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Sodium in PDB 2z1n: Crystal Structure of APE0912 From Aeropyrum Pernix K1

Protein crystallography data

The structure of Crystal Structure of APE0912 From Aeropyrum Pernix K1, PDB code: 2z1n was solved by T.Ichimura, A.Yamamura, F.Mimoto, J.Ohtsuka, K.Miyazono, M.Okai, M.Kamo, W.-C.Lee, K.Nagata, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.19 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.759, 68.869, 69.340, 90.00, 119.00, 90.00
R / Rfree (%) 18.6 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of APE0912 From Aeropyrum Pernix K1 (pdb code 2z1n). 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 APE0912 From Aeropyrum Pernix K1, PDB code: 2z1n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2z1n

Go back to Sodium Binding Sites List in 2z1n
Sodium binding site 1 out of 2 in the Crystal Structure of APE0912 From Aeropyrum Pernix K1


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 APE0912 From Aeropyrum Pernix K1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:28.1
occ:1.00
O A:HOH2136 2.2 31.0 1.0
OD1 A:ASP87 2.7 19.3 1.0
O A:TRP136 2.8 17.0 1.0
CD A:LYS134 3.4 28.9 1.0
CB A:TRP136 3.5 19.8 1.0
CG A:ASP87 3.5 17.4 1.0
C A:TRP136 3.6 17.8 1.0
CB A:LYS134 3.6 21.5 1.0
CE3 A:TRP136 3.6 18.8 1.0
CB A:ASP87 3.8 14.4 1.0
CG A:LYS134 3.9 25.4 1.0
CA A:ASP87 3.9 16.0 1.0
CA A:TRP136 4.0 18.4 1.0
CD2 A:TRP136 4.2 21.9 1.0
CG A:TRP136 4.3 20.2 1.0
N A:TRP136 4.3 19.2 1.0
NZ A:LYS134 4.3 29.7 1.0
O A:HOH2168 4.4 45.3 1.0
CE A:LYS134 4.4 29.6 1.0
N A:GLY137 4.5 15.4 1.0
O A:HOH2120 4.6 36.1 1.0
OD2 A:ASP87 4.6 16.6 1.0
CZ3 A:TRP136 4.7 18.3 1.0
O A:ASP87 4.7 13.3 1.0
O A:ALA86 4.8 18.9 1.0
CA A:GLY137 4.8 14.9 1.0
NZ A:LYS8 4.8 25.8 1.0
C A:ASP87 4.8 14.1 1.0
N A:ASP87 5.0 17.1 1.0

Sodium binding site 2 out of 2 in 2z1n

Go back to Sodium Binding Sites List in 2z1n
Sodium binding site 2 out of 2 in the Crystal Structure of APE0912 From Aeropyrum Pernix K1


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 APE0912 From Aeropyrum Pernix K1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2001

b:28.5
occ:1.00
O A:HOH2074 2.8 32.1 1.0
O A:HOH2020 2.9 25.1 1.0
N A:GLY94 3.0 20.4 1.0
CA A:THR93 3.6 18.8 1.0
CB A:THR93 3.7 19.3 1.0
C A:THR93 3.8 19.6 1.0
CG2 A:ILE67 3.9 24.5 1.0
O A:HOH2079 3.9 34.9 1.0
CD1 A:LEU115 4.0 25.9 1.0
CA A:GLY94 4.0 21.1 1.0
O A:HOH2029 4.2 21.4 1.0
O A:HOH2071 4.2 36.3 1.0
CG2 A:THR93 4.4 19.5 1.0
CB A:ALA14 4.6 19.1 1.0
CB A:ILE67 4.8 24.6 1.0
O A:GLY94 4.8 20.6 1.0
O A:SER92 4.9 16.3 1.0
OG1 A:THR93 4.9 20.0 1.0
C A:GLY94 4.9 20.9 1.0
O A:HOH2038 4.9 26.9 1.0
N A:THR93 4.9 18.0 1.0

Reference:

A.Yamamura, T.Ichimura, F.Mimoto, J.Ohtsuka, K.Miyazono, M.Okai, M.Kamo, W.-C.Lee, K.Nagata, M.Tanokura. A Unique Catalytic Triad Revealed By the Crystal Structure of APE0912, A Short-Chain Dehydrogenase/Reductase Family Protein From Aeropyrum Pernix K1 Proteins V. 70 1640 2008.
ISSN: ISSN 0887-3585
PubMed: 18175326
DOI: 10.1002/PROT.21860
Page generated: Tue Dec 15 06:00:53 2020

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