Manganese in PDB 4r89: Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase

The structure of Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase, PDB code: 4r89 was solved by Y.Cho, G.H.Gwon, Y.R.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 4.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.115, 106.944, 107.541, 90.00, 89.84, 90.00
R / Rfree (%)	22.4 / 27.8

The binding sites of Manganese atom in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase (pdb code 4r89). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase, PDB code: 4r89:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase


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 - 5' Flap Dna Complex with Manganase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:88.4 occ:1.00 OP1 B:DA5 1.8 0.3 1.0 OE2 A:GLU522 2.1 99.7 1.0 OD2 A:ASP507 2.2 0.7 1.0 O A:VAL523 2.2 0.4 1.0 P B:DA5 3.2 0.8 1.0 CD A:GLU522 3.2 97.7 1.0 OE2 A:GLU368 3.3 0.1 1.0 CG A:ASP507 3.3 1.0 1.0 C A:VAL523 3.4 0.8 1.0 CD A:LYS524 3.6 0.5 1.0 O5' B:DA5 3.7 0.5 1.0 OD1 A:ASP507 3.8 0.2 1.0 OE1 A:GLU522 3.8 95.3 1.0 MN A:MN602 3.9 0.9 1.0 C5' B:DA5 3.9 0.9 1.0 N A:VAL523 4.0 0.6 1.0 CG2 A:VAL523 4.0 0.2 1.0 NZ A:LYS524 4.0 0.2 1.0 CG A:GLU368 4.1 0.7 1.0 OP2 B:DA5 4.1 0.3 1.0 CD A:GLU368 4.1 0.7 1.0 O3' B:DC4 4.2 1.0 1.0 CA A:VAL523 4.2 0.7 1.0 CG A:GLU522 4.3 98.6 1.0 CE A:LYS524 4.3 0.1 1.0 N A:LYS524 4.4 0.1 1.0 CB A:ASP507 4.5 0.2 1.0 CA A:LYS524 4.6 0.3 1.0 CG A:LYS524 4.6 0.1 1.0 CB A:VAL523 4.7 0.3 1.0 C A:GLU522 5.0 0.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase


