Magnesium in PDB 4ffr: Semet-Labeled Pylc (Remote)

The structure of Semet-Labeled Pylc (Remote), PDB code: 4ffr was solved by F.Quitterer, A.List, P.Beck, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.830, 61.830, 171.950, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.1

The binding sites of Magnesium atom in the Semet-Labeled Pylc (Remote) (pdb code 4ffr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Semet-Labeled Pylc (Remote), PDB code: 4ffr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Semet-Labeled Pylc (Remote)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Semet-Labeled Pylc (Remote) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:22.9 occ:1.00 O2G A:ATP401 1.9 28.1 1.0 OE2 A:GLU227 1.9 27.9 1.0 OE2 A:GLU239 1.9 20.2 1.0 O1A A:ATP401 1.9 21.9 1.0 O3B A:ATP401 2.0 26.8 1.0 O A:HOH547 2.3 23.2 1.0 PG A:ATP401 2.4 30.6 1.0 CD A:GLU227 2.9 29.5 1.0 CD A:GLU239 3.0 19.0 1.0 PB A:ATP401 3.2 23.5 1.0 PA A:ATP401 3.2 20.9 1.0 MG A:MG404 3.3 21.3 1.0 OE1 A:GLU227 3.3 37.1 1.0 O1G A:ATP401 3.4 32.9 1.0 O3A A:ATP401 3.5 22.6 1.0 O3G A:ATP401 3.6 24.8 1.0 CG A:GLU239 3.7 18.1 1.0 O A:HOH564 3.8 27.8 1.0 O2B A:ATP401 4.0 21.9 1.0 OE1 A:GLU239 4.0 19.7 1.0 O A:HOH612 4.1 36.8 1.0 O5' A:ATP401 4.2 18.6 1.0 C5' A:ATP401 4.2 17.3 1.0 CG A:GLU227 4.3 24.1 1.0 O1B A:ATP401 4.3 23.2 1.0 O2A A:ATP401 4.4 20.2 1.0 OD2 A:ASP241 4.4 21.0 1.0 O3' A:ATP401 4.5 17.2 1.0 CB A:GLU227 4.8 19.5 1.0 C3' A:ATP401 4.9 17.1 1.0

Magnesium binding site 2 out of 4 in the Semet-Labeled Pylc (Remote)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Semet-Labeled Pylc (Remote) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:21.3 occ:1.00 O3G A:ATP401 1.9 24.8 1.0 O2B A:ATP401 1.9 21.9 1.0 OD2 A:ASP241 2.0 21.0 1.0 OE2 A:GLU239 2.2 20.2 1.0 PG A:ATP401 2.4 30.6 1.0 O A:HOH568 2.4 25.9 1.0 OE1 A:GLU239 2.5 19.7 1.0 O3B A:ATP401 2.5 26.8 1.0 PB A:ATP401 2.5 23.5 1.0 CD A:GLU239 2.7 19.0 1.0 CG A:ASP241 3.1 19.9 1.0 O2G A:ATP401 3.2 28.1 1.0 MG A:MG403 3.3 22.9 1.0 OD1 A:ASP241 3.6 21.1 1.0 O1B A:ATP401 3.7 23.2 1.0 O3A A:ATP401 3.7 22.6 1.0 O1G A:ATP401 3.7 32.9 1.0 O A:HOH564 3.9 27.8 1.0 NZ A:LYS104 4.0 20.9 1.0 NH2 A:ARG243 4.1 33.5 1.0 O1A A:ATP401 4.2 21.9 1.0 CG A:GLU239 4.2 18.1 1.0 CA A:SER136 4.3 31.1 1.0 O A:GLU135 4.3 30.4 1.0 CB A:SER136 4.3 32.2 1.0 MG A:MG406 4.3 20.8 1.0 OE2 A:GLU227 4.4 27.9 1.0 O A:HOH543 4.4 23.8 1.0 CB A:ASP241 4.5 19.2 1.0 CE A:LYS104 4.5 23.6 1.0 PA A:ATP401 4.6 20.9 1.0 N A:SER137 4.9 29.2 1.0 CZ A:ARG243 5.0 30.5 1.0

