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Sodium in PDB 4h0s: Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom

Enzymatic activity of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom

All present enzymatic activity of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom, PDB code: 4h0s was solved by F.Zeng, L.Niu, X.Li, M.Teng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.946, 71.436, 53.607, 90.00, 103.53, 90.00
R / Rfree (%) 18.1 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom (pdb code 4h0s). 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 Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom, PDB code: 4h0s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4h0s

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Sodium binding site 1 out of 5 in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:26.7
occ:1.00
 O A:HOH315 3.0 37.9 1.0
N A:TRP77 3.2 18.9 1.0
CA A:SER76 3.8 20.5 0.5
CA A:SER76 3.8 20.3 0.6
CB A:SER76 3.9 21.7 0.5
C A:SER76 4.0 19.5 0.6
C A:SER76 4.0 19.9 0.5
CB A:TRP77 4.0 18.6 1.0
CB A:SER76 4.0 20.5 0.6
O A:TRP77 4.0 19.7 1.0
CA A:TRP77 4.1 17.6 1.0
CD1 A:TRP77 4.4 18.6 1.0
C A:TRP77 4.5 18.6 1.0
CG A:TRP77 4.6 17.4 1.0
OG A:SER76 4.7 21.9 0.6

Sodium binding site 2 out of 5 in 4h0s

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Sodium binding site 2 out of 5 in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:28.0
occ:1.00
 N A:GLU17 3.1 17.6 0.6
N A:GLU17 3.1 18.5 0.4
O A:HOH376 3.3 43.0 1.0
CA B:ASN79 3.4 39.1 1.0
OG A:SER21 3.7 18.7 1.0
CA A:LYS16 3.8 17.2 1.0
C B:ASN79 3.8 33.5 1.0
CB A:GLU17 3.9 19.1 0.6
C A:LYS16 3.9 17.2 1.0
OD1 B:ASN79 4.0 55.0 0.6
CB A:GLU17 4.0 21.3 0.4
CB A:LYS16 4.0 17.8 1.0
CA A:GLU17 4.1 17.9 0.6
CB B:ASN79 4.1 47.3 1.0
CA A:GLU17 4.1 19.5 0.4
CG B:ASN79 4.2 59.6 1.0
N B:ASN79 4.2 34.6 1.0
N B:GLY80 4.3 28.8 1.0
O B:ASN79 4.3 31.6 1.0
CD2 A:LEU20 4.4 33.3 1.0
CG A:LYS16 4.4 19.2 1.0
O A:GLU17 4.6 19.1 0.4
O A:GLU17 4.6 16.9 0.6
OE1 A:GLU17 4.7 29.5 0.4
O A:ASN14 4.9 18.0 1.0
C A:GLU17 4.9 17.4 0.6
C A:GLU17 4.9 19.1 0.4

Sodium binding site 3 out of 5 in 4h0s

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Sodium binding site 3 out of 5 in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:20.9
occ:1.00
 OH B:TYR75 3.1 19.9 1.0
O B:HOH331 3.1 41.3 1.0
NE1 B:TRP77 3.1 18.8 1.0
CE2 B:TYR75 3.7 17.6 1.0
O B:LYS7 3.7 15.4 1.0
CZ B:TYR75 3.8 18.8 1.0
C B:LYS7 3.9 14.7 1.0
CE2 B:TRP77 3.9 17.1 1.0
CZ2 B:TRP77 4.1 17.2 1.0
CB B:LYS7 4.1 17.0 1.0
N B:MET8 4.1 14.3 1.0
CD B:LYS11 4.1 15.0 0.6
CA B:MET8 4.2 13.8 1.0
CD1 B:TRP77 4.2 20.2 1.0
CB B:LYS11 4.2 13.2 0.6
CD B:LYS11 4.2 15.9 0.4
CB B:LYS11 4.2 13.8 0.4
O B:HOH303 4.2 22.1 1.0
CE B:LYS7 4.3 30.0 1.0
CA B:LYS7 4.6 15.4 1.0
CG B:MET8 4.7 15.6 1.0
CG B:LYS11 4.8 14.1 0.6
CG B:LYS11 4.8 15.0 0.4
CD2 B:TYR75 5.0 15.5 1.0

Sodium binding site 4 out of 5 in 4h0s

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Sodium binding site 4 out of 5 in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:31.4
occ:1.00
 N B:ILE19 3.3 19.2 1.0
CB B:GLU17 3.4 20.0 1.0
N B:LEU20 3.5 20.5 1.0
CB B:ILE19 3.6 22.4 1.0
OE1 B:GLU17 3.6 36.2 1.0
C B:GLU17 3.8 15.9 1.0
CA B:ILE19 3.8 21.3 1.0
N B:PRO18 3.9 16.9 1.0
CG1 B:ILE19 4.0 23.7 1.0
CA B:GLU17 4.0 16.9 1.0
C B:ILE19 4.2 22.3 1.0
O B:GLU17 4.2 16.7 1.0
CD B:PRO18 4.2 17.6 1.0
CB B:LEU20 4.3 23.8 1.0
C B:PRO18 4.4 17.6 1.0
CG B:GLU17 4.4 26.9 1.0
CD1 B:ILE19 4.4 26.0 1.0
CD B:GLU17 4.4 34.7 1.0
CA B:LEU20 4.5 21.8 1.0
O C:HOH350 4.5 43.3 1.0
O B:HOH355 4.6 40.4 1.0
CA B:PRO18 4.7 17.2 1.0
CG B:PRO18 4.7 18.2 1.0
O C:HOH338 4.8 34.3 1.0
CG2 B:ILE19 4.9 24.1 1.0

Sodium binding site 5 out of 5 in 4h0s

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Sodium binding site 5 out of 5 in the Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:34.2
occ:1.00
 NZ C:LYS7 3.3 37.5 1.0
NE2 C:GLN4 3.3 36.2 1.0
O C:HOH361 3.6 45.0 1.0
CE1 C:TYR75 3.8 31.1 1.0
CG C:GLN4 4.0 33.2 1.0
CE C:LYS7 4.0 35.5 1.0
CD C:GLN4 4.2 35.5 1.0
OH C:TYR75 4.5 30.5 1.0
CZ C:TYR75 4.5 30.8 1.0
O C:HOH346 4.5 38.1 1.0
CD1 C:TYR75 4.5 31.7 1.0

Reference:

F.Zeng, L.Niu, X.Li, M.Teng. Crystal Structure Analysis of A Basic Phospholipase A2 From Trimeresurus Stejnegeri Venom To Be Published.
Page generated: Mon Oct 7 15:42:53 2024

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