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Sodium in PDB 4eyv: Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica

Enzymatic activity of Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica

All present enzymatic activity of Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica:
5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica, PDB code: 4eyv was solved by H.Bhatt, R.K.Pal, N.Tuteja, N.S.Bhavesh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.03 / 1.97
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 121.252, 144.108, 110.735, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.3

Other elements in 4eyv:

The structure of Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica also contains other interesting chemical elements:

Potassium (K) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica (pdb code 4eyv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica, PDB code: 4eyv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4eyv

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Sodium binding site 1 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:32.8
occ:1.00
 OG A:SER11 2.7 26.6 1.0
N A:ASN14 2.8 32.4 1.0
O A:VAL155 3.0 26.7 1.0
O A:SER11 3.1 23.0 1.0
C A:SER11 3.4 25.0 1.0
N A:ASP13 3.4 28.4 1.0
CA A:ASN14 3.5 32.9 0.5
CA A:ASN14 3.5 32.0 0.5
OD1 A:ASN14 3.6 36.6 0.5
CB A:SER11 3.6 24.3 1.0
N A:ILE12 3.7 24.2 1.0
CG A:LYS157 3.7 33.2 1.0
C A:ILE12 3.8 28.9 1.0
N A:LYS157 3.8 22.9 1.0
C A:VAL155 3.8 26.3 1.0
CA A:ILE12 3.9 24.9 1.0
C A:ASP13 3.9 33.2 1.0
CB A:LYS157 3.9 22.7 1.0
CD A:LYS157 3.9 39.7 1.0
CA A:ASP13 4.0 32.3 1.0
O A:HOH321 4.1 29.8 1.0
CA A:SER11 4.1 24.9 1.0
CG A:ASN14 4.1 32.2 0.5
CB A:VAL155 4.2 29.1 1.0
CA A:VAL156 4.3 22.8 1.0
OD1 A:ASN14 4.4 43.3 0.5
CG1 A:VAL155 4.4 27.2 1.0
N A:VAL156 4.4 23.5 1.0
C A:VAL156 4.4 24.6 1.0
CB A:ASN14 4.4 33.1 0.5
CB A:ASN14 4.4 34.7 0.5
CE A:LYS157 4.5 45.0 1.0
CA A:LYS157 4.5 23.7 1.0
O A:ILE12 4.5 25.7 1.0
C A:ASN14 4.5 32.3 1.0
CA A:VAL155 4.7 26.6 1.0
N A:GLN15 4.7 29.9 1.0
NZ A:LYS157 4.7 46.6 1.0
CG A:ASN14 4.8 37.8 0.5
N A:SER11 4.9 24.3 1.0
ND2 A:ASN14 4.9 34.5 0.5

Sodium binding site 2 out of 10 in 4eyv

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Sodium binding site 2 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:31.4
occ:1.00
 ND1 A:HIS54 2.8 20.5 1.0
O A:THR52 2.8 25.0 1.0
N A:ASP66 2.9 24.3 1.0
O A:HOH306 3.0 29.1 1.0
N A:GLY65 3.4 21.6 1.0
O A:ASP66 3.5 27.9 1.0
CA A:ASP66 3.5 25.0 1.0
CB A:ASP66 3.5 25.3 1.0
CE1 A:HIS54 3.6 22.3 1.0
CG A:HIS54 3.7 20.9 1.0
O A:HOH307 3.7 26.5 1.0
C A:GLY64 3.7 22.4 1.0
C A:ASP66 3.7 26.2 1.0
CA A:GLY64 3.8 20.4 1.0
OG1 A:THR52 3.9 24.5 1.0
C A:THR52 3.9 26.3 1.0
CB A:HIS54 3.9 22.5 1.0
C A:GLY65 3.9 25.9 1.0
N A:HIS54 4.1 22.6 1.0
N A:THR52 4.2 24.2 1.0
CA A:GLY65 4.3 23.3 1.0
O A:GLY64 4.5 21.0 1.0
CA A:HIS70 4.5 32.4 1.0
CA A:THR52 4.6 24.1 1.0
CA A:HIS54 4.7 21.5 1.0
NE2 A:HIS54 4.8 22.2 1.0
CD2 A:HIS54 4.8 22.0 1.0
C A:HIS70 4.8 32.1 1.0
CG A:ASP66 4.8 28.0 1.0
N A:PHE53 4.8 23.5 1.0
N A:PHE67 4.8 25.5 1.0
CA A:PHE53 4.9 22.4 1.0
CB A:THR52 4.9 25.0 1.0
CB A:SER51 4.9 25.7 1.0
C A:PHE53 4.9 23.5 1.0
N A:GLY64 5.0 21.0 1.0

