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Sodium in PDB 2x7j: Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis

Enzymatic activity of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis

All present enzymatic activity of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis:
2.2.1.9;

Protein crystallography data

The structure of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis, PDB code: 2x7j was solved by A.Dawson, M.Chen, P.K.Fyfe, Z.Guo, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.14 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.180, 152.990, 158.499, 90.00, 90.00, 90.00
R / Rfree (%) 17.243 / 22.803

Other elements in 2x7j:

The structure of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis (pdb code 2x7j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis, PDB code: 2x7j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2x7j

Go back to Sodium Binding Sites List in 2x7j
Sodium binding site 1 out of 4 in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1581

b:35.9
occ:1.00
 O A:HIS43 2.3 26.4 1.0
O A:ALA41 2.4 25.2 1.0
O A:ILE46 2.5 24.4 1.0
O A:CYS40 2.7 25.7 1.0
C A:ALA41 3.1 25.2 1.0
O A:HOH2022 3.2 37.0 1.0
C A:HIS43 3.4 26.2 1.0
CA A:ALA41 3.6 24.4 1.0
C A:ILE46 3.7 24.8 1.0
N A:HIS43 3.7 25.7 1.0
C A:CYS40 3.8 25.2 1.0
C A:ALA42 4.0 26.1 1.0
CA A:HIS43 4.1 25.4 1.0
N A:ALA42 4.1 25.4 1.0
N A:ALA41 4.2 24.5 1.0
N A:ILE46 4.4 25.3 1.0
CA A:ILE46 4.4 24.7 1.0
N A:PRO44 4.4 26.4 1.0
O A:ALA42 4.5 26.7 1.0
CA A:ALA42 4.5 25.8 1.0
CB A:ILE46 4.6 24.6 1.0
CB A:HIS43 4.7 24.2 1.0
N A:SER47 4.7 24.9 1.0
CA A:PRO44 4.7 26.7 1.0
CG2 A:VAL48 4.7 26.4 1.0
CA A:SER47 4.9 25.9 1.0
C A:PRO44 4.9 26.8 1.0
CB A:ALA41 5.0 24.4 1.0

Sodium binding site 2 out of 4 in 2x7j

Go back to Sodium Binding Sites List in 2x7j
Sodium binding site 2 out of 4 in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1581

b:33.3
occ:1.00
 O B:ILE46 2.2 28.9 1.0
O B:HOH2022 2.4 34.6 1.0
O B:HIS43 2.4 30.0 1.0
O B:CYS40 2.7 25.9 1.0
O B:ALA41 2.7 26.1 1.0
O B:HOH2024 3.0 44.3 1.0
C B:ALA41 3.4 26.3 1.0
C B:ILE46 3.4 28.2 1.0
C B:HIS43 3.5 29.5 1.0
CA B:ALA41 3.7 25.9 1.0
C B:CYS40 3.8 25.9 1.0
N B:HIS43 3.9 28.8 1.0
CA B:HIS43 4.2 28.7 1.0
CA B:ILE46 4.2 28.4 1.0
N B:ILE46 4.2 29.0 1.0
N B:ALA41 4.2 25.8 1.0
C B:ALA42 4.4 27.9 1.0
N B:ALA42 4.4 26.7 1.0
CB B:ILE46 4.4 27.8 1.0
N B:SER47 4.4 27.3 1.0
N B:PRO44 4.5 29.6 1.0
CG2 B:VAL48 4.6 26.0 1.0
CA B:SER47 4.6 27.7 1.0
CB B:HIS43 4.7 27.9 1.0
CA B:PRO44 4.8 29.5 1.0
N B:VAL48 4.8 27.2 1.0
O B:ALA42 4.8 29.2 1.0
CA B:ALA42 4.9 27.0 1.0
C B:PRO44 4.9 29.3 1.0
O B:HOH2010 4.9 46.1 1.0

