Calcium in PDB 8uke: Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah

The structure of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah, PDB code: 8uke was solved by W.Kim, Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.69 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.973, 79.581, 98.379, 90, 105.62, 90
R / Rfree (%)	18.9 / 24.9

The binding sites of Calcium atom in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah (pdb code 8uke). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah, PDB code: 8uke:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.8 occ:1.00 OD2 A:ASP181 2.3 15.4 1.0 OD1 A:ASP155 2.3 18.0 1.0 OD1 A:ASN182 2.5 15.0 1.0 OD2 A:ASP155 2.9 17.6 1.0 CG A:ASP155 2.9 15.2 1.0 CG A:ASP181 3.4 13.8 1.0 CG A:ASN182 3.5 18.5 1.0 ND2 A:ASN182 3.9 15.1 1.0 CB A:ASP181 4.0 12.7 1.0 O A:MET53 4.1 23.7 1.0 CG2 A:VAL55 4.3 15.9 1.0 NZ A:LYS158 4.3 16.4 1.0 OD1 A:ASP181 4.4 17.8 1.0 CB A:ASP155 4.4 15.4 1.0 CB A:ASN182 4.9 15.1 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:17.7 occ:1.00 O C:VAL104 2.3 18.1 1.0 OE1 A:GLU129 2.4 22.1 1.0 O A:VAL104 2.4 18.7 1.0 OE1 C:GLU129 2.4 21.2 1.0 CD A:GLU129 3.4 21.8 1.0 CD C:GLU129 3.4 22.8 1.0 C A:VAL104 3.5 19.2 1.0 C C:VAL104 3.6 15.8 1.0 CG C:GLU129 3.8 17.6 1.0 CG A:GLU129 3.9 16.1 1.0 CA A:ASN105 4.2 15.8 1.0 CA C:ASN105 4.3 17.8 1.0 N A:ASN105 4.3 18.8 1.0 N C:ASN105 4.4 17.4 1.0 N A:LYS106 4.4 18.6 1.0 OE2 A:GLU129 4.5 16.3 1.0 OE2 C:GLU129 4.5 20.3 1.0 N C:LYS106 4.6 18.8 1.0 CA C:VAL104 4.6 15.2 1.0 CA A:VAL104 4.6 18.6 1.0 C A:ASN105 4.9 21.5 1.0 CB C:VAL104 4.9 16.1 1.0 CB A:VAL104 4.9 18.3 1.0 C C:ASN105 5.0 20.4 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:16.3 occ:1.00 OD1 B:ASP155 2.4 21.0 1.0 OD1 B:ASN182 2.4 10.2 1.0 O B:HOH425 2.5 17.0 1.0 OD2 B:ASP181 2.6 17.1 1.0 CG B:ASP155 3.2 21.2 1.0 OD2 B:ASP155 3.3 20.5 1.0 CG B:ASN182 3.3 14.3 1.0 CG B:ASP181 3.5 15.9 1.0 ND2 B:ASN182 3.6 11.2 1.0 CB B:ASP181 3.6 17.5 1.0 NZ B:LYS158 4.1 14.7 1.0 CB B:ASP155 4.6 18.4 1.0 OD1 B:ASP181 4.6 15.3 1.0 O B:MET53 4.7 20.0 1.0 CB B:ASN182 4.7 10.5 1.0 N B:ASN182 4.8 16.4 1.0 C B:ASP181 4.9 16.1 1.0 CA B:ASP181 4.9 17.0 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:21.5 occ:1.00 OE1 B:GLU129 2.3 18.5 1.0 O B:VAL104 2.4 20.3 1.0 CD B:GLU129 3.4 23.1 1.0 C B:VAL104 3.6 20.8 1.0 CG B:GLU129 3.9 23.2 1.0 CA B:ASN105 4.3 21.0 1.0 N B:ASN105 4.4 18.6 1.0 OE2 B:GLU129 4.5 15.4 1.0 N B:LYS106 4.6 20.8 1.0 CA B:VAL104 4.6 17.9 1.0 CB B:VAL104 4.9 23.2 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:26.2 occ:1.00 OD1 C:ASP155 2.4 24.2 1.0 OD1 C:ASN182 2.4 17.1 1.0 O C:HOH413 2.5 22.2 