Sodium binding site 3 out of 10 in 4eyv

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Sodium binding site 3 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:46.5
occ:1.00
 O A:ASN42 2.6 30.1 1.0
N A:THR49 2.7 25.3 1.0
O A:LEU39 2.8 25.2 1.0
N A:TYR48 3.0 26.5 1.0
OG1 A:THR49 3.2 30.8 1.0
C A:GLY47 3.2 29.1 1.0
CB A:THR49 3.4 27.6 1.0
C A:ASN42 3.4 32.1 1.0
CA A:GLY47 3.4 29.8 1.0
O A:ALA40 3.6 24.4 1.0
CA A:THR49 3.6 26.5 1.0
C A:TYR48 3.7 25.9 1.0
OG A:SER161 3.7 25.9 1.0
CA A:TYR48 3.8 26.2 1.0
K A:K201 3.9 31.8 1.0
O A:PRO43 3.9 35.1 1.0
N A:GLY47 3.9 32.3 1.0
O A:GLY47 3.9 27.2 1.0
CA A:ASN42 4.0 30.8 1.0
CB A:ASN42 4.0 29.2 1.0
N A:ASN42 4.0 29.5 1.0
C A:LEU39 4.0 24.0 1.0
C A:ALA40 4.0 24.4 1.0
C A:PRO43 4.2 35.9 1.0
CA A:ALA40 4.3 22.8 1.0
CB A:TYR48 4.4 23.9 1.0
N A:PRO43 4.4 34.1 1.0
O A:THR49 4.5 27.6 1.0
C A:LYS41 4.6 30.2 1.0
C A:THR49 4.6 26.9 1.0
N A:ALA40 4.7 22.4 1.0
N A:ALA44 4.7 36.5 1.0
CA A:PRO43 4.7 35.0 1.0
N A:LYS41 4.8 25.6 1.0
C A:GLN46 4.8 34.7 1.0
CG2 A:THR49 4.9 26.6 1.0
O A:TYR48 4.9 25.4 1.0
O A:LYS41 5.0 30.8 1.0

Sodium binding site 4 out of 10 in 4eyv

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Sodium binding site 4 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:52.0
occ:1.00
 O A:HOH480 2.1 51.1 1.0
O A:HOH455 2.6 38.6 1.0
N A:GLY135 3.1 25.0 1.0
OD1 A:ASP137 3.7 32.6 0.5
CA A:GLU134 3.9 28.1 1.0
C A:GLU134 4.0 26.9 1.0
CA A:GLY135 4.0 23.9 1.0
N A:MET136 4.2 23.7 1.0
CB A:GLU134 4.5 27.7 1.0
C A:GLY135 4.6 24.6 1.0
CG A:ASP137 4.9 32.6 0.5
O A:HOH408 4.9 59.0 1.0

Sodium binding site 5 out of 10 in 4eyv

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Sodium binding site 5 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:32.4
occ:1.00
 O B:LYS94 2.7 27.6 1.0
OG1 B:THR115 2.8 21.2 1.0
O B:VAL117 2.8 23.2 1.0
N B:THR119 3.3 23.9 1.0
CB B:THR115 3.3 21.7 1.0
OG1 B:THR119 3.5 24.8 1.0
CG2 B:THR115 3.6 22.0 1.0
CA B:VAL118 3.6 26.4 1.0
C B:LYS94 3.6 28.6 1.0
C B:VAL117 3.8 26.1 1.0
CB B:HIS92 3.8 23.1 1.0
C B:VAL118 3.9 27.0 1.0
CD1 B:LEU97 3.9 21.7 1.0
O B:HIS92 3.9 29.9 1.0
C B:HIS92 4.0 27.7 1.0
CA B:HIS92 4.1 25.4 1.0
N B:VAL118 4.2 25.7 1.0
N B:LYS94 4.3 29.0 1.0
CB B:THR119 4.3 26.3 1.0
CA B:PRO95 4.3 27.6 1.0
N B:PRO95 4.3 28.4 1.0
CA B:THR119 4.4 25.1 1.0
CG B:LEU97 4.4 22.7 1.0
CG2 B:THR119 4.4 24.8 1.0
CB B:LEU97 4.5 21.5 1.0
N B:THR93 4.6 27.2 1.0
CA B:LYS94 4.6 28.8 1.0
CG B:HIS92 4.7 23.3 1.0
CD2 B:HIS92 4.8 22.6 1.0
CA B:THR115 4.8 21.1 1.0
CB B:VAL118 4.8 27.4 1.0
C B:PRO95 4.9 25.4 1.0
CG1 B:VAL118 5.0 26.4 1.0

