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Sodium in PDB 6lzh: Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18

Protein crystallography data

The structure of Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18, PDB code: 6lzh was solved by H.Wang, J.Yu, W.G.Wang, Y.Matsuda, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.67 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.683, 55.010, 67.272, 101.71, 100.51, 114.28
R / Rfree (%) 17.8 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18 (pdb code 6lzh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18, PDB code: 6lzh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6lzh

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Sodium binding site 1 out of 4 in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18


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 Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:14.7
occ:1.00
O A:ILE263 2.4 16.9 1.0
OD1 A:ASP262 2.4 15.6 1.0
O A:HOH507 2.5 19.3 1.0
O A:HOH549 2.8 26.7 1.0
C A:ILE263 3.5 16.9 1.0
CG A:ASP262 3.5 17.6 1.0
OD2 A:ASP262 4.0 14.3 1.0
N A:ILE263 4.0 16.2 1.0
O A:HOH502 4.2 22.7 1.0
CA A:ILE263 4.3 14.9 1.0
N A:LEU264 4.4 16.4 1.0
CA A:LEU264 4.5 16.3 1.0
NH1 A:ARG283 4.6 17.5 1.0
C A:ASP262 4.7 16.3 1.0
N A:LYS265 4.7 20.3 1.0
CB A:ASP262 4.8 18.1 1.0
CA A:ASP262 4.9 16.0 1.0
CD2 A:LEU264 4.9 14.3 1.0
CB A:ILE263 4.9 17.1 1.0

Sodium binding site 2 out of 4 in 6lzh

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Sodium binding site 2 out of 4 in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18


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 Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:19.1
occ:1.00
O A:TRP218 2.2 24.8 1.0
O A:SER215 2.3 24.9 1.0
O A:HOH535 2.4 35.3 1.0
O A:HOH566 2.5 29.0 1.0
O A:HOH408 2.6 36.0 1.0
C A:TRP218 3.4 23.7 1.0
C A:SER215 3.4 26.3 1.0
O A:HOH474 4.1 20.4 1.0
CA A:SER215 4.1 27.9 1.0
CB A:SER215 4.2 25.3 1.0
CA A:TRP218 4.2 21.1 1.0
N A:TRP218 4.2 22.3 1.0
OD1 A:ASP142 4.3 38.5 1.0
N A:LEU216 4.4 23.8 1.0
N A:ASN219 4.4 23.5 1.0
CB A:TRP218 4.4 22.8 1.0
CA A:LEU216 4.5 22.9 1.0
CA A:ASN219 4.5 21.9 1.0
OG1 A:THR144 4.6 40.6 1.0
C A:LEU216 4.6 25.5 1.0
O A:HOH593 4.7 28.6 1.0
O A:HOH568 4.7 28.4 1.0
N A:SER143 4.7 37.3 1.0
O A:LEU216 4.8 23.9 1.0
OG A:SER215 4.9 38.4 1.0
CD1 A:TRP218 4.9 21.8 1.0

Sodium binding site 3 out of 4 in 6lzh

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Sodium binding site 3 out of 4 in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:20.2
occ:1.00
O B:TRP218 2.2 26.3 1.0
O B:HOH474 2.3 30.8 1.0
O B:SER215 2.3 30.3 1.0
O B:HOH493 2.3 35.2 1.0
O B:HOH441 2.5 36.6 1.0
O B:HOH510 2.5 36.1 1.0
C B:SER215 3.4 31.5 1.0
C B:TRP218 3.4 23.1 1.0
OD1 B:ASP142 4.1 39.2 1.0
CA B:SER215 4.2 29.4 1.0
CA B:TRP218 4.2 26.6 1.0
CB B:SER215 4.3 31.6 1.0
OG B:SER215 4.3 38.0 1.0
N B:TRP218 4.3 24.4 1.0
N B:LEU216 4.3 27.8 1.0
CA B:LEU216 4.3 27.4 1.0
CB B:TRP218 4.3 23.2 1.0
O B:HOH465 4.4 22.2 1.0
N B:ASN219 4.4 25.0 1.0
OG1 B:THR144 4.4 36.5 1.0
O B:HOH524 4.5 38.9 1.0
CA B:ASN219 4.6 25.8 1.0
C B:LEU216 4.6 25.7 1.0
O B:LEU216 4.7 27.4 1.0
N B:SER143 4.8 38.3 1.0
CD1 B:TRP218 5.0 20.6 1.0

Sodium binding site 4 out of 4 in 6lzh

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Sodium binding site 4 out of 4 in the Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Alpha/Beta Hydrolase Grgf From Penicillium Sp. SH18 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:25.8
occ:1.00
OD1 B:ASP166 2.5 40.6 1.0
O B:HOH475 3.3 34.8 1.0
CG B:ASP166 3.5 33.4 1.0
OD2 B:ASP166 3.9 41.2 1.0
O A:HOH595 4.1 31.6 1.0
CB B:ASP166 4.8 35.1 1.0

Reference:

W.G.Wang, H.Wang, L.Q.Du, M.Li, L.Chen, J.Yu, G.G.Cheng, M.T.Zhan, Q.F.Hu, L.Zhang, M.Yao, Y.Matsuda. Molecular Basis For the Biosynthesis of An Unusual Chain-Fused Polyketide, Gregatin A. J.Am.Chem.Soc. V. 142 8464 2020.
ISSN: ESSN 1520-5126
PubMed: 32275405
DOI: 10.1021/JACS.0C02337
Page generated: Tue Dec 15 12:34:22 2020

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