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Sodium 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:

Nickel (Ni) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3h0n

Go back to Sodium Binding Sites List in 3h0n
Sodium 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 Sodium with other atoms in the Na 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:Na203

b:10.8
occ:1.00
O A:CYS152 2.3 9.0 1.0
O A:HOH232 2.3 13.6 1.0
O A:HOH210 2.4 8.2 1.0
O A:CYS147 2.4 9.6 1.0
O A:ALA149 2.4 9.4 1.0
O A:HOH449 2.8 16.4 0.5
C A:CYS152 3.4 8.1 1.0
C A:CYS147 3.5 8.9 1.0
C A:ALA149 3.5 8.8 1.0
C A:ASN148 3.7 10.0 1.0
N A:ALA149 3.7 8.1 1.0
N A:CYS152 3.8 8.4 1.0
CA A:ASN148 4.0 9.7 1.0
O A:ASN148 4.1 10.5 1.0
CA A:CYS152 4.1 8.5 1.0
N A:ASN148 4.1 8.8 1.0
CA A:ALA149 4.2 7.9 1.0
O A:HOH449 4.3 13.5 0.5
N A:ASP153 4.4 9.8 1.0
CB A:CYS152 4.5 9.0 1.0
O A:HOH301 4.5 22.5 1.0
CA A:CYS147 4.6 8.6 1.0
CB A:CYS147 4.6 9.2 1.0
N A:HIS150 4.6 8.3 1.0
CA A:ASP153 4.6 9.4 1.0
O A:HOH381 4.7 31.0 1.0
N A:ARG151 4.7 8.4 1.0
CA A:HIS150 4.8 8.3 1.0
C A:HIS150 4.9 9.2 1.0

Sodium binding site 2 out of 2 in 3h0n

Go back to Sodium Binding Sites List in 3h0n
Sodium 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 Sodium with other atoms in the Na 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:Na204

b:16.1
occ:1.00
O A:HIS95 2.3 13.3 1.0
O A:HOH274 2.4 18.8 1.0
O A:LEU92 2.5 12.2 1.0
O A:ARG93 2.6 13.7 1.0
C A:ARG93 3.2 12.8 1.0
C A:HIS95 3.3 16.7 1.0
C A:LEU92 3.5 12.4 1.0
CA A:ARG93 3.6 12.8 1.0
N A:HIS95 3.8 12.1 1.0
N A:ARG93 4.0 13.7 1.0
N A:ALA97 4.1 14.6 1.0
N A:LYS94 4.1 12.2 1.0
N A:PRO96 4.2 21.2 1.0
CA A:HIS95 4.2 14.8 1.0
CA A:PRO96 4.2 18.5 1.0
C A:LYS94 4.3 12.1 1.0
O A:HOH370 4.4 29.8 1.0
OXT A:ACT209 4.4 26.4 1.0
O A:ACT209 4.6 22.7 1.0
CB A:ALA97 4.6 13.5 1.0
C A:PRO96 4.6 15.4 1.0
CA A:LYS94 4.8 12.1 1.0
O A:LYS94 4.8 14.9 1.0
CA A:LEU92 4.8 11.3 1.0
CB A:ARG93 4.9 14.2 1.0
CA A:ALA97 5.0 13.5 1.0

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: Tue Dec 15 06:13:01 2020

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