Atomistry » Sodium » PDB 3h0n-3hwd » 3h0n
Atomistry »
  Sodium »
    PDB 3h0n-3hwd »
      3h0n »

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: Sun Aug 17 15:17:37 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy