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Sodium in PDB 2y85: Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp:
5.3.1.16; 5.3.1.24;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp, PDB code: 2y85 was solved by J.Kuper, A.Geerlof, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.980, 121.070, 81.140, 90.00, 95.60, 90.00
R / Rfree (%) 21.281 / 28.726

Other elements in 2y85:

The structure of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp (pdb code 2y85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp, PDB code: 2y85:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 2y85

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Sodium binding site 1 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


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 Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1245

b:55.4
occ:1.00
 O A:ILE224 2.7 27.5 1.0
O2P A:1371247 2.8 26.2 1.0
N A:VAL203 3.2 33.7 1.0
N A:GLY201 3.3 25.7 1.0
O A:HOH2036 3.4 25.1 1.0
CB A:VAL203 3.4 34.8 1.0
C A:GLY201 3.5 28.6 1.0
N A:GLY202 3.5 29.9 1.0
CG2 A:VAL203 3.5 33.8 1.0
CA A:GLY201 3.6 26.6 1.0
O5' A:1371247 3.7 24.9 1.0
P A:1371247 3.7 24.2 1.0
C A:ILE224 3.8 27.1 1.0
CA A:VAL225 3.8 29.3 1.0
O1P A:1371247 3.9 26.5 1.0
CA A:VAL203 3.9 35.6 1.0
O A:GLY201 3.9 29.6 1.0
C5' A:1371247 4.2 24.9 1.0
C A:GLY202 4.3 34.2 1.0
N A:VAL225 4.3 27.9 1.0
CA A:GLY202 4.4 32.1 1.0
O A:HOH2027 4.4 17.1 1.0
C A:SER200 4.5 25.2 1.0
CG2 A:VAL225 4.5 32.0 1.0
N A:GLY226 4.5 29.7 1.0
CB A:VAL225 4.6 31.3 1.0
O A:VAL203 4.7 36.6 1.0
C A:VAL225 4.8 29.4 1.0
CG1 A:VAL203 4.8 37.1 1.0
C A:VAL203 4.8 37.3 1.0
CG1 A:VAL225 4.8 32.9 1.0
O A:HOH2035 4.9 29.4 1.0
CA A:SER200 4.9 25.0 1.0

Sodium binding site 2 out of 11 in 2y85

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Sodium binding site 2 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


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 Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1248

b:47.1
occ:1.00
 OD1 A:ASP130 2.3 20.3 1.0
OG1 A:THR170 2.8 20.5 1.0
O A:VAL168 3.0 22.4 1.0
O A:LEU129 3.2 26.1 1.0
CB A:THR170 3.3 22.4 1.0
NH2 A:ARG143 3.3 21.2 1.0
C A:LEU129 3.4 26.0 1.0
N A:LEU129 3.4 26.2 1.0
N A:THR170 3.4 23.9 1.0
CG A:ASP130 3.5 22.7 1.0
N A:ASP130 3.7 25.2 1.0
C A:VAL168 3.7 23.4 1.0
C A:GLY128 4.0 25.6 1.0
CA A:THR170 4.0 23.9 1.0
CA A:ASP130 4.0 24.9 1.0
CA A:GLY128 4.0 24.8 1.0
CA A:LEU129 4.0 26.8 1.0
C A:VAL169 4.1 24.1 1.0
CG1 A:VAL168 4.1 21.3 1.0
N A:VAL169 4.2 24.2 1.0
CA A:VAL169 4.3 24.5 1.0
CB A:ASP130 4.4 23.6 1.0
CZ A:ARG143 4.4 20.7 1.0
OD2 A:ASP130 4.4 22.0 1.0
CB A:VAL168 4.6 22.3 1.0
CG2 A:THR170 4.7 22.3 1.0
CA A:VAL168 4.8 23.4 1.0
NE A:ARG143 4.8 19.6 1.0
O A:GLY128 4.9 25.8 1.0
O A:VAL169 4.9 24.4 1.0
O A:THR170 5.0 25.1 1.0
C A:THR170 5.0 25.1 1.0

Sodium binding site 3 out of 11 in 2y85

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Sodium binding site 3 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


