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Sodium in PDB 5xwz: Crystal Structure of A Lactonase From Cladophialophora Bantiana

Protein crystallography data

The structure of Crystal Structure of A Lactonase From Cladophialophora Bantiana, PDB code: 5xwz was solved by Y.Y.Zheng, W.T.Liu, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.863, 104.399, 116.834, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Lactonase From Cladophialophora Bantiana (pdb code 5xwz). 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 A Lactonase From Cladophialophora Bantiana, PDB code: 5xwz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5xwz

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Sodium binding site 1 out of 4 in the Crystal Structure of A Lactonase From Cladophialophora Bantiana


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 Lactonase From Cladophialophora Bantiana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:28.6
occ:1.00
 O A:HOH621 2.1 30.0 1.0
O A:VAL122 2.2 17.2 1.0
O A:HOH581 2.2 30.0 1.0
O A:HOH552 2.4 30.3 1.0
O A:PRO119 2.5 20.4 1.0
CG1 A:VAL207 3.2 27.3 1.0
C A:VAL122 3.3 19.2 1.0
O C:HOH664 3.6 42.3 1.0
O A:HOH453 3.6 44.1 1.0
C A:PRO119 3.6 20.6 1.0
O A:HOH662 3.9 41.2 1.0
O C:HOH552 3.9 32.3 1.0
N A:VAL122 4.1 15.5 1.0
CB A:VAL207 4.1 26.0 1.0
N A:ARG123 4.2 17.3 1.0
CA A:ARG123 4.2 18.6 1.0
CA A:VAL122 4.2 17.7 1.0
O C:HOH441 4.3 22.7 1.0
C A:GLU120 4.3 20.1 1.0
O A:ARG123 4.4 17.4 1.0
CA A:GLU120 4.5 21.2 1.0
N A:GLU120 4.5 18.1 1.0
O A:GLU120 4.5 22.0 1.0
CA A:PRO119 4.5 17.8 1.0
C A:ARG123 4.6 19.5 1.0
CB A:VAL122 4.8 18.2 1.0
O C:HOH581 4.8 30.0 1.0
N A:ARG121 4.9 17.1 1.0
O C:HOH525 5.0 30.0 1.0

Sodium binding site 2 out of 4 in 5xwz

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Sodium binding site 2 out of 4 in the Crystal Structure of A Lactonase From Cladophialophora Bantiana


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 Lactonase From Cladophialophora Bantiana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:25.4
occ:1.00
 O B:HOH614 2.3 30.0 1.0
O B:HOH622 2.3 30.0 1.0
O B:PRO119 2.3 20.0 1.0
O B:HOH620 2.3 33.3 1.0
O B:VAL122 2.4 20.5 1.0
CG1 B:VAL207 3.3 20.9 1.0
C B:PRO119 3.4 19.6 1.0
C B:VAL122 3.5 19.6 1.0
N B:VAL122 4.1 20.6 1.0
O B:HOH655 4.1 30.0 1.0
CA B:GLU120 4.2 21.5 1.0
N B:GLU120 4.3 21.3 1.0
CA B:VAL122 4.3 18.4 1.0
CB B:VAL207 4.3 21.2 1.0
O B:HOH547 4.3 30.0 1.0
C B:GLU120 4.3 22.1 1.0
N B:ARG123 4.3 17.9 1.0
CA B:PRO119 4.4 20.1 1.0
CA B:ARG123 4.5 17.9 1.0
O B:GLU120 4.5 23.6 1.0
O B:HOH438 4.7 30.5 1.0
N B:ARG121 4.7 20.8 1.0
CB B:VAL122 4.8 20.4 1.0
CB B:PRO119 4.8 23.6 1.0
O B:HOH411 4.9 42.9 1.0
O B:ARG123 4.9 20.1 1.0
C B:ARG123 4.9 20.0 1.0

Sodium binding site 3 out of 4 in 5xwz

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Sodium binding site 3 out of 4 in the Crystal Structure of A Lactonase From Cladophialophora Bantiana


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 A Lactonase From Cladophialophora Bantiana within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:30.2
occ:1.00
 O C:VAL122 2.3 17.4 1.0
O C:HOH581 2.3 30.0 1.0
O C:PRO119 2.4 25.2 1.0
O C:HOH552 2.6 32.3 1.0
CG1 C:VAL207 3.3 27.4 1.0
O C:HOH525 3.3 30.0 1.0
C C:VAL122 3.4 19.1 1.0
C C:PRO119 3.5 24.3 1.0
O A:HOH662 3.7 41.2 1.0
O C:HOH664 3.9 42.3 1.0
N C:VAL122 4.1 17.0 1.0
O A:HOH552 4.1 30.3 1.0
CB C:VAL207 4.1 28.0 1.0
N C:ARG123 4.2 15.5 1.0
O A:HOH431 4.2 23.5 1.0
CA C:VAL122 4.3 18.5 1.0
CA C:ARG123 4.3 15.8 1.0
C C:GLU120 4.3 22.1 1.0
CA C:GLU120 4.4 22.6 1.0
N C:GLU120 4.4 19.6 1.0
CA C:PRO119 4.4 21.2 1.0
O C:ARG123 4.5 16.0 1.0
O C:GLU120 4.6 25.1 1.0
C C:ARG123 4.7 19.6 1.0
O A:HOH581 4.8 30.0 1.0
CB C:VAL122 4.8 19.3 1.0
N C:ARG121 4.8 20.8 1.0
O A:HOH621 4.9 30.0 1.0
CB C:PRO119 4.9 22.8 1.0

Sodium binding site 4 out of 4 in 5xwz

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Sodium binding site 4 out of 4 in the Crystal Structure of A Lactonase From Cladophialophora Bantiana


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 A Lactonase From Cladophialophora Bantiana within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:39.0
occ:1.00
 O D:HOH550 2.3 30.0 1.0
O D:SER65 2.3 24.2 1.0
O D:HOH552 2.4 30.0 1.0
O D:HOH538 2.4 41.6 1.0
OG D:SER68 2.6 29.5 1.0
O D:HOH563 2.7 48.1 1.0
C D:SER65 3.3 24.6 1.0
CB D:SER68 3.3 30.7 1.0
O D:HOH504 3.9 34.0 1.0
CA D:SER65 4.0 23.9 1.0
N D:ARG66 4.2 22.4 1.0
CA D:ARG66 4.4 23.6 1.0
N D:SER68 4.4 20.4 1.0
O D:HOH568 4.5 50.7 1.0
N D:SER65 4.5 23.0 1.0
CA D:SER68 4.5 22.9 1.0
O D:HOH521 4.7 47.5 1.0
O D:HOH581 4.7 55.3 1.0
C D:ARG66 5.0 24.9 1.0
O D:HOH587 5.0 46.1 1.0

Reference:

R.Hui, X.Hu, W.Liu, W.Liu, Y.Zheng, Y.Chen, R.T.Guo, J.Jin, C.C.Chen. Characterization and Crystal Structure of A Novel Zearalenone Hydrolase From Cladophialophora Bantiana Acta Crystallogr F Struct V. 73 515 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28876230
DOI: 10.1107/S2053230X17011840
Page generated: Tue Oct 8 01:20:14 2024

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