Sodium binding site 6 out of 10 in 4eyv

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Sodium binding site 6 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:32.1
occ:1.00
 O B:THR52 2.7 25.3 1.0
ND1 B:HIS54 2.8 22.0 1.0
O B:HOH317 2.8 34.4 1.0
N B:ASP66 2.9 23.9 1.0
N B:GLY65 3.4 22.0 1.0
CB B:ASP66 3.5 24.7 1.0
O B:ASP66 3.5 28.8 1.0
CA B:ASP66 3.5 24.8 1.0
CE1 B:HIS54 3.6 21.9 1.0
C B:GLY64 3.7 22.9 1.0
CA B:GLY64 3.7 22.2 1.0
CG B:HIS54 3.7 20.4 1.0
C B:ASP66 3.8 25.8 1.0
O B:HOH324 3.8 28.5 1.0
C B:THR52 3.9 26.1 1.0
C B:GLY65 4.0 25.1 1.0
OG1 B:THR52 4.0 27.8 1.0
CB B:HIS54 4.0 22.1 1.0
N B:HIS54 4.2 21.1 1.0
CA B:GLY65 4.2 23.2 1.0
N B:THR52 4.3 25.4 1.0
O B:GLY64 4.5 22.2 1.0
CA B:HIS70 4.6 32.6 1.0
CA B:THR52 4.6 25.6 1.0
N B:PHE67 4.7 26.7 1.0
NE2 B:HIS54 4.7 22.7 1.0
CG B:ASP66 4.8 27.3 1.0
CA B:HIS54 4.8 20.1 1.0
CD2 B:HIS54 4.8 21.4 1.0
C B:HIS70 4.8 32.4 1.0
CB B:SER51 4.9 26.4 1.0
N B:PHE53 4.9 24.1 1.0
CA B:PHE53 4.9 23.3 1.0
N B:GLY64 5.0 21.7 1.0
O B:GLN63 5.0 20.9 1.0
C B:PHE53 5.0 23.2 1.0

Sodium binding site 7 out of 10 in 4eyv

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Sodium binding site 7 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:31.5
occ:1.00
 O B:LEU90 2.7 26.9 1.0
O B:HOH303 2.8 23.8 1.0
N B:VAL128 2.8 21.1 1.0
O B:HOH315 3.3 23.9 1.0
CA B:PHE88 3.4 26.8 1.0
CA B:VAL127 3.5 20.4 1.0
C B:VAL127 3.7 22.1 1.0
O B:ASN87 3.7 25.3 1.0
C B:LEU90 3.7 28.0 1.0
O B:HIS126 3.7 21.1 1.0
CB B:VAL128 3.7 22.3 1.0
C B:PHE88 3.7 28.2 1.0
N B:LEU90 3.8 26.9 1.0
CA B:VAL128 3.8 22.2 1.0
O B:VAL128 3.9 21.9 1.0
CG2 B:VAL128 4.0 22.4 1.0
CA B:LEU90 4.1 27.7 1.0
CD1 B:PHE88 4.1 24.3 1.0
CG1 B:VAL127 4.1 20.4 1.0
CB B:PHE88 4.2 26.5 1.0
O B:PHE88 4.2 26.4 1.0
N B:GLN89 4.2 27.4 1.0
CB B:LEU90 4.2 27.3 1.0
C B:VAL128 4.4 21.0 1.0
CB B:VAL127 4.4 20.9 1.0
N B:PHE88 4.4 26.0 1.0
C B:ASN87 4.4 27.1 1.0
C B:HIS126 4.5 21.9 1.0
N B:VAL127 4.5 21.6 1.0
CG B:PHE88 4.6 25.6 1.0
C B:GLN89 4.7 30.8 1.0
OD1 B:ASN87 4.8 26.6 1.0
O B:VAL127 4.9 21.9 1.0
N B:LYS91 4.9 26.6 1.0
CG2 B:VAL127 4.9 20.6 1.0

Sodium binding site 8 out of 10 in 4eyv

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Sodium binding site 8 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:33.2
occ:1.00
 OD1 B:ASP85 2.8 25.9 1.0
O B:GLY104 2.9 29.0 1.0
N B:THR107 2.9 23.2 1.0
CB B:ASN102 3.2 22.6 1.0
N B:HIS106 3.2 26.4 1.0
OD2 B:ASP85 3.4 24.1 1.0
CG B:ASP85 3.4 27.3 1.0
CG B:ASN102 3.4 25.2 1.0
ND2 B:ASN102 3.4 21.4 1.0
ND2 B:ASN108 3.5 22.8 1.0
N B:ASN108 3.6 23.0 1.0
OD1 B:ASN108 3.6 23.4 1.0
OG1 B:THR107 3.6 23.9 1.0
CG B:ASN108 3.7 26.3 1.0
CA B:HIS106 3.7 27.4 1.0
O B:HOH314 3.7 21.9 1.0
C B:HIS106 3.8 27.5 1.0
C B:THR107 3.8 24.4 1.0
CA B:THR107 3.8 23.3 1.0
C B:PRO105 3.8 27.2 1.0
O B:HOH323 3.8 26.2 1.0
C B:GLY104 4.0 29.8 1.0
OD1 B:ASN102 4.2 25.6 1.0
CA B:PRO105 4.3 28.7 1.0
CB B:THR107 4.3 25.4 1.0
CA B:ASN108 4.4 23.8 1.0
O B:THR107 4.5 24.2 1.0
O B:PRO105 4.5 25.9 1.0
N B:PRO105 4.6 28.9 1.0
CA B:ASN102 4.6 24.4 1.0
CB B:ASN108 4.6 22.5 1.0
CB B:ASP85 4.8 24.3 1.0
O B:PHE83 4.8 24.6 1.0
O B:HIS106 5.0 25.0 1.0

