Manganese in PDB 4e7i: Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn)

All present enzymatic activity of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn):
2.7.7.49; 2.7.7.7; 3.1.26.4;

The structure of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn), PDB code: 4e7i was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.84 / 2.53
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.150, 160.150, 124.240, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.1

The structure of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn) (pdb code 4e7i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn), PDB code: 4e7i:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:44.7 occ:1.00 OP1 D:DA18 2.2 50.5 1.0 OD1 A:ASP128 2.3 49.9 1.0 O D:HOH202 2.4 47.2 1.0 O A:HOH624 2.4 53.4 1.0 OD1 A:ASP185 2.4 46.1 1.0 O A:HOH502 2.4 42.7 1.0 CG A:ASP185 3.3 47.8 1.0 CG A:ASP128 3.4 49.3 1.0 P D:DA18 3.5 58.8 1.0 OD2 A:ASP185 3.5 44.7 1.0 OD2 A:ASP128 3.8 45.5 1.0 MN A:MN403 3.8 55.0 1.0 C5' D:DA18 3.9 49.6 1.0 O1 A:MES412 3.9 74.5 0.8 OP2 D:DA18 4.1 54.3 1.0 O5' D:DA18 4.1 58.2 1.0 O A:HOH559 4.2 49.4 1.0 N A:TYR129 4.2 42.4 1.0 C2 A:MES412 4.2 70.2 0.8 O A:HOH642 4.3 52.4 1.0 O D:HOH217 4.3 67.9 1.0 O A:TYR129 4.4 43.6 1.0 O A:HOH501 4.6 42.9 1.0 CB A:ASP128 4.6 45.1 1.0 O3' D:DA17 4.7 51.0 1.0 CB A:ASP185 4.7 45.7 1.0 C6 A:MES412 4.8 48.4 0.8 CA A:ASP128 4.8 40.2 1.0 O A:HOH537 4.9 51.2 1.0

Manganese binding site 2 out of 3 in the Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:55.0 occ:1.00 OD2 A:ASP128 2.2 45.5 1.0 OE2 A:GLU221 2.3 43.5 1.0 O A:HOH501 2.4 42.9 1.0 OP1 D:DA18 2.4 50.5 1.0 OE1 A:GLU221 2.4 45.9 1.0 O3' D:DA17 2.5 51.0 1.0 CD A:GLU221 2.7 46.5 1.0 P D:DA18 3.0 58.8 1.0 CG A:ASP128 3.2 49.3 1.0 OD1 A:ASP128 3.5 49.9 1.0 ND2 A:ASN224 3.7 37.2 1.0 C3' D:DA17 3.7 45.1 1.0 O A:HOH559 3.8 49.4 1.0 MN A:MN402 3.8 44.7 1.0 C4' D:DA17 3.9 43.8 1.0 OP2 D:DA18 4.0 54.3 1.0 O5' D:DA18 4.1 58.2 1.0 O A:TYR129 4.2 43.6 1.0 CG A:GLU221 4.2 40.9 1.0 C5' D:DA18 4.3 49.6 1.0 O A:HOH624 4.3 53.4 1.0 CB A:ASP128 4.5 45.1 1.0 OP1 D:DA17 4.5 46.7 1.0 C2' D:DA17 4.5 33.5 1.0 C1' D:DA17 4.6 38.3 1.0 OD1 A:ASP185 4.7 46.1 1.0 C5' D:DA17 4.8 36.1 1.0 O4' D:DA17 4.8 48.3 1.0 O D:HOH203 4.9 62.5 1.0 O3' D:DC16 4.9 48.0 1.0

Manganese binding site 3 out of 3 in the Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pfv Intasome Freeze-Trapped Prior to 3'-Processing, Mn-Bound Form (Ui- Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:58.1 occ:1.00 OD1 B:ASP185 2.2 39.7 1.0 O B:HOH501 2.4 51.0 1.0 O B:HOH502 2.4 59.2 1.0 OD1 B:ASP128 2.5 68.3 1.0 O B:HOH545 2.5 58.2 1.0 OD2 B:ASP128 3.1 59.8 1.0 CG B:ASP128 3.1 60.1 1.0 CG B:ASP185 3.3 53.7 1.0 OD2 B:ASP185 3.7 52.3 1.0 O B:HOH511 4.2 49.2 1.0 O B:HOH539 4.2 52.2 1.0 O B:HOH517 4.4 57.4 1.0 O B:TYR129 4.4 56.2 1.0 N B:TYR129 4.5 49.0 1.0 CB B:ASP128 4.5 49.5 1.0 CB B:ASP185 4.6 38.3 1.0 O B:HOH518 4.6 68.2 1.0 CA B:ASP128 5.0 45.5 1.0

S.Hare, G.N.Maertens, P.Cherepanov. 3'-Processing and Strand Transfer Catalysed By Retroviral Integrase in Crystallo. Embo J. V. 31 3020 2012.
ISSN: ISSN 0261-4189
PubMed: 22580823
DOI: 10.1038/EMBOJ.2012.118