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 Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1249

b:30.6
occ:1.00
 O A:ASP175 2.6 28.9 1.0
O A:ILE172 2.8 27.4 1.0
OE1 B:GLN132 2.8 25.8 1.0
N A:ASP175 3.5 30.2 1.0
C A:ASP175 3.5 29.2 1.0
CG2 A:THR177 3.5 32.7 1.0
C A:THR173 3.5 32.3 1.0
O A:THR173 3.6 33.9 1.0
C A:ILE172 3.7 27.4 1.0
CD B:GLN132 3.7 25.0 1.0
CA A:ASP175 3.8 28.8 1.0
NE2 B:GLN132 3.8 23.9 1.0
O A:HOH2026 3.8 32.8 1.0
CA A:THR173 3.9 30.9 1.0
N A:LYS174 3.9 32.0 1.0
CB A:ASP175 4.0 27.7 1.0
C A:LYS174 4.0 32.1 1.0
N A:THR173 4.1 28.9 1.0
CA A:LYS174 4.4 33.1 1.0
O A:LYS174 4.6 33.4 1.0
N A:GLY176 4.7 29.5 1.0
CA A:ILE172 4.9 26.3 1.0
CB A:THR177 4.9 34.3 1.0

Sodium binding site 4 out of 11 in 2y85

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Sodium binding site 4 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


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 Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1245

b:39.2
occ:1.00
 O1P B:1371247 2.7 24.4 1.0
O B:ILE224 2.9 21.5 1.0
C B:GLY201 3.0 23.1 1.0
N B:GLY201 3.0 21.8 1.0
CA B:GLY201 3.1 22.1 1.0
N B:VAL203 3.2 23.5 1.0
N B:GLY202 3.3 23.0 1.0
O B:GLY201 3.3 24.4 1.0
CB B:VAL203 3.6 24.2 1.0
CG2 B:VAL203 3.7 24.4 1.0
P B:1371247 3.7 25.2 1.0
O2P B:1371247 3.7 24.6 1.0
O B:HOH2048 3.8 23.6 1.0
O5' B:1371247 3.9 24.2 1.0
CA B:VAL203 3.9 24.0 1.0
C B:ILE224 4.0 21.2 1.0
C5' B:1371247 4.0 26.2 1.0
CA B:VAL225 4.1 22.2 1.0
C B:GLY202 4.1 24.4 1.0
C B:SER200 4.2 22.1 1.0
CA B:GLY202 4.2 23.7 1.0
O B:HOH2040 4.3 26.6 1.0
N B:VAL225 4.5 21.6 1.0
O B:VAL203 4.7 24.7 1.0
CG2 B:VAL225 4.7 24.5 1.0
CA B:SER200 4.8 22.2 1.0
C B:VAL203 4.8 24.3 1.0
N B:GLY226 4.8 22.2 1.0
CB B:VAL225 4.9 23.3 1.0
O B:HOH2049 4.9 15.4 1.0
CG1 B:VAL203 4.9 25.1 1.0

Sodium binding site 5 out of 11 in 2y85

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Sodium binding site 5 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


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 Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1248

b:32.1
occ:1.00
 O B:VAL168 2.5 21.7 1.0
OG1 B:THR170 2.6 20.3 1.0
O B:LEU129 3.0 20.2 1.0
OD1 B:ASP130 3.0 17.4 1.0
N B:THR170 3.1 22.3 1.0
CB B:THR170 3.2 20.6 1.0
C B:VAL168 3.3 22.7 1.0
C B:LEU129 3.3 21.6 1.0
N B:LEU129 3.4 23.5 1.0
C B:VAL169 3.6 22.4 1.0
CA B:VAL169 3.7 23.2 1.0
N B:VAL169 3.7 22.9 1.0
CA B:THR170 3.8 21.7 1.0
CG1 B:VAL168 3.8 22.8 1.0
N B:ASP130 3.9 20.9 1.0
C B:GLY128 3.9 24.1 1.0
CA B:LEU129 4.0 23.0 1.0
NH2 B:ARG143 4.0 21.5 1.0
CA B:GLY128 4.0 23.8 1.0
CG B:ASP130 4.2 18.6 1.0
CA B:ASP130 4.2 20.2 1.0
CB B:VAL168 4.3 23.1 1.0
CA B:VAL168 4.4 23.5 1.0
O B:VAL169 4.4 22.0 1.0
O B:HOH2039 4.6 21.4 1.0
CG2 B:THR170 4.6 20.9 1.0
CB B:ASP130 4.8 19.6 1.0
O B:THR170 4.8 22.6 1.0
C B:THR170 4.9 22.5 1.0
O B:GLY128 4.9 25.3 1.0
CB B:SER200 4.9 21.5 1.0
CB B:LEU129 4.9 24.0 1.0
CZ B:ARG143 5.0 21.3 1.0