1.0 OD2 C:ASP181 2.6 17.3 1.0 CG C:ASP155 3.1 19.6 1.0 OD2 C:ASP155 3.2 23.3 1.0 CG C:ASN182 3.3 19.6 1.0 CG C:ASP181 3.6 16.4 1.0 ND2 C:ASN182 3.6 13.6 1.0 CB C:ASP181 4.0 15.0 1.0 NZ C:LYS158 4.1 17.9 1.0 O C:MET53 4.5 22.5 1.0 CB C:ASP155 4.6 16.2 1.0 OD1 C:ASP181 4.6 16.2 1.0 CB C:ASN182 4.7 17.9 1.0 CG2 C:VAL55 4.8 23.8 1.0 O C:ASP155 5.0 16.1 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:18.4 occ:1.00 OD1 D:ASP155 2.4 26.4 1.0 OD1 D:ASN182 2.4 14.8 1.0 OD2 D:ASP181 2.4 16.2 1.0 O D:HOH402 2.5 21.4 1.0 O D:HOH452 2.7 19.2 1.0 CG D:ASP155 2.9 14.1 1.0 OD2 D:ASP155 3.0 14.1 1.0 CG D:ASN182 3.3 16.8 1.0 CG D:ASP181 3.4 17.8 1.0 ND2 D:ASN182 3.4 12.6 1.0 CB D:ASP181 3.8 16.4 1.0 CB D:ASP155 4.3 14.6 1.0 OD1 D:ASP181 4.4 19.7 1.0 O D:MET53 4.5 21.8 1.0 NZ D:LYS158 4.6 15.3 1.0 CB D:ASN182 4.7 16.4 1.0 N D:ASN182 4.9 14.2 1.0 O D:HOH409 4.9 22.1 1.0 CA D:ASP155 5.0 17.8 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:26.2 occ:1.00 OD1 E:ASN182 2.4 18.8 1.0 OD1 E:ASP155 2.4 25.7 1.0 OD2 E:ASP181 2.5 15.8 1.0 CG E:ASP155 3.2 20.4 1.0 OD2 E:ASP155 3.3 22.3 1.0 CG E:ASN182 3.3 13.8 1.0 CG E:ASP181 3.3 16.8 1.0 ND2 E:ASN182 3.6 13.0 1.0 CB E:ASP181 3.9 17.7 1.0 OD1 E:ASP181 4.2 19.1 1.0 O E:MET53 4.3 22.8 1.0 NZ E:LYS158 4.3 19.5 1.0 CG2 E:VAL55 4.4 24.5 1.0 CB E:ASP155 4.7 16.6 1.0 CB E:ASN182 4.7 17.5 1.0 CG E:SAH301 4.8 32.4 1.0 N E:ASN182 5.0 15.1 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca303 b:21.8 occ:1.00 O E:VAL104 2.3 18.1 1.0 OE1 E:GLU129 2.3 20.5 1.0 CD E:GLU129 3.4 21.5 1.0 C E:VAL104 3.6 20.1 1.0 CG E:GLU129 3.9 17.6 1.0 CA E:ASN105 4.3 17.8 1.0 N E:ASN105 4.3 18.2 1.0 OE2 E:GLU129 4.5 16.6 1.0 CA E:VAL104 4.6 16.3 1.0 N E:LYS106 4.7 15.9 1.0 CB E:VAL104 4.9 19.3 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Norbelladine O-Methyltransferase Variant in Complex with Sah within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca302 b:28.2 occ:1.00 OD1 F:ASN182 2.4 18.5 1.0 OD1 F:ASP155 2.5 28.5 1.0 OD2 F:ASP181 2.8 19.9 1.0 CG F:ASP155 3.2 24.1 1.0 OD2 F:ASP155 3.3 20.9 1.0 CG F:ASN182 3.4 19.0 1.0 CG F:ASP181 3.6 20.7 1.0 ND2 F:ASN182 3.6 16.9 1.0 CB F:ASP181 3.9 18.3 1.0 NZ F:LYS158 4.4 17.4 1.0 O F:MET53 4.5 25.0 1.0 OD1 F:ASP181 4.6 23.4 1.0 CB F:ASP155 4.7 15.7 1.0 CB F:ASN182 4.8 17.0 1.0 N F:ASN182 5.0 16.4 1.0

S.D'oelsnitz, D.J.Diaz, W.Kim, D.J.Acosta, T.L.Dangerfield, M.W.Schechter, M.B.Minus, J.R.Howard, H.Do, J.M.Loy, H.S.Alper, Y.J.Zhang, A.D.Ellington. Biosensor and Machine Learning-Aided Engineering of An Amaryllidaceae Enzyme. Nat Commun V. 15 2084 2024.
ISSN: ESSN 2041-1723
PubMed: 38453941
DOI: 10.1038/S41467-024-46356-Y