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Potassium in PDB 5ice: Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline

Enzymatic activity of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline

All present enzymatic activity of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline:
2.1.1.128;

Protein crystallography data

The structure of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline, PDB code: 5ice was solved by A.Y.Robin, M.Graindorge, C.Giustini, R.Dumas, M.Matringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.85 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.720, 109.130, 40.950, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.7

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline (pdb code 5ice). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline, PDB code: 5ice:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5ice

Go back to Potassium Binding Sites List in 5ice
Potassium binding site 1 out of 3 in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline


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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:10.0
occ:0.50
O A:HOH604 3.1 9.3 1.0
NE2 A:HIS124 3.3 9.0 1.0
CE A:MET120 4.0 10.2 1.0
CD2 A:HIS124 4.1 7.0 1.0
CE1 A:HIS124 4.3 8.9 1.0
CB A:MET120 4.4 7.4 1.0
SD A:MET120 4.8 7.2 1.0

Potassium binding site 2 out of 3 in 5ice

Go back to Potassium Binding Sites List in 5ice
Potassium binding site 2 out of 3 in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline


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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:15.2
occ:1.00
OG1 A:THR297 3.2 9.2 1.0
O A:HOH559 3.2 32.0 1.0
N A:ASP289 3.2 12.5 1.0
NH1 A:ARG300 3.3 9.7 1.0
CD A:ARG300 3.6 8.6 1.0
CB A:ASP289 3.7 12.1 1.0
ND1 A:HIS294 3.8 13.1 1.0
CA A:THR297 3.8 6.8 1.0
CB A:THR297 3.9 8.2 1.0
O A:ASP289 3.9 16.0 1.0
CA A:ASP289 4.0 13.0 1.0
CG2 A:THR297 4.1 8.1 1.0
O A:ILE287 4.1 13.5 1.0
CD1 A:LEU288 4.1 11.4 0.5
C A:LEU288 4.2 10.1 1.0
CA A:LEU288 4.3 10.6 0.5
CZ A:ARG300 4.3 9.2 1.0
CA A:LEU288 4.3 11.1 0.5
N A:THR297 4.4 6.1 1.0
NE A:ARG300 4.4 6.9 1.0
C A:ASP289 4.4 14.7 1.0
CG A:HIS294 4.6 11.2 1.0
CB A:HIS294 4.6 9.7 1.0
CE1 A:HIS294 4.7 6.4 1.0
CB A:ARG300 4.7 7.8 1.0
CG A:ARG300 4.8 8.3 1.0
CG A:LEU288 5.0 8.1 0.5
C A:THR297 5.0 7.2 1.0
C A:TYR296 5.0 6.8 1.0
O A:SER292 5.0 14.4 1.0

Potassium binding site 3 out of 3 in 5ice

Go back to Potassium Binding Sites List in 5ice
Potassium binding site 3 out of 3 in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline


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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine and Norlaudanosoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:27.8
occ:1.00
CA A:HIS155 3.4 9.2 1.0
C A:HIS155 3.5 10.3 1.0
N A:GLU157 3.5 8.8 1.0
O A:HOH538 3.5 13.8 1.0
CB A:HIS155 3.6 8.9 1.0
N A:PRO156 3.6 8.2 1.0
CD A:PRO156 3.9 9.8 1.0
CB A:GLU157 3.9 11.5 1.0
O A:HIS155 4.0 9.7 1.0
N A:LYS158 4.1 8.8 1.0
CD2 A:HIS155 4.1 10.0 1.0
CG A:HIS155 4.2 9.2 1.0
CA A:GLU157 4.2 8.8 1.0
C A:PRO156 4.4 7.5 1.0
CG A:LYS158 4.5 9.2 1.0
CA A:PRO156 4.5 9.8 1.0
CG A:PRO156 4.6 15.3 1.0
C A:GLU157 4.7 7.5 1.0
N A:HIS155 4.8 8.8 1.0
CB A:LYS158 4.9 7.0 1.0

Reference:

A.Y.Robin, C.Giustini, M.Graindorge, M.Matringe, R.Dumas. Crystal Structure of Norcoclaurine-6-O-Methyltransferase, A Key Rate-Limiting Step in the Synthesis of Benzylisoquinoline Alkaloids. Plant J. V. 87 641 2016.
ISSN: ESSN 1365-313X
PubMed: 27232113
DOI: 10.1111/TPJ.13225
Page generated: Sun Dec 13 23:59:20 2020

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