Magnesium in PDB 5dph: Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine

The structure of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine, PDB code: 5dph was solved by A.B.Dippel, G.M.Olenginski, N.Maurici, M.T.Liskov, S.H.Brewer, C.M.Phillips-Piro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.00 / 1.42
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	47.270, 47.270, 344.550, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.8

The binding sites of Magnesium atom in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine (pdb code 5dph). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine, PDB code: 5dph:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.8 occ:1.00 HB2 A:ARG30 2.8 31.5 1.0 HG1 A:THR49 3.0 30.1 1.0 HB3 A:SER28 3.3 25.9 1.0 HG21 A:THR49 3.4 31.7 1.0 O A:VAL29 3.5 20.4 1.0 HG2 A:GLU17 3.7 25.1 1.0 CB A:ARG30 3.7 26.2 1.0 OG1 A:THR49 3.8 25.1 1.0 C A:VAL29 3.8 19.6 1.0 HH21 A:ARG30 3.8 49.9 1.0 HA A:ARG30 3.9 30.8 1.0 HD3 A:ARG30 3.9 47.9 1.0 N A:ARG30 4.0 20.9 1.0 HB2 A:SER28 4.1 25.9 1.0 NH2 A:ARG30 4.1 41.6 1.0 CA A:ARG30 4.1 25.6 1.0 CG2 A:THR49 4.1 26.4 1.0 CB A:SER28 4.1 21.5 1.0 HG23 A:THR49 4.2 31.7 1.0 HB3 A:ARG30 4.2 31.5 1.0 HA A:GLU17 4.3 27.3 1.0 O A:HOH503 4.3 31.5 1.0 HH22 A:ARG30 4.3 49.9 1.0 H A:VAL29 4.3 25.7 1.0 O A:HOH425 4.4 31.1 1.0 HB3 A:GLU17 4.4 24.2 1.0 N A:VAL29 4.4 21.4 1.0 H A:LEU18 4.4 24.0 1.0 H A:ARG30 4.5 25.1 1.0 CB A:THR49 4.5 24.7 1.0 CG A:GLU17 4.5 21.0 1.0 CD A:ARG30 4.6 39.9 1.0 CZ A:ARG30 4.6 40.2 1.0 CG A:ARG30 4.6 32.7 1.0 CA A:VAL29 4.7 22.6 1.0 HG3 A:ARG30 4.7 39.2 1.0 HB A:THR49 4.8 29.7 1.0 NE A:ARG30 4.8 38.2 1.0 CB A:GLU17 4.8 20.2 1.0 C A:SER28 4.8 19.0 1.0 HG22 A:THR49 4.9 31.7 1.0 HA A:VAL29 4.9 27.1 1.0 CA A:GLU17 5.0 22.7 1.0

Magnesium binding site 2 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:29.3 occ:1.00 HB3 A:LYS126 3.6 27.2 1.0 O A:LYS107 3.6 16.9 1.0 HB2 A:LYS107 3.8 20.9 1.0 HA A:THR108 3.9 21.2 1.0 HB2 A:ARG109 3.9 23.7 1.0 HB3 A:GLU124 4.1 26.2 1.0 O A:GLU124 4.1 18.6 1.0 H A:LYS126 4.1 19.0 1.0 C A:LYS107 4.1 17.3 1.0 HB3 A:ARG109 4.2 23.7 1.0 HB3 A:LYS107 4.3 20.9 1.0 HB2 A:LYS126 4.3 27.2 1.0 H A:ARG109 4.3 19.6 1.0 HA A:LEU125 4.4 20.7 1.0 CB A:LYS126 4.4 22.7 1.0 N A:ARG109 4.4 16.4 1.0 CB A:LYS107 4.5 17.4 1.0 N A:LYS126 4.5 15.8 1.0 CA A:THR108 4.5 17.7 1.0 CB A:ARG109 4.5 19.8 1.0 N A:THR108 4.5 17.6 1.0 O A:HOH616 4.5 27.8 1.0 C A:THR108 4.5 16.8 1.0 C A:GLU124 4.6 18.5 1.0 O A:HOH518 4.6 20.6 1.0 HB2 A:GLU124 4.8 26.2 1.0 CB A:GLU124 4.9 21.8 1.0 CA A:LEU125 4.9 17.2 1.0 C A:LEU125 4.9 19.2 1.0 CA A:LYS107 5.0 15.9 1.0 N A:LEU125 5.0 16.9 1.0

