Calcium in PDB 5y7g: Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap

All present enzymatic activity of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap:
3.1.4.1;

The structure of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap, PDB code: 5y7g was solved by Y.Cho, H.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.58 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	140.290, 143.258, 172.712, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 28

The binding sites of Calcium atom in the Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap (pdb code 5y7g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap, PDB code: 5y7g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:92.2 occ:1.00 O A:VAL523 2.0 0.3 1.0 OP1 J:DC6 2.2 0.9 1.0 OE2 A:GLU368 2.3 0.7 1.0 OE2 A:GLU522 2.4 0.2 1.0 OD2 A:ASP507 2.5 84.9 1.0 P J:DC6 3.2 0.1 1.0 C A:VAL523 3.3 0.8 1.0 CG A:ASP507 3.4 93.2 1.0 CD A:GLU368 3.5 0.3 1.0 OD1 A:ASP507 3.6 0.2 1.0 CD A:GLU522 3.6 92.4 1.0 O5' J:DC6 3.6 0.1 1.0 OP2 J:DC6 3.8 0.2 1.0 CD A:LYS524 3.9 0.7 1.0 OD2 A:ASP528 4.1 0.6 1.0 CA A:LYS524 4.1 0.9 1.0 N A:LYS524 4.1 0.0 1.0 CG A:GLU368 4.2 94.2 1.0 NZ A:LYS524 4.2 0.1 1.0 OE1 A:GLU522 4.3 89.7 1.0 N A:VAL523 4.3 86.6 1.0 CA A:VAL523 4.3 88.6 1.0 CE A:LYS524 4.3 0.3 1.0 CA A:CA602 4.4 0.8 1.0 C5' J:DC6 4.5 0.2 1.0 OE1 A:GLU368 4.5 0.2 1.0 CG A:GLU522 4.6 0.8 1.0 O3' J:DA5 4.6 0.0 1.0 CG A:LYS524 4.6 0.1 1.0 CB A:VAL523 4.7 90.8 1.0 CB A:ASP507 4.8 0.2 1.0 CB A:LYS524 4.9 0.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:0.8 occ:1.00 OD1 A:ASP507 2.4 0.2 1.0 OP1 J:DC6 2.6 0.9 1.0 OE1 A:GLU386 2.7 0.5 1.0 O3' J:DA5 2.7 0.0 1.0 P J:DC6 3.2 0.1 1.0 CG A:ASP507 3.5 93.2 1.0 C3' J:DA5 3.6 0.2 1.0 OH A:TYR384 3.7 0.4 1.0 C4' J:DA5 3.8 0.9 1.0 CD A:GLU386 3.9 0.5 1.0 OD2 A:ASP507 4.1 84.9 1.0 C5' J:DC6 4.2 0.2 1.0 O5' J:DC6 4.2 0.1 1.0 OE2 A:GLU368 4.3 0.7 1.0 CA A:CA601 4.4 92.2 1.0 OP2 J:DC6 4.4 0.2 1.0 CD A:GLU368 4.5 0.3 1.0 C5' J:DA5 4.5 0.4 1.0 OE2 A:GLU386 4.5 0.8 1.0 CB A:ASP507 4.5 0.2 1.0 CZ A:TYR384 4.6 0.2 1.0 CG A:GLU368 4.6 94.2 1.0 CA A:ASP507 4.8 0.8 1.0 CB A:GLU386 4.8 86.4 1.0 OE2 A:GLU522 4.9 0.2 1.0 OE1 A:GLU368 5.0 0.2 1.0 CG A:GLU386 5.0 0.6 1.0 C2' J:DA5 5.0 0.0 1.0 O4' J:DA5 5.0 0.