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Sodium in PDB 4j07: Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae

Enzymatic activity of Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae

All present enzymatic activity of Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae:
2.5.1.78;

Protein crystallography data

The structure of Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae, PDB code: 4j07 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.25 / 1.95
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.950, 109.950, 288.330, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae (pdb code 4j07). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae, PDB code: 4j07:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4j07

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Sodium binding site 1 out of 5 in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae


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 Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:19.0
occ:1.00
 O A:ALA70 2.2 25.2 1.0
OG1 A:THR110 2.3 20.1 1.0
O A:HIS73 2.4 27.7 1.0
O A:HOH363 2.4 24.1 1.0
O A:HOH327 2.6 37.1 1.0
O A:HOH375 2.7 29.3 1.0
CB A:THR110 3.4 19.7 1.0
C A:ALA70 3.5 25.1 1.0
CG2 A:THR110 3.5 19.5 1.0
C A:HIS73 3.6 25.6 1.0
N A:HIS73 4.2 27.5 1.0
O A:THR108 4.2 20.1 1.0
C A:ARG71 4.3 28.1 1.0
CA A:ALA70 4.3 23.0 1.0
O A:ARG71 4.4 26.4 1.0
N A:ARG71 4.4 26.1 1.0
O A:HOH349 4.5 26.4 1.0
CA A:ARG71 4.5 28.0 1.0
N A:ASP74 4.5 25.0 1.0
CA A:ASP74 4.5 23.9 1.0
CA A:HIS73 4.5 26.1 1.0
N A:HIS72 4.6 28.7 1.0
CA A:THR110 4.7 19.0 1.0
CB A:THR108 4.9 18.6 1.0
CB A:ALA70 4.9 22.5 1.0
NH2 A:ARG19 5.0 44.2 1.0
C A:ASP74 5.0 21.9 1.0

Sodium binding site 2 out of 5 in 4j07

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Sodium binding site 2 out of 5 in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae


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 Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:16.7
occ:1.00
 O B:ALA70 2.3 21.9 1.0
O B:HOH344 2.3 21.5 1.0
O B:HOH353 2.4 23.9 1.0
O B:HOH366 2.5 21.5 1.0
OG1 B:THR110 2.5 19.6 1.0
O B:HIS73 2.5 19.8 1.0
C B:ALA70 3.5 20.6 1.0
CB B:THR110 3.6 19.0 1.0
CG2 B:THR110 3.7 19.3 1.0
C B:HIS73 3.7 20.0 1.0
N B:HIS73 4.0 22.7 1.0
O B:THR108 4.2 18.7 1.0
C B:ARG71 4.2 24.4 1.0
CA B:ARG71 4.4 22.9 1.0
N B:ARG71 4.4 21.3 1.0
O B:ARG71 4.4 23.8 1.0
CA B:ALA70 4.5 20.0 1.0
CA B:HIS73 4.5 21.2 1.0
O B:HOH301 4.5 19.9 1.0
N B:HIS72 4.5 25.6 1.0
N B:ASP74 4.6 20.8 1.0
NH2 B:ARG19 4.7 46.3 1.0
CA B:ASP74 4.8 20.6 1.0
CB B:THR108 4.8 17.7 1.0
CA B:THR110 4.8 18.2 1.0
C B:HIS72 4.9 25.0 1.0

Sodium binding site 3 out of 5 in 4j07

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Sodium binding site 3 out of 5 in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae


