Atomistry » Magnesium » PDB 5djh-5drz » 5dph
Atomistry »
  Magnesium »
    PDB 5djh-5drz »
      5dph »

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

Protein crystallography data

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

Magnesium Binding Sites:

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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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 5dph

Go back to Magnesium Binding Sites List in 5dph
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

Reference:

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
Page generated: Mon Dec 14 20:12:58 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy