Manganese in PDB 1fa0: Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp

All present enzymatic activity of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp:
2.7.7.19;

The structure of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp, PDB code: 1fa0 was solved by J.Bard, A.M.Zhelkovsky, S.Helmling, C.L.Moore, A.Bohm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.800, 109.100, 238.500, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.8

The binding sites of Manganese atom in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp (pdb code 1fa0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp, PDB code: 1fa0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn600 b:54.2 occ:1.00 O1A A:3AT604 2.0 73.5 1.0 OD2 A:ASP100 2.1 49.0 1.0 O3G A:3AT604 2.2 69.0 1.0 O A:HOH871 2.2 37.2 1.0 OD1 A:ASP102 2.3 51.5 1.0 O2B A:3AT604 2.4 69.0 1.0 CG A:ASP100 3.0 49.4 1.0 PA A:3AT604 3.1 73.3 1.0 O3A A:3AT604 3.2 70.9 1.0 CG A:ASP102 3.2 52.0 1.0 MN A:MN601 3.3 60.3 1.0 PB A:3AT604 3.3 68.8 1.0 OD1 A:ASP100 3.3 47.7 1.0 OD2 A:ASP102 3.3 54.1 1.0 PG A:3AT604 3.5 68.6 1.0 O3B A:3AT604 3.7 69.1 1.0 O A:ASP100 3.9 51.6 1.0 O5' A:3AT604 3.9 77.2 1.0 C5' A:3AT604 3.9 81.3 1.0 C A:ASP100 4.4 51.2 1.0 O2A A:3AT604 4.4 73.1 1.0 O2G A:3AT604 4.4 68.9 1.0 CB A:ASP100 4.4 50.8 1.0 O A:HOH831 4.5 48.7 1.0 N A:SER89 4.5 49.7 1.0 CB A:SER89 4.5 50.2 1.0 N A:ASP100 4.5 51.4 1.0 CB A:ASP102 4.6 50.4 1.0 O1G A:3AT604 4.6 69.1 1.0 O1B A:3AT604 4.7 68.4 1.0 CA A:ASP100 4.7 51.1 1.0 N A:ASP102 4.7 50.6 1.0 OD1 A:ASP154 4.9 57.3 1.0

Manganese binding site 2 out of 4 in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:60.3 occ:1.00 OD1 A:ASP154 1.9 57.3 1.0 OD1 A:ASP100 2.2 47.7 1.0 OD2 A:ASP102 2.2 54.1 1.0 O1A A:3AT604 2.2 73.5 1.0 C3' A:3AD606 2.9 81.5 0.8 CG A:ASP154 3.1 59.0 1.0 CG A:ASP100 3.2 49.4 1.0 CG A:ASP102 3.2 52.0 1.0 MN A:MN600 3.3 54.2 1.0 PA A:3AT604 3.4 73.3 1.0 OD2 A:ASP100 3.5 49.0 1.0 OD1 A:ASP102 3.6 51.5 1.0 C5' A:3AT604 3.9 81.3 1.0 O2A A:3AT604 3.9 73.1 1.0 CB A:ASP154 3.9 58.7 1.0 C2' A:3AD606 4.0 82.2 0.8 OD2 A:ASP154 4.0 59.5 1.0 O5' A:3AT604 4.0 77.2 1.0 O2' A:3AD606 4.1 81.7 0.8 C4' A:3AD606 4.1 81.2 0.8 CB A:ASP102 4.5 50.4 1.0 CB A:ASP100 4.6 50.8 1.0 C5' A:3AD606 4.6 80.1 0.8 O3A A:3AT604 4.7 70.9 1.0 CA A:ASP102 5.0 49.4 1.0

Manganese binding site 3 out of 4 in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:61.8 occ:1.00 O1A B:3AT605 2.0 83.8 1.0 O1B B:3AT605 2.1 80.8 1.0 OD2 B:ASP100 2.2 63.8 1.0 O1G B:3AT605 2.2 82.2 1.0 OD1 B:ASP102 2.3 65.6 1.0 PB B:3AT605 3.1 81.0 1.0 CG B:ASP102 3.1 64.3 1.0 PA B:3AT605 3.2 84.9 1.0 O3A B:3AT605 3.2 83.9 1.0 O3B B:3AT605 3.3 81.8 1.0 OD2 B:ASP102 3.3 64.0 1.0 PG B:3AT605 3.3 81.6 1.0 CG B:ASP100 3.3 62.0 1.0 OG B:SER89 3.6 56.5 1.0 MN B:MN603 3.7 67.4 1.0 OD1 B:ASP100 3.8 60.5 1.0 O B:ASP100 3.9 64.6 1.0 O B:HOH611 4.1 55.4 1.0 O2G B:3AT605 4.1 81.4 1.0 O5' B:3AT605 4.1 88.1 1.0 C B:ASP100 4.3 64.2 1.0 O2A B:3AT605 4.3 84.5 1.0 N B:ASP100 4.4 63.0 1.0 O2B B:3AT605 4.5 79.6 1.0 O3G B:3AT605 4.5 80.9 1.0 N B:SER89 4.5 57.7 1.0 CB B:ASP102 4.5 62.9 1.0 N B:ASP102 4.5 61.2 1.0 CB B:ASP100 4.6 62.5 1.0 CA B:ASP100 4.7 63.3 1.0 CB B:SER89 4.7 57.8 1.0 N B:ILE101 4.9 63.9 1.0

Manganese binding site 4 out of 4 in the Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Yeast Poly(A) Polymerase Bound to Manganate and 3'-Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn603 b:67.4 occ:1.00 OD2 B:ASP102 1.9 64.0 1.0 OD2 B:ASP154 1.9 62.6 1.0 O1A B:3AT605 2.2 83.8 1.0 OD1 B:ASP100 2.7 60.5 1.0 C3' B:3AD607 2.8 93.1 0.9 PA B:3AT605 3.0 84.9 1.0 O5' B:3AT605 3.0 88.1 1.0 O5' B:3AD607 3.1 91.8 0.9 CG B:ASP102 3.1 64.3 1.0 CG B:ASP154 3.1 63.3 1.0 O2A B:3AT605 3.5 84.5 1.0 CG B:ASP100 3.6 62.0 1.0 C4' B:3AD607 3.6 93.1 0.9 OD1 B:ASP102 3.7 65.6 1.0 OD2 B:ASP100 3.7 63.8 1.0 MN B:MN602 3.7 61.8 1.0 C5' B:3AD607 3.9 92.2 0.9 CB B:ASP154 3.9 61.7 1.0 C2' B:3AD607 4.0 93.5 0.9 OD1 B:ASP154 4.1 65.2 1.0 CB B:ASP102 4.3 62.9 1.0 C5' B:3AT605 4.3 91.5 1.0 O3A B:3AT605 4.4 83.9 1.0 O2' B:3AD607 4.4 93.4 0.9 CA B:ASP102 4.9 60.5 1.0 O4' B:3AD607 5.0 93.6 0.9

J.Bard, A.M.Zhelkovsky, S.Helmling, T.N.Earnest, C.L.Moore, A.Bohm. Structure of Yeast Poly(A) Polymerase Alone and in Complex with 3'-Datp. Science V. 289 1346 2000.
ISSN: ISSN 0036-8075
PubMed: 10958780
DOI: 10.1126/SCIENCE.289.5483.1346