Manganese in PDB 5z6w: Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese

All present enzymatic activity of Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese:
3.1.4.1;

The structure of Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese, PDB code: 5z6w was solved by H.Jin, Y.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.874, 104.969, 105.490, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.8

The binding sites of Manganese atom in the Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese (pdb code 5z6w). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese, PDB code: 5z6w:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:89.2 occ:1.00 OD1 A:ASP507 2.3 84.4 1.0 OE1 A:GLU386 2.3 97.0 1.0 OE2 A:GLU386 2.3 99.3 1.0 CD A:GLU386 2.6 94.1 1.0 MN A:MN602 3.0 0.6 1.0 CG A:ASP507 3.4 83.1 1.0 OD2 A:ASP507 3.8 89.1 1.0 CG A:GLU386 4.2 86.9 1.0 OE2 A:GLU522 4.2 0.0 1.0 OH A:TYR384 4.3 68.9 1.0 OE2 A:GLU368 4.6 0.8 1.0 O A:HOH701 4.6 63.6 1.0 CB A:ASP507 4.7 75.4 1.0 NE2 A:GLN534 4.8 69.0 1.0 CD A:GLU368 4.8 0.3 1.0 OE1 A:GLU522 4.9 0.7 1.0 CD A:GLU522 5.0 0.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of PAFAN1 Bound to 2NT 5'Flap Dna with Gap with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:0.6 occ:1.00 OE2 A:GLU522 2.2 0.0 1.0 OD2 A:ASP507 2.4 89.1 1.0 O A:VAL523 2.8 86.6 1.0 MN A:MN601 3.0 89.2 1.0 OD1 A:ASP507 3.1 84.4 1.0 CG A:ASP507 3.1 83.1 1.0 CD A:GLU522 3.3 0.2 1.0 O A:HOH701 3.7 63.6 1.0 CD A:LYS524 3.9 93.6 1.0 NZ A:LYS524 3.9 0.2 1.0 OE2 A:GLU368 3.9 0.8 1.0 C A:VAL523 4.0 82.5 1.0 OE1 A:GLU522 4.0 0.7 1.0 OE1 A:GLU386 4.2 97.0 1.0 CG A:GLU522 4.3 95.7 1.0 NE2 A:GLN534 4.4 69.0 1.0 CE A:LYS524 4.4 99.2 1.0 N A:VAL523 4.5 74.2 1.0 CB A:ASP507 4.7 75.4 1.0 CD A:GLU368 4.7 0.3 1.0 CA A:VAL523 4.8 75.7 1.0 CG A:GLU368 4.9 0.0 1.0 N A:LYS524 5.0 84.4 1.0

H.Jin, U.Roy, G.Lee, O.D.Scharer, Y.Cho. Structural Mechanism of Dna Interstrand Cross-Link Unhooking By the Bacterial FAN1 Nuclease. J. Biol. Chem. V. 293 6482 2018.
ISSN: ESSN 1083-351X
PubMed: 29514982
DOI: 10.1074/JBC.RA118.002171