Atomistry » Sodium » PDB 4gxj-4hfc » 4h0s
Atomistry »
  Sodium »
    PDB 4gxj-4hfc »
      4h0s »

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

Go back to Sodium Binding Sites List in 4h0s
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

Go back to Sodium Binding Sites List in 4h0s
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

Go back to Sodium Binding Sites List in 4h0s
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

Go back to Sodium Binding Sites List in 4h0s
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

Go back to Sodium Binding Sites List in 4h0s
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: Sun Aug 17 19:35:45 2025

Last articles

Na in 4TKX
Na in 4TL5
Na in 4RYF
Na in 4RU4
Na in 4S0N
Na in 4S2L
Na in 4RZR
Na in 4RZM
Na in 4RYD
Na in 4RU5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy