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Potassium in PDB 3ik4: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus, PDB code: 3ik4 was solved by Y.Patskovsky, R.Toro, M.Dickey, M.Iizuka, J.M.Sauder, J.A.Gerlt, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.026, 93.344, 85.914, 90.00, 112.60, 90.00
R / Rfree (%) 21.7 / 27.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus (pdb code 3ik4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus, PDB code: 3ik4:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3ik4

Go back to Potassium Binding Sites List in 3ik4
Potassium binding site 1 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus


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 Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K364

b:37.8
occ:0.50
OD2 A:ASP244 3.0 35.9 1.0
O A:HOH453 3.0 30.7 1.0
OE2 A:GLU219 3.0 39.5 1.0
OD2 A:ASP191 3.2 51.4 1.0
NZ A:LYS268 3.2 32.1 1.0
O A:HOH449 3.5 41.7 1.0
O A:HOH387 3.5 36.2 1.0
NZ A:LYS161 3.7 58.8 1.0
CD A:GLU219 4.0 39.6 1.0
CG A:ASP191 4.1 42.5 1.0
CG A:ASP244 4.1 31.1 1.0
CE A:LYS268 4.2 26.9 1.0
O A:HOH411 4.2 28.7 1.0
OE1 A:GLU219 4.3 40.8 1.0
OD1 A:ASP191 4.4 37.0 1.0
ND2 A:ASN266 4.6 26.6 1.0
CE A:LYS161 4.7 51.1 1.0
CB A:ASP244 4.9 19.2 1.0
OD1 A:ASP244 4.9 30.8 1.0

Potassium binding site 2 out of 4 in 3ik4

Go back to Potassium Binding Sites List in 3ik4
Potassium binding site 2 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus


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 Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K365

b:47.4
occ:0.50
OD1 B:ASP191 3.0 28.7 1.0
OE1 B:GLU245 3.1 31.4 1.0
OD2 B:ASP244 3.3 40.0 1.0
OE2 B:GLU219 3.8 50.9 1.0
CD B:GLU245 3.9 64.3 1.0
OE2 B:GLU245 3.9 41.4 1.0
CA B:ASN193 3.9 32.5 1.0
OD1 B:ASN193 4.0 55.2 1.0
CG B:ASP191 4.0 39.2 1.0
CB B:GLN220 4.1 24.3 1.0
CG B:ASP244 4.2 34.5 1.0
OD2 B:ASP191 4.2 47.1 1.0
CB B:ASP244 4.2 26.6 1.0
N B:ASN193 4.2 31.8 1.0
CD B:GLU219 4.5 44.9 1.0
NZ B:LYS163 4.5 56.2 1.0
O B:HOH452 4.5 22.1 1.0
CG B:GLN220 4.6 26.2 1.0
CG B:GLU219 4.7 38.6 1.0
O B:HOH455 4.7 45.2 1.0
O B:GLN220 4.7 31.4 1.0
C B:ASN193 4.7 31.5 1.0
CB B:ASN193 4.8 40.8 1.0
CG B:ASN193 4.8 49.3 1.0
N B:CYS194 4.9 29.7 1.0

Potassium binding site 3 out of 4 in 3ik4

Go back to Potassium Binding Sites List in 3ik4
Potassium binding site 3 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus


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 Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K365

b:48.5
occ:0.50
O C:HOH374 2.7 49.5 1.0
OD2 C:ASP244 2.9 49.6 1.0
O C:HOH391 3.3 35.9 1.0
OD1 C:ASN193 3.4 58.1 1.0
OE2 C:GLU245 3.4 62.4 1.0
OE1 C:GLU245 3.9 58.8 1.0
OD2 C:ASP191 3.9 43.0 1.0
CD C:GLU245 4.0 71.7 1.0
CG C:ASP244 4.1 27.2 1.0
NZ C:LYS268 4.1 27.5 1.0
OD1 C:ASP191 4.4 32.5 1.0
CG C:ASN193 4.4 59.4 1.0
NZ C:LYS163 4.5 57.6 1.0
CG C:ASP191 4.6 40.2 1.0
OE2 C:GLU219 4.7 36.3 1.0
CB C:ASP244 4.7 35.0 1.0
OD1 C:ASP244 5.0 47.8 1.0

Potassium binding site 4 out of 4 in 3ik4

Go back to Potassium Binding Sites List in 3ik4
Potassium binding site 4 out of 4 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus


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 Mandelate Racemase/Muconate Lactonizing Protein From Herpetosiphon Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K364

b:67.1
occ:0.50
OD2 D:ASP244 2.6 28.6 1.0
OE1 D:GLU245 3.0 33.4 1.0
OE2 D:GLU219 3.3 58.6 1.0
OD1 D:ASN193 3.4 61.7 1.0
OE2 D:GLU245 3.5 79.0 1.0
CG D:ASP244 3.7 43.2 1.0
CD D:GLU245 3.7 54.7 1.0
OD1 D:ASP191 3.7 37.7 1.0
OD2 D:ASP191 3.9 47.3 1.0
CB D:ASP244 4.0 25.8 1.0
CG D:ASP191 4.2 37.3 1.0
CG D:ASN193 4.3 56.8 1.0
NZ D:LYS268 4.4 54.8 1.0
CD D:GLU219 4.4 57.0 1.0
CB D:GLN220 4.6 33.0 1.0
CA D:ASN193 4.7 46.3 1.0
CB D:ASN193 4.7 51.1 1.0
OD1 D:ASP244 4.8 56.8 1.0
CG D:GLN220 4.9 32.3 1.0

Reference:

T.Lukk, A.Sakai, C.Kalyanaraman, S.D.Brown, H.J.Imker, L.Song, A.A.Fedorov, E.V.Fedorov, R.Toro, B.Hillerich, R.Seidel, Y.Patskovsky, M.W.Vetting, S.K.Nair, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Homology Models Guide Discovery of Diverse Enzyme Specificities Among Dipeptide Epimerases in the Enolase Superfamily. Proc.Natl.Acad.Sci.Usa V. 109 4122 2012.
ISSN: ISSN 0027-8424
PubMed: 22392983
DOI: 10.1073/PNAS.1112081109
Page generated: Sun Dec 13 23:19:52 2020

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