Magnesium binding site 3 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:33.0 occ:1.00 HB3 A:ASP129 4.3 23.1 1.0 O A:HOH634 4.4 27.0 1.0 CG A:ASP129 4.7 20.2 1.0 OD1 A:ASP129 4.7 21.7 1.0 OD2 A:ASP129 5.0 24.3 1.0 O A:HOH550 5.0 25.6 1.0

Magnesium binding site 4 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:23.2 occ:1.00 O A:HOH654 1.9 72.0 1.0 HA A:HIS148 2.7 22.7 1.0 O A:HOH446 2.9 24.9 1.0 HH21 A:ARG168 3.0 25.2 1.0 N A:4CF149 3.1 20.2 1.0 O A:HOH485 3.4 19.2 1.0 HB3 A:HIS148 3.5 20.1 1.0 CA A:HIS148 3.5 18.9 1.0 O B:HOH496 3.6 26.4 1.0 HD2 A:HIS148 3.7 22.2 1.0 C A:HIS148 3.8 18.6 1.0 NH2 A:ARG168 3.8 21.0 1.0 CB A:HIS148 4.0 16.7 1.0 CA A:4CF149 4.0 21.8 1.0 HH22 A:ARG168 4.1 25.2 1.0 HE A:ARG168 4.2 29.7 1.0 CD2 A:4CF149 4.2 25.9 1.0 O A:4CF149 4.2 21.1 1.0 CB A:4CF149 4.3 21.4 1.0 CD2 A:HIS148 4.4 18.5 1.0 O A:SER147 4.4 16.6 1.0 O B:HOH583 4.5 28.9 1.0 CG A:HIS148 4.6 16.9 1.0 CG A:4CF149 4.6 24.0 1.0 C A:4CF149 4.6 23.6 1.0 HE2 A:TYR151 4.6 39.2 1.0 HH12 B:ARG73 4.6 35.3 1.0 O A:LYS166 4.6 23.1 1.0 N A:HIS148 4.7 16.0 1.0 CZ A:ARG168 4.7 26.0 1.0 NE A:ARG168 4.8 24.8 1.0 HB2 A:HIS148 4.8 20.1 1.0 O A:HIS148 4.9 21.0 1.0

Magnesium binding site 5 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:32.1 occ:1.00 O B:HOH542 2.0 69.6 1.0 O A:HOH520 2.2 46.9 1.0 HB3 A:PRO75 2.7 38.9 1.0 H A:ASP76 3.0 49.0 1.0 HA A:PRO75 3.3 39.8 1.0 HH B:TYR151 3.4 41.0 1.0 CB A:PRO75 3.6 32.4 1.0 O A:HOH409 3.7 30.1 1.0 N A:ASP76 3.7 40.8 1.0 CA A:PRO75 3.8 33.1 1.0 CE2 B:4CF149 3.9 34.6 1.0 H A:HIS77 4.0 42.8 1.0 OH B:TYR151 4.0 34.2 1.0 CZ B:4CF149 4.1 27.1 1.0 HB2 A:PRO75 4.1 38.9 1.0 ND1 A:HIS77 4.1 38.1 1.0 O A:HOH665 4.1 36.6 1.0 C A:PRO75 4.2 38.0 1.0 HB2 A:ASP76 4.2 48.5 1.0 HE1 A:HIS77 4.3 40.9 1.0 CD2 B:4CF149 4.3 28.9 1.0 OD2 A:ASP76 4.3 41.4 1.0 HG3 A:PRO75 4.3 38.1 1.0 C1 B:4CF149 4.4 31.3 1.0 CE1 A:HIS77 4.6 34.1 1.0 CG A:PRO75 4.6 31.8 1.0 CE1 B:4CF149 4.6 29.0 1.0 CG A:ASP76 4.6 43.8 1.0 CB A:ASP76 4.7 40.4 1.0 CA A:ASP76 4.8 40.3 1.0 O B:HOH414 4.8 24.1 1.0 N A:HIS77 4.8 35.7 1.0 CG B:4CF149 4.9 28.5 1.0 N1 B:4CF149 4.9 31.7 1.0

