B:HIS215 4.2 20.5 1.0
CD2 B:HIS115 4.3 15.9 1.0
C B:ASP117 4.4 18.1 1.0
CB B:ASP117 4.5 18.4 1.0
CD2 B:PHE120 4.6 25.1 1.0
CA B:SER118 4.6 20.2 1.0
CG B:ASP117 4.6 19.1 1.0
NH1 B:ARG279 4.6 24.5 1.0
CD2 B:HIS215 4.7 19.4 1.0
CZ B:PHE120 4.7 26.0 1.0
NE2 B:HIS115 4.7 15.8 1.0
O B:SER116 4.9 18.2 1.0
MN B:MN401 4.9 16.8 1.0
OD1 B:ASN111 5.0 23.9 1.0

Potassium binding site 3 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 3 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K403

b:62.6
occ:1.00
O D:HOH572 2.7 48.2 1.0
O D:HOH654 2.8 51.2 1.0
O D:HOH646 3.4 61.2 1.0
O D:HOH528 3.6 39.5 1.0
N D:SER118 3.8 30.8 1.0
OD1 D:ASP117 3.8 32.8 1.0
O D:HOH597 3.8 33.2 1.0
NE2 D:HIS215 3.9 26.8 1.0
CE2 D:PHE120 4.1 36.2 1.0
CA D:ASP117 4.1 30.2 1.0
NH1 D:ARG279 4.2 39.7 1.0
CE1 D:HIS215 4.4 27.5 1.0
CD2 D:HIS115 4.4 31.4 1.0
CG D:ASP117 4.5 31.8 1.0
C D:ASP117 4.5 30.4 1.0
CB D:ASP117 4.5 31.3 1.0
NE2 D:HIS115 4.7 32.2 1.0
CA D:SER118 4.7 32.5 1.0
CZ D:PHE120 4.7 37.2 1.0
MN D:MN401 4.7 29.9 1.0
NH2 D:ARG279 4.8 39.1 1.0
OD1 D:ASN111 4.9 37.1 1.0
OG D:SER118 4.9 33.6 1.0
CD2 D:HIS215 5.0 27.3 1.0
CZ D:ARG279 5.0 40.0 1.0

Potassium binding site 4 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 4 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K403

b:69.5
occ:1.00
O E:HOH543 2.2 36.6 1.0
O E:HOH511 3.3 24.6 1.0
OD1 E:ASP117 3.7 31.3 1.0
N E:SER118 3.9 29.9 1.0
NH1 E:ARG279 4.0 44.0 1.0
O E:HOH596 4.2 34.1 1.0
CE2 E:PHE120 4.2 39.4 1.0
CA E:ASP117 4.3 28.1 1.0
CG E:ASP117 4.5 30.4 1.0
NE2 E:HIS215 4.5 30.5 1.0
NH2 E:ARG279 4.5 45.2 1.0
CB E:ASP117 4.6 28.1 1.0
C E:ASP117 4.7 29.1 1.0
CD2 E:HIS115 4.7 26.4 1.0
OG E:SER118 4.7 37.3 1.0
CZ E:PHE120 4.7 40.2 1.0
MN E:MN401 4.8 27.2 1.0
CZ E:ARG279 4.8 43.8 1.0
CA E:SER118 4.9 32.9 1.0
NE2 E:HIS115 4.9 26.7 1.0
OD1 E:ASN111 4.9 35.0 1.0

Potassium binding site 5 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 5 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K403

b:45.8
occ:1.00
O F:HOH718 2.6 39.7 1.0
NE2 F:HIS215 3.4 20.9 1.0
O F:HOH513 3.5 17.3 1.0
N F:SER118 3.6 17.2 1.0
O F:HOH713 3.7 40.2 1.0
CA F:ASP117 4.0 17.3 1.0
OD1 F:ASP117 4.0 16.3 1.0
CE2 F:PHE120 4.0 21.0 1.0
CE1 F:HIS215 4.1 20.5 1.0
CD2 F:HIS115 4.1 14.8 1.0
C F:ASP117 4.3 17.1 1.0
CD2 F:HIS215 4.4 20.7 1.0
CB F:ASP117 4.5 17.5 1.0
CA F:SER118 4.5 19.0 1.0
NE2 F:HIS115 4.6 14.8 1.0
CG F:ASP117 4.6 17.9 1.0
NH1 F:ARG279 4.7 43.6 1.0
O F:SER116 4.8 16.5 1.0
CZ F:PHE120 4.8 22.2 1.0
MN F:MN401 4.8 17.3 1.0
CD2 F:PHE120 4.8 20.9 1.0
O F:HOH656 4.9 42.3 1.0
CE1 F:PHE107 5.0 43.3 1.0
N F:ASP117 5.0 16.9 1.0

Potassium binding site 6 out of 6 in 5bke

Go back to Potassium Binding Sites List in 5bke
Potassium binding site 6 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


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 Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K403

b:48.7
occ:1.00
O G:HOH681 2.6 35.2 1.0
O G:HOH551 3.3 18.0 1.0
O G:HOH695 3.5 34.1 1.0
N G:SER118 3.7 18.7 1.0
NE2 G:HIS215 3.7 21.6 1.0
OD1 G:ASP117 3.9 17.1 1.0
CE2 G:PHE120 3.9 29.9 1.0
CA G:ASP117 4.1 18.7 1.0
CE1 G:HIS215 4.3 21.1 1.0
CD2 G:HIS115 4.4 16.6 1.0
NH1 G:ARG279 4.4 31.7 1.0
C G:ASP117 4.5 18.3 1.0
CE1 G:PHE107 4.5 38.8 1.0
CG G:ASP117 4.5 18.4 1.0
CB G:ASP117 4.5 18.1 1.0
CZ G:PHE120 4.6 29.4 1.0
CA G:SER118 4.7 20.6 1.0
NE2 G:HIS115 4.8 17.1 1.0
O G:HOH508 4.8 51.6 1.0
CD2 G:HIS215 4.8 20.6 1.0
MN G:MN401 4.9 17.5 1.0
CD2 G:PHE120 4.9 29.0 1.0

Reference:

J.R.Chekan, C.Ongpipattanakul, T.R.Wright, B.Zhang, J.M.Bollinger Jr., L.J.Rajakovich, C.Krebs, R.M.Cicchillo, S.K.Nair. Molecular Basis For Enantioselective Herbicide Degradation Imparted By Aryloxyalkanoate Dioxygenases in Transgenic Plants. Proc.Natl.Acad.Sci.Usa V. 116 13299 2019.
ISSN: ESSN 1091-6490
PubMed: 31209034
DOI: 10.1073/PNAS.1900711116
Page generated: Mon Aug 12 13:00:03 2024

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