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

Protein crystallography data

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

Other elements in 3h0n:

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

Nickel Binding Sites:

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 3h0n

Go back to Nickel Binding Sites List in 3h0n
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 3h0n

Go back to Nickel Binding Sites List in 3h0n
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

Reference:

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
Page generated: Wed Dec 16 01:23:56 2020

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