Sodium binding site 6 out of 11 in 2y85

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Sodium binding site 6 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1245

b:42.1
occ:1.00
 O C:ILE224 2.7 17.1 1.0
O3P C:1371247 3.0 21.8 1.0
N C:VAL203 3.1 21.1 1.0
O C:HOH2044 3.1 18.0 1.0
C C:GLY201 3.2 19.3 1.0
N C:GLY201 3.2 19.0 1.0
CG2 C:VAL203 3.3 22.0 1.0
CA C:GLY201 3.3 19.2 1.0
CB C:VAL203 3.4 21.6 1.0
N C:GLY202 3.4 19.5 1.0
O C:GLY201 3.6 19.0 1.0
O C:HOH2049 3.7 21.7 1.0
P C:1371247 3.7 21.0 1.0
CA C:VAL203 3.8 21.8 1.0
O5' C:1371247 3.9 23.3 1.0
C C:ILE224 3.9 17.6 1.0
CA C:VAL225 3.9 18.9 1.0
O2P C:1371247 4.0 22.5 1.0
C5' C:1371247 4.1 25.5 1.0
C C:GLY202 4.2 21.5 1.0
CA C:GLY202 4.3 20.8 1.0
N C:VAL225 4.4 17.8 1.0
CG2 C:VAL225 4.4 19.3 1.0
C C:SER200 4.5 19.2 1.0
CB C:VAL225 4.5 19.9 1.0
CG1 C:VAL225 4.6 20.6 1.0
O C:VAL203 4.6 21.5 1.0
N C:GLY226 4.7 19.5 1.0
CG1 C:VAL203 4.7 21.9 1.0
C C:VAL203 4.8 22.3 1.0
C C:VAL225 4.9 19.0 1.0

Sodium binding site 7 out of 11 in 2y85

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Sodium binding site 7 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1248

b:29.2
occ:1.00
 OG1 C:THR170 2.6 20.6 1.0
OD1 C:ASP130 2.6 18.1 1.0
O C:VAL168 2.6 22.2 1.0
O C:LEU129 3.2 22.2 1.0
N C:THR170 3.4 20.7 1.0
CB C:THR170 3.4 20.0 1.0
C C:VAL168 3.4 21.5 1.0
C C:LEU129 3.5 23.0 1.0
N C:LEU129 3.5 23.7 1.0
C C:VAL169 3.8 20.7 1.0
CG C:ASP130 3.9 21.7 1.0
NH2 C:ARG143 3.9 16.7 1.0
N C:ASP130 3.9 23.0 1.0
CA C:GLY128 3.9 23.6 1.0
C C:GLY128 4.0 23.7 1.0
CA C:THR170 4.0 20.4 1.0
N C:VAL169 4.0 21.2 1.0
CA C:VAL169 4.0 21.4 1.0
CG1 C:VAL168 4.1 20.0 1.0
CA C:ASP130 4.1 22.3 1.0
CB C:VAL168 4.2 20.7 1.0
CA C:LEU129 4.2 23.8 1.0
CA C:VAL168 4.4 21.5 1.0
O C:HOH2040 4.5 21.3 1.0
CB C:ASP130 4.6 22.3 1.0
O C:VAL169 4.6 20.9 1.0
CG2 C:THR170 4.7 19.3 1.0
OD2 C:ASP130 4.8 23.4 1.0
CZ C:ARG143 4.8 16.4 1.0
CB C:SER200 4.8 19.6 1.0
O C:GLY128 4.9 24.3 1.0

Sodium binding site 8 out of 11 in 2y85

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Sodium binding site 8 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1249

b:23.8
occ:1.00
 O C:ILE172 2.6 24.0 1.0
O C:ASP175 2.7 25.1 1.0
N C:ASP175 3.0 25.1 1.0
C C:THR173 3.3 25.9 1.0
O C:THR173 3.4 26.5 1.0
C C:ASP175 3.5 24.2 1.0
N C:LYS174 3.5 25.4 1.0
C C:ILE172 3.5 23.4 1.0
CA C:ASP175 3.5 24.0 1.0
CB C:ASP175 3.6 24.1 1.0
C C:LYS174 3.7 25.7 1.0
CA C:THR173 3.8 25.9 1.0
CG2 C:THR177 3.9 25.0 1.0
CA C:LYS174 4.0 26.4 1.0
N C:THR173 4.1 24.4 1.0
O C:LYS174 4.5 25.9 1.0
CA C:ILE172 4.6 22.4 1.0
N C:GLY176 4.7 23.4 1.0
O C:ASP171 4.9 21.4 1.0
CG C:ASP175 4.9 24.2 1.0