Magnesium binding site 6 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:19.9 occ:1.00 H B:TRP57 2.5 19.4 1.0 O B:HOH519 2.8 31.6 1.0 O B:HOH530 3.0 23.1 1.0 HA B:PRO56 3.0 19.2 1.0 HD1 B:TRP57 3.0 20.9 1.0 O B:HOH576 3.2 19.2 1.0 N B:TRP57 3.3 16.2 1.0 HB2 B:TRP57 3.3 17.8 1.0 HD3 B:PRO58 3.5 22.3 1.0 HD1 B:TYR143 3.5 20.5 1.0 HB3 B:PRO56 3.6 21.3 1.0 HD2 B:PRO58 3.7 22.3 1.0 CA B:PRO56 3.8 16.0 1.0 CD1 B:TRP57 3.8 17.5 1.0 CD B:PRO58 4.0 18.6 1.0 C B:PRO56 4.0 14.5 1.0 CB B:TRP57 4.0 14.8 1.0 O B:HOH656 4.1 25.9 1.0 CD1 B:TYR143 4.2 17.1 1.0 CB B:PRO56 4.2 17.7 1.0 O B:HOH619 4.2 63.2 1.0 CA B:TRP57 4.3 15.5 1.0 CG B:TRP57 4.3 16.0 1.0 O B:HOH472 4.4 18.4 1.0 HE1 B:TYR143 4.4 24.2 1.0 HB2 B:TYR143 4.5 27.2 1.0 CE1 B:TYR143 4.7 20.1 1.0 HB2 B:PRO56 4.7 21.3 1.0 HZ1 B:LYS209 4.7 28.4 1.0 HB3 B:TRP57 4.9 17.8 1.0 HA B:TRP57 4.9 18.6 1.0 NE1 B:TRP57 4.9 20.1 1.0 HA B:TYR143 5.0 28.1 1.0

Magnesium binding site 7 out of 7 in the Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Sfgfp Mutant - 149 P-Cyano-L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:34.1 occ:1.00 HB2 B:ARG109 3.6 27.7 1.0 HB3 B:ARG109 3.7 27.7 1.0 HB2 B:GLU124 4.0 24.6 1.0 H B:ARG109 4.1 19.9 1.0 CB B:ARG109 4.1 23.1 1.0 O B:GLU124 4.1 17.4 1.0 O B:LYS107 4.1 16.6 1.0 HB3 B:GLU124 4.2 24.6 1.0 N B:ARG109 4.2 16.6 1.0 HA B:THR108 4.2 22.1 1.0 O B:HOH401 4.4 31.6 1.0 C B:THR108 4.4 17.2 1.0 HB3 B:LYS107 4.4 26.2 1.0 HB2 B:LYS107 4.5 26.2 1.0 CB B:GLU124 4.6 20.5 1.0 C B:LYS107 4.6 16.8 1.0 HB3 B:LYS126 4.6 23.2 1.0 CA B:THR108 4.7 18.4 1.0 C B:GLU124 4.7 13.7 1.0 OE1 B:GLU124 4.8 29.4 1.0 CA B:ARG109 4.8 17.8 1.0 N B:THR108 4.8 17.4 1.0 O B:THR108 4.9 18.7 1.0 H B:LYS126 4.9 23.7 1.0 HB2 B:LYS126 4.9 23.2 1.0 CB B:LYS107 4.9 21.9 1.0 HA B:LEU125 4.9 21.2 1.0 HD2 B:ARG109 5.0 30.0 1.0

A.B.Dippel, G.M.Olenginski, N.Maurici, M.T.Liskov, S.H.Brewer, C.M.Phillips-Piro. Probing the Effectiveness of Spectroscopic Reporter Unnatural Amino Acids: A Structural Study. Acta Crystallogr D Struct V. 72 121 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894540
DOI: 10.1107/S2059798315022858