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 Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:22.1
occ:1.00
 O C:ALA70 2.3 24.8 1.0
O C:HOH309 2.3 19.5 1.0
OG1 C:THR110 2.4 18.3 1.0
O C:HOH393 2.5 30.9 1.0
O C:HIS73 2.5 22.1 1.0
O C:HOH328 2.6 26.4 1.0
C C:ALA70 3.6 24.9 1.0
CB C:THR110 3.6 17.6 1.0
CG2 C:THR110 3.7 18.0 1.0
C C:HIS73 3.7 22.2 1.0
N C:HIS73 4.1 24.1 1.0
O C:HOH314 4.2 19.6 1.0
O C:THR108 4.2 19.4 1.0
C C:ARG71 4.2 28.4 1.0
O C:ARG71 4.4 31.7 1.0
CA C:ARG71 4.4 28.4 1.0
CA C:ALA70 4.5 24.1 1.0
N C:ARG71 4.5 25.9 1.0
N C:HIS72 4.5 26.5 1.0
CA C:HIS73 4.6 23.3 1.0
N C:ASP74 4.6 21.7 1.0
O C:HOH357 4.6 36.0 1.0
CA C:ASP74 4.7 20.4 1.0
CA C:THR110 4.7 18.1 1.0
O C:HOH365 4.9 35.7 1.0
CB C:ALA70 5.0 24.1 1.0
CB C:THR108 5.0 18.1 1.0
C C:HIS72 5.0 27.1 1.0

Sodium binding site 4 out of 5 in 4j07

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Sodium binding site 4 out of 5 in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae


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 Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na203

b:25.6
occ:1.00
 O D:HIS73 2.3 20.6 1.0
O D:ALA70 2.3 27.1 1.0
OG1 D:THR110 2.4 19.4 1.0
O D:HOH329 2.4 29.0 1.0
O D:HOH326 2.4 27.4 1.0
O D:HOH334 2.7 24.3 1.0
CB D:THR110 3.5 20.0 1.0
C D:HIS73 3.6 21.5 1.0
C D:ALA70 3.6 25.7 1.0
CG2 D:THR110 3.6 20.5 1.0
N D:HIS73 4.0 23.8 1.0
C D:ARG71 4.3 31.5 1.0
O D:THR108 4.3 22.3 1.0
O D:HOH323 4.4 22.7 1.0
CA D:HIS73 4.5 22.1 1.0
N D:ARG71 4.5 28.4 1.0
N D:ASP74 4.5 21.2 1.0
CA D:ALA70 4.5 23.0 1.0
CA D:ARG71 4.5 30.8 1.0
CA D:ASP74 4.5 21.2 1.0
O D:ARG71 4.5 33.4 1.0
N D:HIS72 4.6 31.1 1.0
CA D:THR110 4.7 19.8 1.0
C D:HIS72 5.0 26.5 1.0
C D:ASP74 5.0 19.7 1.0
CB D:ALA70 5.0 23.4 1.0

Sodium binding site 5 out of 5 in 4j07

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Sodium binding site 5 out of 5 in the Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:20.1
occ:1.00
 O E:ALA70 2.2 19.7 1.0
O E:HIS73 2.2 19.7 1.0
O E:HOH316 2.5 20.1 1.0
OG1 E:THR110 2.5 17.5 1.0
O E:HOH369 2.5 22.6 1.0
O E:HOH328 2.9 18.4 1.0
C E:HIS73 3.4 19.1 1.0
C E:ALA70 3.4 20.8 1.0
CG2 E:THR110 3.5 17.6 1.0
CB E:THR110 3.6 17.5 1.0
N E:HIS73 3.8 20.6 1.0
CA E:HIS73 4.3 19.8 1.0
C E:ARG71 4.3 24.1 1.0
CA E:ALA70 4.3 19.8 1.0
N E:ASP74 4.4 18.9 1.0
O E:THR108 4.4 17.2 1.0
N E:ARG71 4.4 21.8 1.0
CA E:ARG71 4.5 23.4 1.0
N E:HIS72 4.5 24.1 1.0
O E:HOH354 4.5 27.2 1.0
CA E:ASP74 4.5 18.9 1.0
O E:ARG71 4.6 24.8 1.0
C E:HIS72 4.7 24.9 1.0
CA E:THR110 4.8 17.1 1.0
C E:ASP74 4.9 17.9 1.0
O E:HOH382 4.9 28.6 1.0
CB E:ALA70 5.0 19.5 1.0
CA E:HIS72 5.0 25.7 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of A Probable Riboflavin Synthase, Beta Chain Ribh (6,7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae To Be Published.
Page generated: Sun Aug 17 19:55:44 2025

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