Nickel in PDB 7a1f: Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp

The structure of Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp, PDB code: 7a1f was solved by J.A.Newman, H.T.Baddock, S.M.M.Mukhopadhyay, N.A.Burgess-Brown, F.Vondelft, C.H.Arrowshmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.95 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.121, 54.183, 72.109, 75.48, 74.33, 63.09
R / Rfree (%)	17.7 / 22.3

The structure of Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp (pdb code 7a1f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp, PDB code: 7a1f:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:26.2 occ:1.00 O A:HOH547 1.9 25.2 1.0 O2P A:D5M404 2.1 31.0 1.0 ND1 A:HIS33 2.2 27.3 1.0 NE2 A:HIS31 2.2 27.1 1.0 NE2 A:HIS99 2.2 19.8 1.0 OD2 A:ASP120 2.3 24.7 1.0 CE1 A:HIS33 3.1 23.2 1.0 CE1 A:HIS31 3.1 27.7 1.0 CD2 A:HIS99 3.2 21.4 1.0 CE1 A:HIS99 3.2 21.3 1.0 CG A:HIS33 3.2 25.4 1.0 CD2 A:HIS31 3.2 24.6 1.0 FE A:FE401 3.2 33.8 1.0 P A:D5M404 3.3 38.4 1.0 CG A:ASP120 3.4 29.9 1.0 O3P A:D5M404 3.5 35.5 1.0 CB A:HIS33 3.6 25.2 1.0 CB A:ASP120 3.8 21.1 1.0 O5' A:D5M404 3.9 38.8 1.0 H5'2 A:D5M404 4.1 41.5 1.0 NE2 A:HIS36 4.2 29.3 1.0 ND1 A:HIS31 4.3 26.8 1.0 NE2 A:HIS33 4.3 29.6 1.0 ND1 A:HIS99 4.3 19.1 1.0 CD2 A:HIS36 4.3 28.6 1.0 CG A:HIS99 4.3 25.1 1.0 CD2 A:HIS33 4.3 26.9 1.0 CG A:HIS31 4.3 26.7 1.0 OD1 A:ASP120 4.5 23.2 1.0 O1P A:D5M404 4.5 31.2 1.0 C5' A:D5M404 4.5 34.6 1.0 H1 A:D5M404 4.6 47.9 1.0 CE1 A:HIS276 4.6 23.2 1.0 OD1 A:ASP35 4.6 28.8 1.0 NE2 A:HIS276 4.9 23.7 1.0 O A:HOH594 4.9 31.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni402 b:21.4 occ:1.00 ND1 L:HIS33 2.0 19.8 1.0 O L:HOH557 2.1 22.1 1.0 O3P L:D5M404 2.2 28.1 1.0 NE2 L:HIS99 2.2 19.9 1.0 OD2 L:ASP120 2.3 21.8 1.0 NE2 L:HIS31 2.3 20.9 1.0 CE1 L:HIS33 2.9 24.2 1.0 CG L:HIS33 3.1 26.5 1.0 CD2 L:HIS31 3.2 19.4 1.0 CE1 L:HIS99 3.2 19.7 1.0 CD2 L:HIS99 3.2 20.8 1.0 P L:D5M404 3.2 32.6 1.0 FE L:FE401 3.3 25.7 1.0 CG L:ASP120 3.3 18.8 1.0 CE1 L:HIS31 3.4 26.8 1.0 CB L:HIS33 3.5 21.4 1.0 O1P L:D5M404 3.6 26.3 1.0 CB L:ASP120 3.7 15.3 1.0 O5' L:D5M404 3.8 35.1 1.0 H5'2 L:D5M404 4.0 44.2 1.0 NE2 L:HIS33 4.1 24.2 1.0 CD2 L:HIS33 4.2 21.6 1.0 NE2 L:HIS36 4.2 17.5 1.0 ND1 L:HIS99 4.3 22.9 1.0 CG L:HIS99 4.3 19.2 1.0 CD2 L:HIS36 4.3 16.3 1.0 CG L:HIS31 4.4 24.6 1.0 ND1 L:HIS31 4.4 21.1 1.0 OD1 L:ASP120 4.4 20.8 1.0 C5' L:D5M404 4.5 36.8 1.0 O2P L:D5M404 4.6 32.2 1.0 CE1 L:HIS276 4.6 18.0 1.0 OD1 L:ASP35 4.7 22.4 1.0 H1 L:D5M404 4.7 43.2 1.0 O L:HOH702 4.8 28.1 1.0 NE2 L:HIS276 4.9 18.1 1.0 H5'1 L:D5M404 4.9 44.2 1.0 CA L:HIS33 5.0 21.9 1.0

J.A.Newman, H.T.Baddock, S.M.M.Mukhopadhyay, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowshmith, A.Edwards, C.Bountra, O.Gileadi. Crystal Structure of Human 5' Exonuclease Appollo in Complex with 5'Damp To Be Published.