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Manganese in PDB 4e7l: Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

Enzymatic activity of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

All present enzymatic activity of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution., PDB code: 4e7l was solved by G.N.Maertens, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.95 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.078, 159.078, 126.814, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.4

Other elements in 4e7l:

The structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. (pdb code 4e7l). 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 Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution., PDB code: 4e7l:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4e7l

Go back to Manganese Binding Sites List in 4e7l
Manganese binding site 1 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:67.4
occ:1.00
OD2 A:ASP128 2.5 67.6 1.0
OE1 A:GLU221 2.6 50.9 1.0
OE2 A:GLU221 2.6 58.0 1.0
O3' D:DA17 2.8 54.4 1.0
CD A:GLU221 2.9 49.1 1.0
OD1 A:ASP128 3.0 53.9 1.0
MN A:MN403 3.0 66.4 1.0
OP1 T:DC0 3.1 45.2 1.0
CG A:ASP128 3.1 54.2 1.0
P T:DC0 3.6 88.9 1.0
C3' D:DA17 3.9 35.8 1.0
C4' D:DA17 3.9 27.1 1.0
O A:TYR129 4.0 43.0 1.0
O3' t:DG-1 4.0 47.7 1.0
C5' T:DC0 4.2 45.6 1.0
OD1 A:ASP185 4.2 58.2 1.0
ND2 A:ASN224 4.3 37.9 1.0
CG A:GLU221 4.4 34.3 1.0
O5' T:DC0 4.4 54.0 1.0
C2' D:DA17 4.5 38.3 1.0
CB A:ASP128 4.6 52.6 1.0
OP2 T:DC0 4.7 95.8 1.0
C1' D:DA17 4.8 47.3 1.0
OP1 D:DA17 4.8 40.8 1.0
C5' D:DA17 4.9 35.2 1.0
O4' D:DA17 4.9 42.9 1.0

Manganese binding site 2 out of 3 in 4e7l

Go back to Manganese Binding Sites List in 4e7l
Manganese binding site 2 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:66.4
occ:1.00
OD1 A:ASP185 2.4 58.2 1.0
O3' t:DG-1 2.5 47.7 1.0
OD1 A:ASP128 2.7 53.9 1.0
OP1 T:DC0 3.0 45.2 1.0
MN A:MN402 3.0 67.4 1.0
CG A:ASP128 3.5 54.2 1.0
CG A:ASP185 3.5 60.9 1.0
C3' t:DG-1 3.7 58.2 1.0
OD2 A:ASP128 3.7 67.6 1.0
OD2 A:ASP185 3.9 62.9 1.0
O A:TYR129 3.9 43.0 1.0
C4' t:DG-1 4.0 41.7 1.0
N A:TYR129 4.1 52.4 1.0
C2' t:DG-1 4.2 41.1 1.0
P T:DC0 4.4 88.9 1.0
O3' D:DA17 4.7 54.4 1.0
CB A:ASP185 4.8 57.0 1.0
CB A:ASP128 4.8 52.6 1.0
CA A:TYR129 4.8 47.7 1.0
C A:TYR129 4.8 42.2 1.0
CB A:TYR129 4.8 53.9 1.0
C5' T:DC0 4.9 45.6 1.0
CA A:ASP128 4.9 44.9 1.0
OE2 A:GLU221 4.9 58.0 1.0
C1' t:DG-1 5.0 54.4 1.0

Manganese binding site 3 out of 3 in 4e7l

Go back to Manganese Binding Sites List in 4e7l
Manganese binding site 3 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:53.6
occ:1.00
OD2 B:ASP128 2.4 56.0 1.0
OD1 B:ASP128 2.4 56.7 1.0
CG B:ASP128 2.7 56.9 1.0
OD1 B:ASP185 2.7 42.0 1.0
OD2 B:ASP185 3.4 55.4 1.0
CG B:ASP185 3.5 52.0 1.0
CB B:ASP128 4.1 46.4 1.0
N B:TYR129 4.2 55.7 1.0
O B:TYR129 4.3 59.4 1.0
CA B:ASP128 4.6 52.8 1.0
CE2 B:PHE190 4.9 55.4 1.0
CB B:ASP185 5.0 52.2 1.0
C B:ASP128 5.0 50.0 1.0

Reference:

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
Page generated: Tue Dec 15 04:19:53 2020

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