Sodium binding site 9 out of 10 in 4eyv

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Sodium binding site 9 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:37.9
occ:1.00
 OD1 C:ASP85 2.7 28.5 1.0
N C:THR107 2.8 25.1 1.0
O C:GLY104 2.9 31.1 1.0
CB C:ASN102 3.1 24.1 1.0
N C:HIS106 3.1 26.7 1.0
OD2 C:ASP85 3.3 27.6 1.0
CG C:ASN102 3.4 24.1 1.0
CG C:ASP85 3.4 28.8 1.0
ND2 C:ASN102 3.4 22.9 1.0
ND2 C:ASN108 3.6 25.2 1.0
OD1 C:ASN108 3.6 26.3 1.0
N C:ASN108 3.6 24.0 1.0
OG1 C:THR107 3.6 25.6 1.0
CA C:HIS106 3.7 27.4 1.0
CG C:ASN108 3.7 27.2 1.0
CA C:THR107 3.7 24.3 1.0
C C:HIS106 3.8 27.3 1.0
O C:HOH317 3.8 27.5 1.0
C C:THR107 3.8 25.8 1.0
C C:PRO105 3.8 27.1 1.0
O C:HOH325 3.8 29.8 1.0
C C:GLY104 4.0 30.8 1.0
OD1 C:ASN102 4.1 27.8 1.0
CA C:PRO105 4.3 29.8 1.0
CB C:THR107 4.3 26.4 1.0
CA C:ASN108 4.5 24.7 1.0
O C:PRO105 4.5 25.8 1.0
CA C:ASN102 4.6 24.9 1.0
N C:PRO105 4.6 31.5 1.0
O C:THR107 4.6 26.1 1.0
CB C:ASN108 4.7 24.0 1.0
CB C:ASP85 4.9 25.5 1.0
O C:HIS106 4.9 26.7 1.0
O C:PHE83 4.9 25.7 1.0
N C:ASP85 5.0 24.8 1.0

Sodium binding site 10 out of 10 in 4eyv

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Sodium binding site 10 out of 10 in the Crystal Structure of Cyclophilin A Like Protein From Piriformospora Indica


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 Cyclophilin A Like Protein From Piriformospora Indica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na204

b:44.0
occ:1.00
 OG1 C:THR159 2.9 25.1 1.0
O C:HOH358 2.9 43.7 1.0
OD1 C:ASN16 2.9 26.2 1.0
O C:ILE10 2.9 24.7 1.0
C C:ILE10 3.4 26.4 1.0
CG2 C:THR159 3.7 27.1 1.0
CG C:ASN16 3.7 30.1 1.0
N C:ILE10 3.7 24.2 1.0
CB C:THR159 3.8 27.4 1.0
CA C:ASN16 3.8 27.1 1.0
N C:SER11 3.9 25.0 1.0
O C:HOH342 3.9 40.1 1.0
CB C:ASN16 4.0 27.5 1.0
CB C:ASP9 4.0 24.4 1.0
O C:HOH383 4.0 53.8 1.0
C C:ASP9 4.1 24.8 1.0
CB C:SER11 4.2 25.6 1.0
CA C:ILE10 4.3 22.9 1.0
CA C:SER11 4.3 25.4 1.0
N C:ALA17 4.6 25.8 1.0
CA C:ASP9 4.6 25.1 1.0
O C:ASP9 4.6 24.5 1.0
C C:ASN16 4.8 28.7 1.0
N C:ASN16 4.8 28.1 1.0
ND2 C:ASN16 4.8 26.9 1.0
O C:GLY18 4.8 27.0 1.0

Reference:

D.K.Trivedi, H.Bhatt, R.K.Pal, R.Tuteja, B.Garg, A.K.Johri, N.S.Bhavesh, N.Tuteja. Structure of Rna-Interacting Cyclophilin A-Like Protein From Piriformospora Indica That Provides Salinity-Stress Tolerance in Plants Sci Rep V. 3 3001 2013.
ISSN: ESSN 2045-2322
PubMed: 24141523
DOI: 10.1038/SREP03001
Page generated: Mon Oct 7 15:13:46 2024

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