Manganese in PDB 2phn: Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus

The structure of Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus, PDB code: 2phn was solved by B.Nocek, E.Evdokimova, M.Kudritska, A.Edwards, A.Savchenko, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.367, 98.367, 94.347, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19

The binding sites of Manganese atom in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus (pdb code 2phn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus, PDB code: 2phn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2001 b:11.9 occ:1.00 OE1 A:GLU208 2.1 12.5 1.0 O2A A:GDP2696 2.1 11.6 1.0 O A:HOH4080 2.1 12.8 1.0 O2B A:GDP2696 2.2 11.3 1.0 O A:HOH4042 2.2 14.1 1.0 OG1 A:THR151 2.2 12.5 1.0 CD A:GLU208 3.1 13.2 1.0 CB A:THR151 3.1 12.2 1.0 PB A:GDP2696 3.2 11.6 1.0 PA A:GDP2696 3.3 12.2 1.0 OE2 A:GLU208 3.4 13.6 1.0 O3A A:GDP2696 3.5 11.5 1.0 O3B A:GDP2696 3.6 12.4 1.0 CG2 A:THR151 4.0 13.8 1.0 O A:HOH4046 4.1 20.7 1.0 ND2 A:ASN203 4.1 10.6 1.0 O A:HOH4028 4.2 14.7 1.0 N A:THR151 4.3 10.9 1.0 O A:GLY207 4.3 13.7 1.0 CA A:THR151 4.3 11.7 1.0 CA A:GLU208 4.3 14.1 1.0 O5' A:GDP2696 4.4 11.5 1.0 CG A:GLU208 4.4 14.4 1.0 C5' A:GDP2696 4.4 10.8 1.0 O1A A:GDP2696 4.4 12.7 1.0 O1B A:GDP2696 4.6 14.1 1.0 CB A:GLU208 4.6 14.2 1.0 O A:HOH4065 4.7 14.7 1.0 O A:HOH4091 4.8 24.1 1.0 O A:HOH4121 4.9 20.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn2002 b:13.0 occ:1.00 O A:HOH4092 2.1 14.9 1.0 O3B A:GDP2696 2.2 12.4 1.0 OD2 A:ASP109 2.2 19.0 1.0 OD1 A:ASP150 2.2 11.3 1.0 O A:HOH4065 2.2 14.7 1.0 O A:HOH4008 2.2 16.5 1.0 CG A:ASP150 3.2 11.8 1.0 CG A:ASP109 3.3 18.9 1.0 PB A:GDP2696 3.3 11.6 1.0 OD2 A:ASP150 3.5 15.3 1.0 CB A:ASP109 3.7 18.2 1.0 O1B A:GDP2696 3.8 14.1 1.0 O A:HOH4042 3.9 14.1 1.0 O2B A:GDP2696 4.0 11.3 1.0 OG1 A:THR41 4.2 13.6 1.0 OG A:SER40 4.4 12.4 1.0 O A:HOH4121 4.4 20.6 1.0 OD1 A:ASP109 4.4 20.0 1.0 O A:HOH4027 4.4 18.9 1.0 O A:HOH4188 4.4 39.8 1.0 O A:HOH4083 4.5 35.2 1.0 CB A:ASP150 4.6 10.8 1.0 O A:HOH4091 4.6 24.1 1.0 O3A A:GDP2696 4.6 11.5 1.0 N A:THR151 4.6 10.9 1.0 O A:THR151 4.7 13.2 1.0 O A:GLY107 4.9 20.2 1.0 CA A:ASP109 4.9 18.5 1.0 CA A:ASP150 5.0 10.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:10.7 occ:0.85 O B:HOH3045 2.1 13.7 1.0 OE1 B:GLU208 2.1 13.3 1.0 O1A B:GDP2697 2.2 11.9 1.0 O2B B:GDP2697 2.2 11.9 1.0 OG1 B:THR151 2.2 13.4 1.0 O B:HOH3061 2.2 15.1 1.0 CD B:GLU208 3.1 13.9 1.0 CB B:THR151 3.1 12.6 1.0 PB B:GDP2697 3.2 11.9 1.0 PA B:GDP2697 3.3 12.4 1.0 OE2 B:GLU208 3.4 14.0 1.0 O3A B:GDP2697 3.4 12.2 1.0 O3B B:GDP2697 3.7 11.8 1.0 CG2 B:THR151 4.0 14.7 1.0 O B:HOH3084 4.1 21.6 1.0 OD1 B:ASN203 4.1 13.4 1.0 O B:HOH3033 4.2 15.7 1.0 O B:GLY207 4.2 14.2 1.0 N B:THR151 4.2 11.2 1.0 CA B:THR151 4.3 11.5 1.0 CA B:GLU208 4.3 15.1 1.0 O5' B:GDP2697 4.3 11.2 1.0 C5' B:GDP2697 4.3 11.4 1.0 CG B:GLU208 4.4 13.9 1.0 O2A B:GDP2697 4.4 14.7 1.0 O1B B:GDP2697 4.6 14.8 1.0 O B:HOH3269 4.6 24.8 1.0 CB B:GLU208 4.6 15.2 1.0 O B:HOH3066 4.7 16.0 1.0 O B:HOH3114 4.9 22.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of An Amide Bond Forming F420-Gamma Glutamyl Ligase From Archaeoglobus Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:13.4 occ:1.00 O3B B:GDP2697 2.1 11.8 1.0 O B:HOH3052 2.2 16.7 1.0 OD2 B:ASP109 2.2 17.8 1.0 OD1 B:ASP150 2.2 12.3 1.0 O B:HOH3066 2.2 16.0 1.0 O B:HOH3167 2.2 16.9 1.0 CG B:ASP150 3.2 12.5 1.0 CG B:ASP109 3.2 17.4 1.0 PB B:GDP2697 3.3 11.9 1.0 OD2 B:ASP150 3.4 16.6 1.0 CB B:ASP109 3.6 17.6 1.0 O1B B:GDP2697 3.8 14.8 1.0 O B:HOH3061 3.9 15.1 1.0 O2B B:GDP2697 4.0 11.9 1.0 O B:HOH3017 4.1 35.3 1.0 OG1 B:THR41 4.2 13.7 1.0 OD1 B:ASP109 4.4 19.9 1.0 O B:HOH3010 4.4 19.7 1.0 OG B:SER40 4.4 12.6 1.0 O B:HOH3069 4.4 31.0 1.0 O B:HOH3114 4.5 22.2 1.0 O B:HOH3269 4.5 24.8 1.0 CB B:ASP150 4.6 11.2 1.0 N B:THR151 4.6 11.2 1.0 O3A B:GDP2697 4.6 12.2 1.0 O B:THR151 4.7 13.0 1.0 CA B:ASP109 4.9 17.7 1.0 CA B:ASP150 4.9 11.1 1.0

B.Nocek, E.Evdokimova, M.Proudfoot, M.Kudritska, L.L.Grochowski, R.H.White, A.Savchenko, A.F.Yakunin, A.Edwards, A.Joachimiak. Structure of An Amide Bond Forming F(420):Gammagamma-Glutamyl Ligase From Archaeoglobus Fulgidus - A Member of A New Family of Non-Ribosomal Peptide Synthases. J.Mol.Biol. V. 372 456 2007.
ISSN: ISSN 0022-2836
PubMed: 17669425
DOI: 10.1016/J.JMB.2007.06.063