Magnesium binding site 3 out of 4 in the Semet-Labeled Pylc (Remote)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Semet-Labeled Pylc (Remote) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:26.6 occ:1.00 OE1 A:GLU171 2.6 22.5 1.0 OG1 A:THR185 2.8 17.1 1.0 O A:SER169 3.0 16.6 1.0 OG A:SER169 3.0 21.1 1.0 O A:LYS183 3.3 17.7 1.0 CD A:GLU171 3.3 22.6 1.0 C A:SER169 3.3 17.4 1.0 OE2 A:GLU171 3.4 25.0 1.0 O A:HOH507 3.5 19.2 1.0 CB A:SER169 3.6 18.9 1.0 CB A:THR248 3.6 15.2 1.0 CG2 A:THR185 3.6 16.2 1.0 CB A:THR185 3.7 15.4 1.0 N A:LEU170 3.8 15.7 1.0 CA A:LEU170 3.9 16.4 1.0 CG2 A:THR248 4.0 15.6 1.0 OG1 A:THR248 4.0 16.4 1.0 N A:THR185 4.0 14.3 1.0 CA A:SER169 4.1 17.5 1.0 CG2 A:VAL252 4.1 15.1 1.0 N A:GLU171 4.1 16.8 1.0 C A:LEU170 4.3 17.2 1.0 CA A:THR185 4.5 14.4 1.0 C A:LYS183 4.5 16.5 1.0 C A:GLU184 4.7 15.6 1.0 CG A:GLU171 4.7 19.6 1.0 CA A:THR248 4.8 14.6 1.0 N A:SER169 4.9 17.2 1.0 CA A:GLU184 4.9 16.9 1.0 O A:THR248 5.0 14.9 1.0

Magnesium binding site 4 out of 4 in the Semet-Labeled Pylc (Remote)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Semet-Labeled Pylc (Remote) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:20.8 occ:1.00 OD1 A:ASP241 1.9 21.1 1.0 O A:ILE240 2.2 17.2 1.0 O A:SER101 2.2 19.9 1.0 O A:HOH543 2.4 23.8 1.0 O A:HOH534 2.6 18.2 1.0 OE1 A:GLU239 2.8 19.7 1.0 CG A:ASP241 3.0 19.9 1.0 C A:SER101 3.3 17.6 1.0 C A:ILE240 3.4 16.4 1.0 OD2 A:ASP241 3.6 21.0 1.0 O A:HOH568 3.8 25.9 1.0 CD A:GLU239 3.9 19.0 1.0 O A:HOH523 3.9 18.6 1.0 CA A:ASP241 4.1 16.4 1.0 CB A:GLU239 4.1 17.4 1.0 N A:ILE240 4.1 15.7 1.0 CB A:ASP241 4.1 19.2 1.0 N A:ASP241 4.1 15.8 1.0 CA A:SER101 4.2 17.3 1.0 N A:ARG102 4.2 18.1 1.0 MG A:MG404 4.3 21.3 1.0 CA A:ARG102 4.4 20.5 1.0 CB A:SER101 4.4 16.9 1.0 CA A:ILE240 4.4 15.8 1.0 NZ A:LYS104 4.4 20.9 1.0 CG A:GLU239 4.5 18.1 1.0 CG A:LYS104 4.5 21.0 1.0 C A:ARG102 4.6 20.8 1.0 O A:ARG102 4.6 23.9 1.0 OG A:SER107 4.7 18.0 1.0 O2B A:ATP401 4.7 21.9 1.0 CE A:LYS104 4.8 23.6 1.0 OE2 A:GLU239 4.8 20.2 1.0 OG A:SER101 4.8 17.0 1.0 C A:GLU239 4.9 15.9 1.0 CA A:GLU239 5.0 16.8 1.0

F.Quitterer, A.List, P.Beck, A.Bacher, M.Groll. Biosynthesis of the 22ND Genetically Encoded Amino Acid Pyrrolysine: Structure and Reaction Mechanism of Pylc at 1.5A Resolution. J.Mol.Biol. V. 424 270 2012.
ISSN: ISSN 0022-2836
PubMed: 22985965
DOI: 10.1016/J.JMB.2012.09.007