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Manganese in PDB 2w42: The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.

Protein crystallography data

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex., PDB code: 2w42 was solved by J.S.Parker, S.M.Roe, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.06 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.838, 61.384, 103.540, 75.80, 75.86, 79.47
R / Rfree (%) 20.5 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. (pdb code 2w42). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex., PDB code: 2w42:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2w42

Go back to Manganese Binding Sites List in 2w42
Manganese binding site 1 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1428

b:14.6
occ:1.00
OP3 P:DT1 2.0 19.5 1.0
OE1 A:GLN159 2.0 14.5 1.0
OP1 P:DC3 2.1 19.4 1.0
O A:HOH2244 2.2 18.8 1.0
OXT A:LEU427 2.2 13.6 1.0
O A:LEU427 2.5 11.4 1.0
C A:LEU427 2.7 12.7 1.0
CD A:GLN159 3.0 18.4 1.0
P P:DT1 3.3 17.5 1.0
NE2 A:GLN159 3.4 24.3 1.0
P P:DC3 3.5 23.1 1.0
OP1 P:DT1 3.6 19.4 1.0
O3' P:DT2 3.9 20.2 1.0
NZ A:LYS163 3.9 14.7 1.0
NH2 A:ARG380 4.2 21.0 1.0
CA A:LEU427 4.2 12.4 1.0
NE A:ARG380 4.2 21.6 1.0
OP2 P:DC3 4.2 26.7 1.0
O5' P:DT1 4.2 18.7 1.0
O A:HOH2243 4.3 17.4 1.0
C5' P:DT1 4.3 20.1 1.0
OP2 P:DT1 4.3 12.4 1.0
CG A:GLN159 4.4 19.3 1.0
NE2 A:GLN137 4.5 15.3 1.0
O A:HOH2242 4.5 31.3 1.0
CE A:LYS163 4.5 14.1 1.0
O P:HOH2002 4.6 29.0 1.0
O5' P:DC3 4.6 21.3 1.0
OE1 A:GLN137 4.6 20.7 1.0
CZ A:ARG380 4.7 20.1 1.0
CB A:LEU427 4.8 11.9 1.0
CG A:ARG380 4.9 18.3 1.0
C5' P:DC3 4.9 29.0 1.0
CB A:GLN159 5.0 16.9 1.0

Manganese binding site 2 out of 2 in 2w42

Go back to Manganese Binding Sites List in 2w42
Manganese binding site 2 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus Complexed with A 16NT Dna Duplex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1428

b:23.3
occ:1.00
OXT B:LEU427 1.9 20.8 1.0
OP3 R:DT1 2.1 26.1 1.0
OP1 R:DC3 2.1 29.8 1.0
O B:HOH2143 2.2 24.9 1.0
OE1 B:GLN159 2.2 21.6 1.0
O B:LEU427 2.5 22.2 1.0
C B:LEU427 2.6 21.6 1.0
CD B:GLN159 3.2 24.9 1.0
P R:DT1 3.4 25.5 1.0
P R:DC3 3.4 28.9 1.0
OP1 R:DT1 3.6 22.8 1.0
NE2 B:GLN159 3.6 24.9 1.0
NZ B:LYS163 3.9 23.6 1.0
O3' R:DT2 4.0 28.4 1.0
CA B:LEU427 4.1 20.9 1.0
NE B:ARG380 4.1 24.3 1.0
OP2 R:DC3 4.2 31.0 1.0
NH2 B:ARG380 4.3 27.1 1.0
O5' R:DT1 4.3 26.6 1.0
OP2 R:DT1 4.3 24.2 1.0
O B:HOH2141 4.3 35.2 1.0
C5' R:DT1 4.4 32.4 1.0
CE B:LYS163 4.5 24.5 1.0
O B:HOH2142 4.5 37.1 1.0
NE2 B:GLN137 4.5 24.7 1.0
O5' R:DC3 4.5 28.8 1.0
CG B:GLN159 4.6 21.3 1.0
O R:HOH2005 4.6 36.7 1.0
CZ B:ARG380 4.7 27.3 1.0
OE1 B:GLN137 4.7 21.7 1.0
CB B:LEU427 4.7 20.4 1.0
CG B:ARG380 4.7 21.0 1.0
C5' R:DC3 4.8 32.4 1.0

Reference:

J.S.Parker, E.A.Parizotto, M.Wang, S.M.Roe, D.Barford. Enhancement of the Seed-Target Recognition Step in Rna Silencing By A Piwi-Mid Domain Protein Mol.Cell V. 33 204 2009.
ISSN: ISSN 1097-2765
PubMed: 19187762
DOI: 10.1016/J.MOLCEL.2008.12.012
Page generated: Tue Dec 15 04:06:04 2020

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