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 - 5' Flap Dna Complex with Manganase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:0.9 occ:1.00 OE1 A:GLU386 2.2 0.3 1.0 OD1 A:ASP507 2.2 0.2 1.0 O3' B:DC4 2.3 1.0 1.0 OP1 B:DA5 2.9 0.3 1.0 CG A:ASP507 3.0 1.0 1.0 OD2 A:ASP507 3.2 0.7 1.0 P B:DA5 3.2 0.8 1.0 CD A:GLU386 3.4 0.9 1.0 C3' B:DC4 3.4 0.1 1.0 C4' B:DC4 3.6 0.6 1.0 MN A:MN601 3.9 88.4 1.0 OH A:TYR384 3.9 0.5 1.0 O5' B:DA5 4.0 0.5 1.0 CB A:GLU386 4.1 0.6 1.0 C2' B:DC4 4.1 1.0 1.0 OE2 A:GLU386 4.2 0.4 1.0 OE1 A:GLU522 4.2 95.3 1.0 OE2 A:GLU368 4.3 0.1 1.0 CB A:ASP507 4.3 0.2 1.0 CG A:GLU386 4.4 0.2 1.0 OE2 A:GLU522 4.4 99.7 1.0 OP2 B:DA5 4.4 0.3 1.0 O4' B:DC4 4.5 0.8 1.0 CE1 A:TYR384 4.6 0.9 1.0 C5' B:DC4 4.7 0.1 1.0 CD A:GLU522 4.7 97.7 1.0 CZ A:TYR384 4.8 0.0 1.0 CD A:GLU368 4.8 0.7 1.0 CG A:GLU368 4.8 0.7 1.0 O5' B:DC4 4.8 0.4 1.0 CA A:ASP507 4.8 0.7 1.0 C1' B:DC4 4.9 0.9 1.0 NE2 A:GLN534 4.9 88.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn601 b:95.1 occ:1.00 OP1 F:DA5 1.8 0.6 1.0 OE2 E:GLU522 2.1 91.9 1.0 OD2 E:ASP507 2.2 0.5 1.0 O E:VAL523 2.2 0.3 1.0 P F:DA5 3.2 0.4 1.0 CD E:GLU522 3.3 90.3 1.0 OE2 E:GLU368 3.3 0.2 1.0 CG E:ASP507 3.3 0.2 1.0 C E:VAL523 3.4 0.7 1.0 CD E:LYS524 3.6 0.9 1.0 O5' F:DA5 3.6 0.3 1.0 OD1 E:ASP507 3.8 0.7 1.0 OE1 E:GLU522 3.9 88.3 1.0 MN E:MN602 3.9 0.9 1.0 C5' F:DA5 3.9 0.6 1.0 CG2 E:VAL523 4.0 0.2 1.0 N E:VAL523 4.0 0.3 1.0 NZ E:LYS524 4.0 0.2 1.0 CG E:GLU368 4.0 0.1 1.0 CD E:GLU368 4.1 0.7 1.0 OP2 F:DA5 4.1 0.1 1.0 O3' F:DC4 4.1 0.0 1.0 CA E:VAL523 4.2 1.0 1.0 CG E:GLU522 4.4 91.3 1.0 CE E:LYS524 4.4 0.9 1.0 N E:LYS524 4.4 0.1 1.0 CB E:ASP507 4.5 0.6 1.0 CA E:LYS524 4.6 0.9 1.0 CG E:LYS524 4.6 0.5 1.0 CB E:VAL523 4.7 0.4 1.0 C E:GLU522 5.0 0.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of PAFAN1 - 5' Flap Dna Complex with Manganase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn602 b:0.9 occ:1.00 OD1 E:ASP507 2.2 0.7 1.0 OE1 E:GLU386 2.2 0.9 1.0 O3' F:DC4 2.3 0.0 1.0 OP1 F:DA5 2.9 0.6 1.0 CG E:ASP507 3.0 0.2 1.0 P F:DA5 3.2 0.4 1.0 OD2 E:ASP507 3.2 0.5 1.0 C3' F:DC4 3.3 0.5 1.0 CD E:GLU386 3.4 0.9 1.0 C4' F:DC4 3.5 0.9 1.0 MN E:MN601 3.9 95.1 1.0 O5' F:DA5 4.0 0.3 1.0 OH E:TYR384 4.1 0.2 1.0 OE1 E:GLU522 4.1 88.3 1.0 CB E:GLU386 4.1 0.1 1.0 C2' F:DC4 4.1 0.7 1.0 OE2 E:GLU386 4.2 0.4 1.0 CG E:GLU386 4.4 0.6 1.0 OE2 E:GLU522 4.4 91.9 1.0 OP2 F:DA5 4.4 0.1 1.0 CB E:ASP507 4.4 0.6 1.0 O4' F:DC4 4.4 0.2 1.0 OE2 E:GLU368 4.4 0.2 1.0 C5' F:DC4 4.5 0.1 1.0 CD E:GLU522 4.7 90.3 1.0 O5' F:DC4 4.7 0.8 1.0 CE1 E:TYR384 4.7 0.9 1.0 NE2 E:GLN534 4.8 88.5 1.0 CA E:ASP507 4.8 0.5 1.0 CZ E:TYR384 4.9 0.8 1.0 C1' F:DC4 4.9 0.0 1.0 CD E:GLU368 4.9 0.7 1.0 CG E:GLU368 4.9 0.1 1.0

G.H.Gwon, Y.R.Kim, Y.Liu, A.T.Watson, A.Jo, T.J.Etheridge, F.Yuan, Y.Zhang, Y.C.Kim, A.M.Carr, Y.Cho. Crystal Structure of A Fanconi Anemia-Associated Nuclease Homolog Bound to 5' Flap Dna: Basis of Interstrand Cross-Link Repair By FAN1 Genes Dev. V. 28 2276 2014.
ISSN: ISSN 0890-9369
PubMed: 25319828
DOI: 10.1101/GAD.248492.114