Manganese in PDB 4ff3: N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn

The structure of N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn, PDB code: 4ff3 was solved by K.S.Murakami, R.S.Basu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.38 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.019, 111.652, 276.145, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.1

The binding sites of Manganese atom in the N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn (pdb code 4ff3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn, PDB code: 4ff3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1202 b:56.8 occ:1.00 OD1 A:ASP951 2.5 24.6 1.0 O2A A:ATP1201 2.6 33.9 1.0 O3' C:5GP101 2.6 58.0 1.0 OD1 A:ASP559 2.7 48.7 1.0 O A:HOH1555 2.7 25.5 1.0 O C:HOH229 3.1 52.0 1.0 OD2 A:ASP559 3.4 47.2 1.0 CG A:ASP559 3.4 44.4 1.0 CG A:ASP951 3.4 29.2 1.0 MN A:MN1203 3.5 35.2 1.0 OD2 A:ASP951 3.7 23.0 1.0 PA A:ATP1201 3.8 42.6 1.0 C3' C:5GP101 4.0 56.2 1.0 O1A A:ATP1201 4.1 36.0 1.0 OE2 A:GLU557 4.4 38.5 1.0 N A:GLY952 4.4 13.7 1.0 C5' A:ATP1201 4.4 25.8 1.0 O A:HOH1744 4.5 45.6 1.0 O2' C:5GP101 4.5 50.7 1.0 O5' A:ATP1201 4.5 33.8 1.0 C A:ASP951 4.5 18.9 1.0 C4' C:5GP101 4.6 56.0 1.0 CA A:GLY952 4.7 19.1 1.0 CB A:ASP951 4.8 12.1 1.0 O A:ASP951 4.8 23.9 1.0 O A:ILE949 4.8 16.3 1.0 C2' C:5GP101 4.8 48.8 1.0 O1G A:ATP1201 4.8 27.3 1.0 CB A:ASP559 4.9 33.6 1.0

Manganese binding site 2 out of 2 in the N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of N4 Mini-Vrnap Transcription Initiation Complex, 3 Min After Soaking Gtp, Atp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1203 b:35.2 occ:1.00 OD2 A:ASP951 2.3 23.0 1.0 O A:GLY560 2.3 19.3 1.0 O1G A:ATP1201 2.4 27.3 1.0 O2B A:ATP1201 2.4 23.0 1.0 O2A A:ATP1201 2.4 33.9 1.0 OD2 A:ASP559 2.6 47.2 1.0 CG A:ASP951 3.3 29.2 1.0 C A:GLY560 3.4 25.2 1.0 PB A:ATP1201 3.5 42.4 1.0 CG A:ASP559 3.5 44.4 1.0 MN A:MN1202 3.5 56.8 1.0 OD1 A:ASP951 3.7 24.6 1.0 PA A:ATP1201 3.7 42.6 1.0 PG A:ATP1201 3.7 38.2 1.0 N A:GLY560 3.8 18.3 1.0 O3A A:ATP1201 3.8 0.7 1.0 CA A:GLY560 3.9 20.8 1.0 OD1 A:ASP559 3.9 48.7 1.0 O3B A:ATP1201 4.0 59.8 1.0 C5' A:ATP1201 4.2 25.8 1.0 O3G A:ATP1201 4.4 39.8 1.0 CB A:ASN563 4.4 15.1 1.0 O5' A:ATP1201 4.5 33.8 1.0 C A:ASP559 4.5 23.2 1.0 N A:VAL561 4.5 17.5 1.0 N A:ASN563 4.6 16.1 1.0 N A:THR562 4.6 11.4 1.0 CB A:ASP951 4.6 12.1 1.0 CB A:ASP559 4.7 33.6 1.0 O A:ASP951 4.7 23.9 1.0 O2G A:ATP1201 4.8 35.8 1.0 O1B A:ATP1201 4.9 36.4 1.0 O1A A:ATP1201 4.9 36.0 1.0 CA A:VAL561 4.9 14.9 1.0

R.S.Basu, K.S.Murakami. Watching the Bacteriophage N4 Rna Polymerase Transcription By Time-Dependent Soak-Trigger-Freeze X-Ray Crystallography. J.Biol.Chem. V. 288 3305 2013.
ISSN: ISSN 0021-9258
PubMed: 23235152
DOI: 10.1074/JBC.M112.387712