Sodium binding site 3 out of 4 in 2x7j

Go back to Sodium Binding Sites List in 2x7j
Sodium binding site 3 out of 4 in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1579

b:36.9
occ:1.00
 O C:HOH2015 2.3 41.4 1.0
O C:ALA41 2.4 29.1 1.0
O C:HIS43 2.4 30.4 1.0
O C:ILE46 2.5 29.4 1.0
O C:CYS40 2.7 26.4 1.0
O C:HOH2018 3.1 35.5 1.0
C C:ALA41 3.1 28.4 1.0
C C:HIS43 3.5 29.6 1.0
CA C:ALA41 3.6 27.3 1.0
O C:HOH2012 3.6 50.9 1.0
C C:ILE46 3.7 29.3 1.0
N C:HIS43 3.8 29.3 1.0
C C:CYS40 3.8 26.2 1.0
N C:ALA42 4.1 28.6 1.0
C C:ALA42 4.1 29.3 1.0
CA C:HIS43 4.2 28.9 1.0
N C:ALA41 4.2 26.3 1.0
N C:ILE46 4.3 29.7 1.0
CA C:ILE46 4.4 29.4 1.0
O C:HOH2017 4.5 46.6 1.0
N C:PRO44 4.6 30.0 1.0
CA C:ALA42 4.6 29.1 1.0
CB C:ILE46 4.6 30.0 1.0
O C:ALA42 4.7 30.1 1.0
CG2 C:VAL48 4.7 27.0 1.0
CA C:PRO44 4.7 30.2 1.0
N C:SER47 4.7 28.9 1.0
CB C:HIS43 4.7 27.8 1.0
C C:PRO44 4.9 30.2 1.0
CA C:SER47 4.9 29.2 1.0
CB C:ALA41 4.9 26.8 1.0

Sodium binding site 4 out of 4 in 2x7j

Go back to Sodium Binding Sites List in 2x7j
Sodium binding site 4 out of 4 in the Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Menaquinone Biosynthesis Protein Mend From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1581

b:33.8
occ:1.00
 O D:ILE46 2.2 28.6 1.0
O D:HIS43 2.3 30.5 1.0
O D:CYS40 2.5 27.1 1.0
O D:ALA41 2.6 27.4 1.0
C D:ALA41 3.3 28.2 1.0
C D:HIS43 3.4 30.6 1.0
C D:ILE46 3.4 29.5 1.0
CA D:ALA41 3.6 28.2 1.0
C D:CYS40 3.7 27.0 1.0
N D:HIS43 3.8 30.0 1.0
CA D:HIS43 4.1 30.1 1.0
N D:ALA41 4.1 26.9 1.0
N D:ILE46 4.1 30.1 1.0
CA D:ILE46 4.1 29.8 1.0
C D:ALA42 4.2 29.8 1.0
N D:ALA42 4.2 29.0 1.0
CB D:ILE46 4.3 30.1 1.0
O D:HOH2016 4.3 39.6 1.0
N D:SER47 4.5 29.1 1.0
N D:PRO44 4.5 31.0 1.0
CB D:HIS43 4.6 29.6 1.0
O D:ALA42 4.6 30.5 1.0
CA D:SER47 4.6 29.6 1.0
CG2 D:VAL48 4.7 28.1 1.0
CA D:PRO44 4.7 30.9 1.0
CA D:ALA42 4.7 29.2 1.0
C D:PRO44 4.8 30.9 1.0
CA D:CYS40 4.9 26.6 1.0
N D:VAL48 5.0 28.6 1.0
CG2 D:ILE46 5.0 29.5 1.0

Reference:

A.Dawson, M.Chen, P.K.Fyfe, Z.Guo, W.N.Hunter. Structure and Reactivity of Bacillus Subtilis Mend Catalyzing the First Committed Step in Menaquinone Biosynthesis. J.Mol.Biol. V. 401 253 2010.
ISSN: ISSN 0022-2836
PubMed: 20600129
DOI: 10.1016/J.JMB.2010.06.025
Page generated: Mon Oct 7 05:04:54 2024

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