Sodium binding site 9 out of 11 in 2y85

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Sodium binding site 9 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1245

b:48.4
occ:1.00
 O3P D:1371247 2.6 24.3 1.0
O D:ILE224 2.8 21.9 1.0
N D:GLY201 3.2 20.8 1.0
C D:GLY201 3.3 21.1 1.0
CA D:GLY201 3.3 20.8 1.0
N D:VAL203 3.4 22.0 1.0
N D:GLY202 3.5 20.9 1.0
CB D:VAL203 3.5 22.6 1.0
CG2 D:VAL203 3.6 22.7 1.0
P D:1371247 3.6 25.8 1.0
O D:GLY201 3.7 22.5 1.0
CA D:VAL225 3.8 21.6 1.0
C D:ILE224 3.9 21.9 1.0
O5' D:1371247 3.9 26.3 1.0
O D:HOH2040 3.9 24.3 1.0
CA D:VAL203 4.0 22.3 1.0
C5' D:1371247 4.1 28.5 1.0
O1P D:1371247 4.1 24.8 1.0
N D:VAL225 4.3 21.5 1.0
C D:GLY202 4.4 21.7 1.0
N D:GLY226 4.4 21.2 1.0
CG2 D:VAL225 4.5 22.7 1.0
CA D:GLY202 4.5 21.3 1.0
C D:SER200 4.5 21.3 1.0
CB D:VAL225 4.5 22.0 1.0
CG1 D:VAL225 4.6 22.1 1.0
O D:VAL203 4.6 22.8 1.0
C D:VAL225 4.7 21.7 1.0
C D:VAL203 4.8 22.7 1.0
CG1 D:VAL203 4.8 22.4 1.0
O4' D:1371247 4.9 32.7 1.0
CA D:SER200 5.0 22.0 1.0

Sodium binding site 10 out of 11 in 2y85

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Sodium binding site 10 out of 11 in the Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Mycobacterium Tuberculosis Phosphoribosyl Isomerase with Bound Rcdrp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1248

b:31.6
occ:1.00
 OD1 D:ASP130 2.4 22.5 1.0
OG1 D:THR170 2.6 24.1 1.0
O D:VAL168 3.0 25.8 1.0
N D:LEU129 3.4 25.9 1.0
O D:LEU129 3.5 24.1 1.0
C D:LEU129 3.5 24.1 1.0
CB D:THR170 3.6 23.4 1.0
N D:THR170 3.6 24.2 1.0
NH2 D:ARG143 3.6 24.1 1.0
C D:VAL168 3.6 26.3 1.0
CG D:ASP130 3.7 22.0 1.0
CA D:GLY128 3.8 26.9 1.0
N D:ASP130 3.8 23.4 1.0
C D:GLY128 3.8 26.7 1.0
C D:VAL169 4.1 24.5 1.0
CG1 D:VAL168 4.1 24.9 1.0
N D:VAL169 4.1 26.1 1.0
CA D:LEU129 4.1 25.5 1.0
CA D:ASP130 4.2 22.2 1.0
CA D:VAL169 4.2 25.8 1.0
CA D:THR170 4.2 23.7 1.0
CB D:VAL168 4.3 26.6 1.0
O D:HOH2038 4.4 23.6 1.0
OD2 D:ASP130 4.6 21.5 1.0
CB D:ASP130 4.6 21.7 1.0
CA D:VAL168 4.6 27.1 1.0
CZ D:ARG143 4.7 24.0 1.0
O D:GLY128 4.7 27.4 1.0
CG2 D:THR170 4.9 22.3 1.0
O D:VAL169 4.9 24.4 1.0
OG1 D:THR105 4.9 23.6 1.0

Reference:

A.V.Due, J.Kuper, A.Geerlof, J.P.Kries, M.Wilmanns. Bisubstrate Specificity in Histidine/Tryptophan Biosynthesis Isomerase From Mycobacterium Tuberculosis By Active Site Metamorphosis. Proc.Natl.Acad.Sci.Usa V. 108 3554 2011.
ISSN: ISSN 0027-8424
PubMed: 21321225
DOI: 10.1073/PNAS.1015996108
Page generated: Mon Oct 7 05:21:13 2024

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