Nickel in PDB 3h0n: Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution

The structure of Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution, PDB code: 3h0n was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.79 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.750, 59.670, 57.820, 90.00, 128.79, 90.00
R / Rfree (%)	14 / 15.7

The structure of Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Nickel atom in the Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution (pdb code 3h0n). 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 A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution, PDB code: 3h0n:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution


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 A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:14.3 occ:0.35 NI A:NI202 0.0 14.3 0.3 NI A:NI202 1.3 34.0 0.7 ND1 A:HIS112 2.0 13.7 1.0 O A:HOH315 2.2 23.8 1.0 NE2 A:HIS114 2.4 16.3 1.0 O A:HOH448 2.4 27.3 0.5 CE1 A:HIS112 2.9 15.7 1.0 O A:HOH448 3.0 18.3 0.5 CE1 A:HIS114 3.1 18.2 1.0 CG A:HIS112 3.1 11.2 1.0 CD2 A:HIS114 3.5 12.9 1.0 CB A:HIS112 3.6 11.8 1.0 CE A:MSE123 3.7 16.9 0.5 OXT A:ACT207 4.0 14.0 1.0 NE2 A:HIS112 4.0 12.9 1.0 O A:HOH419 4.1 38.0 1.0 CD2 A:HIS112 4.2 13.1 1.0 ND1 A:HIS114 4.3 13.2 1.0 OH A:TYR6 4.4 12.6 1.0 CA A:HIS112 4.5 9.5 1.0 CG A:HIS114 4.6 11.9 1.0 SE A:MSE123 4.6 9.5 0.4 CD1 A:ILE127 4.7 10.3 1.0 C A:ACT207 4.7 15.9 1.0 CH3 A:ACT207 4.8 17.1 1.0 CD2 A:LEU116 4.9 23.3 0.5 O A:HOH385 4.9 32.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution


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 A DUF1470 Family Protein (JANN_2411) From Jannaschia Sp. CCS1 at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:34.0 occ:0.65 NI A:NI202 0.0 34.0 0.7 NI A:NI202 1.3 14.3 0.3 NE2 A:HIS114 2.4 16.3 1.0 ND1 A:HIS112 2.5 13.7 1.0 O A:HOH448 2.7 27.3 0.5 OXT A:ACT207 2.7 14.0 1.0 O A:HOH448 2.9 18.3 0.5 CD2 A:HIS114 3.1 12.9 1.0 CG A:HIS112 3.4 11.2 1.0 O A:HOH315 3.5 23.8 1.0 C A:ACT207 3.5 15.9 1.0 CE1 A:HIS114 3.5 18.2 1.0 CE1 A:HIS112 3.5 15.7 1.0 CB A:HIS112 3.6 11.8 1.0 CH3 A:ACT207 3.6 17.1 1.0 OH A:TYR6 3.8 12.6 1.0 CD1 A:ILE127 3.8 10.3 1.0 CE A:MSE123 4.0 16.9 0.5 CA A:HIS112 4.0 9.5 1.0 CG A:HIS114 4.4 11.9 1.0 ND1 A:HIS114 4.5 13.2 1.0 CG1 A:ILE127 4.6 9.2 1.0 N A:HIS113 4.6 10.2 1.0 CD2 A:HIS112 4.6 13.1 1.0 NE2 A:HIS112 4.6 12.9 1.0 O A:ACT207 4.6 16.7 1.0 C A:HIS112 4.8 10.7 1.0 CZ A:TYR6 4.8 11.8 1.0 CE1 A:TYR6 4.9 13.9 1.0 SE A:MSE123 4.9 9.5 0.4

C.Bakolitsa, A.Bateman, K.K.Jin, D.Mcmullan, S.S.Krishna, M.D.Miller, P.Abdubek, C.Acosta, T.Astakhova, H.L.Axelrod, P.Burra, D.Carlton, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, Y.Elias, J.Feuerhelm, J.C.Grant, A.Grzechnik, S.K.Grzechnik, G.W.Han, L.Jaroszewski, H.E.Klock, M.W.Knuth, P.Kozbial, A.Kumar, D.Marciano, A.T.Morse, K.D.Murphy, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, C.L.Rife, N.Sefcovic, H.Tien, C.B.Trame, C.V.Trout, H.Van Den Bedem, D.Weekes, A.White, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.Lesley, I.A.Wilson. The Structure of JANN_2411 (DUF1470) From Jannaschia Sp. at 1.45  Resolution Reveals A New Fold (the Abate Domain) and Suggests Its Possible Role As A Transcription Regulator. Acta Crystallogr.,Sect.F V. 66 1198 2010.
ISSN: ESSN 1744-3091
PubMed: 20944211
DOI: 10.1107/S1744309109025196