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Manganese in PDB 4e7k: Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution

Enzymatic activity of Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution

All present enzymatic activity of Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution, PDB code: 4e7k 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) 38.01 / 3.02
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 163.914, 163.914, 129.675, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 28.9

Other elements in 4e7k:

The structure of Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution (pdb code 4e7k). 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution, PDB code: 4e7k:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4e7k

Go back to Manganese Binding Sites List in 4e7k
Manganese binding site 1 out of 3 in the Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:47.8
occ:1.00
 OD2 A:ASP128 2.3 50.4 1.0
OP1 T:DC0 2.4 60.8 1.0
OE1 A:GLU221 2.5 48.5 1.0
OE2 A:GLU221 2.5 43.2 1.0
O3' D:DA17 2.6 51.7 1.0
CD A:GLU221 2.8 46.3 1.0
CG A:ASP128 3.0 52.3 1.0
OD1 A:ASP128 3.1 54.5 1.0
P T:DC0 3.5 74.1 1.0
O A:TYR129 3.6 52.7 1.0
ND2 A:ASN224 3.7 46.0 1.0
O5' T:DC0 3.7 66.1 1.0
C3' D:DA17 3.8 48.4 1.0
MN A:MN403 3.9 82.0 1.0
C4' D:DA17 4.0 44.4 1.0
OP1 D:DA17 4.1 42.6 1.0
CG A:GLU221 4.3 45.9 1.0
OP2 T:DC0 4.4 62.2 1.0
CB A:ASP128 4.5 51.8 1.0
C5' T:DC0 4.5 56.5 1.0
O3' T:DG-1 4.7 63.6 1.0
C5' D:DA17 4.7 47.8 1.0
C A:TYR129 4.7 52.3 1.0
C2' D:DA17 4.8 44.7 1.0
O3' D:DC16 4.8 45.1 1.0
C1' D:DA17 5.0 45.4 1.0
OD1 A:ASP185 5.0 56.5 1.0

Manganese binding site 2 out of 3 in 4e7k

Go back to Manganese Binding Sites List in 4e7k
Manganese binding site 2 out of 3 in the Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:82.0
occ:1.00
 OD1 A:ASP128 2.4 54.5 1.0
OP1 T:DC0 2.4 60.8 1.0
O3' T:DG-1 2.5 63.6 1.0
OD1 A:ASP185 2.7 56.5 1.0
P T:DC0 2.9 74.1 1.0
OD2 A:ASP185 3.2 54.3 1.0
CG A:ASP185 3.3 57.8 1.0
CG A:ASP128 3.6 52.3 1.0
C3' T:DG-1 3.7 64.2 1.0
O5' T:DC0 3.8 66.1 1.0
MN A:MN402 3.9 47.8 1.0
C4' T:DG-1 3.9 59.4 1.0
N A:TYR129 4.2 50.8 1.0
OD2 A:ASP128 4.2 50.4 1.0
C5' T:DG-1 4.2 56.5 1.0
OP2 T:DC0 4.3 62.2 1.0
O A:TYR129 4.5 52.7 1.0
OE2 A:GLU221 4.5 43.2 1.0
CB A:ASP128 4.6 51.8 1.0
C2' T:DG-1 4.6 66.5 1.0
CA A:ASP128 4.7 52.2 1.0
CB A:ASP185 4.8 56.1 1.0
O3' D:DA17 4.9 51.7 1.0
C A:ASP128 5.0 52.0 1.0
CA A:TYR129 5.0 52.0 1.0

Manganese binding site 3 out of 3 in 4e7k

Go back to Manganese Binding Sites List in 4e7k
Manganese binding site 3 out of 3 in the Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, 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 Target Capture Complex (Tcc-Mn), Freeze-Trapped Prior to Strand Transfer, at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:52.6
occ:1.00
 OD1 B:ASP185 2.4 50.1 1.0
O B:HOH502 2.6 46.5 1.0
O B:HOH504 2.6 56.4 1.0
OD1 B:ASP128 2.6 57.5 1.0
O B:HOH501 2.7 44.5 1.0
CG B:ASP128 3.1 59.7 1.0
OD2 B:ASP128 3.2 49.5 1.0
CG B:ASP185 3.4 54.4 1.0
OD2 B:ASP185 3.8 57.4 1.0
N B:TYR129 3.9 55.3 1.0
O B:TYR129 4.0 57.8 1.0
CB B:ASP128 4.4 63.9 1.0
CA B:TYR129 4.7 55.5 1.0
CB B:ASP185 4.7 58.7 1.0
CA B:ASP128 4.7 54.5 1.0
CB B:TYR129 4.8 57.0 1.0
C B:ASP128 4.8 55.2 1.0
C B:TYR129 4.8 60.1 1.0
CE2 B:PHE190 4.9 58.1 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 04:19:52 2020

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