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:0.3 occ:1.00 O B:VAL523 2.1 0.4 1.0 OP1 L:DA5 2.4 0.7 1.0 OD2 B:ASP507 2.5 0.1 1.0 OE2 B:GLU522 2.5 0.1 1.0 OE2 B:GLU368 2.6 0.4 1.0 C B:VAL523 3.4 0.0 1.0 CG B:ASP507 3.4 0.9 1.0 P L:DA5 3.5 1.0 1.0 OD1 B:ASP507 3.6 0.1 1.0 O5' L:DA5 3.6 0.1 1.0 C5' L:DA5 3.7 0.1 1.0 CD B:GLU522 3.7 0.8 1.0 CD B:GLU368 3.7 0.8 1.0 CA B:CA602 3.8 0.6 1.0 CD B:LYS524 3.9 0.2 1.0 NZ B:LYS524 4.0 0.5 1.0 CE B:LYS524 4.1 0.5 1.0 CG B:GLU368 4.2 0.4 1.0 N B:LYS524 4.3 0.6 1.0 CA B:LYS524 4.3 0.2 1.0 OP2 L:DA5 4.3 0.0 1.0 N B:VAL523 4.3 0.0 1.0 CA B:VAL523 4.4 0.1 1.0 CG B:GLU522 4.5 0.2 1.0 OD1 B:ASP528 4.5 0.1 1.0 OE1 B:GLU522 4.6 0.5 1.0 CG B:LYS524 4.8 1.0 1.0 O3' L:DC4 4.8 0.4 1.0 OE1 B:GLU368 4.8 0.3 1.0 CB B:ASP507 4.8 0.0 1.0 CB B:VAL523 4.8 0.5 1.0 C4' L:DA5 5.0 0.6 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:0.6 occ:1.00 OD1 B:ASP507 2.4 0.1 1.0 OP1 L:DA5 2.5 0.7 1.0 OE1 B:GLU386 2.6 0.2 1.0 O3' L:DC4 3.1 0.4 1.0 CG B:ASP507 3.3 0.9 1.0 P L:DA5 3.4 1.0 1.0 OH B:TYR384 3.5 0.4 1.0 C5' L:DA5 3.5 0.1 1.0 OE2 B:GLU368 3.7 0.4 1.0 CD B:GLU386 3.7 0.5 1.0 CA B:CA601 3.8 0.3 1.0 OD2 B:ASP507 3.8 0.1 1.0 CD B:GLU368 3.9 0.8 1.0 O5' L:DA5 3.9 0.1 1.0 OE2 B:GLU386 4.2 0.4 1.0 OE1 B:GLU368 4.3 0.3 1.0 OE2 B:GLU522 4.3 0.1 1.0 C3' L:DC4 4.3 0.3 1.0 CZ B:TYR384 4.4 0.9 1.0 CG B:GLU368 4.5 0.4 1.0 C4' L:DC4 4.5 0.5 1.0 CB B:ASP507 4.5 0.0 1.0 OP2 L:DA5 4.7 0.0 1.0 C4' L:DA5 4.8 0.6 1.0 CE1 B:TYR384 4.9 0.9 1.0 CB B:GLU386 4.9 0.6 1.0 CG B:GLU386 4.9 0.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of PAFAN1 Bound to 1NT 5'Flap Dna with Gap within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:0.7 occ:1.00 O C:VAL523 2.2 0.5 1.0 OP1 N:DC6 2.2 0.5 1.0 OD1 C:ASP507 2.3 0.9 1.0 OE2 C:GLU368 2.4 0.7 1.0 OE2 C:GLU522 2.6 0.0 1.0 P N:DC6 3.0 0.3 1.0 OP2 N:DC6 3.3 0.9 1.0 C C:VAL523 3.4 0.6 1.0 O5' N:DC6 3.5 0.6 1.0 CD C:GLU368 3.5 0.6 1.0 CG C:ASP507 3.6 0.4 1.0 NZ C:LYS524 3.7 0.3 1.0 CD C:GLU522 3.7 0.6 1.0 CD C:LYS524 3.9 0.9 1.0 CG C:GLU368 4.0 0.4 1.0 CE C:LYS524 4.0 0.3 1.0 OD2 C:ASP507 4.1 0.8 1.0 N C:VAL523 4.2 0.3 1.0 CA C:VAL523 4.3 0.4 1.0 N C:LYS524 4.4 0.9 1.0 OE1 C:GLU522 4.4 1.0 1.0 CA C:LYS524 4.4 1.0 1.0 O3' N:DA5 4.5 0.4 1.0 C5' N:DC6 4.5 0.9 1.0 OD2 C:ASP528 4.5 0.7 1.0 CB C:VAL523 4.5 0.9 1.0 OE1 C:GLU368 4.6 0.2 1.0 CG C:GLU522 4.7 0.7 1.0 CB C:ASP507 4.7 0.2 1.0 CG C:LYS524 4.8 1.0 1.0 OP2 N:DA7 4.9 0.0 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