Atomistry » Calcium » PDB 1lu1-1m8v » 1m8t
Atomistry »
  Calcium »
    PDB 1lu1-1m8v »
      1m8t »

Calcium in PDB 1m8t: Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form

Enzymatic activity of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form

All present enzymatic activity of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form:
3.1.1.4;

Protein crystallography data

The structure of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form, PDB code: 1m8t was solved by S.Xu, L.Gu, Q.Wang, Y.Shu, Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.99 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 98.060, 98.060, 132.390, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form (pdb code 1m8t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form, PDB code: 1m8t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 1 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:29.1
occ:1.00
 O A:TYR28 2.2 17.7 1.0
OD2 A:ASP49 2.2 25.5 1.0
O A:HOH1020 2.2 19.9 1.0
O A:GLY30 2.4 23.9 1.0
O A:GLY32 2.4 32.2 1.0
OD1 A:ASP49 2.6 25.6 1.0
O A:HOH1077 2.6 27.7 1.0
CG A:ASP49 2.7 24.9 1.0
C A:TYR28 3.4 17.3 1.0
C A:GLY32 3.5 31.3 1.0
C A:GLY30 3.6 24.6 1.0
N A:GLY30 3.8 21.0 1.0
N A:GLY32 4.0 31.4 1.0
CA A:TYR28 4.1 17.8 1.0
CB A:ASP49 4.2 24.3 1.0
CA A:GLY32 4.2 30.9 1.0
O A:HOH1092 4.3 30.8 1.0
O A:HOH1079 4.3 28.4 1.0
C A:SER31 4.4 31.3 1.0
N A:GLY33 4.4 30.7 1.0
O A:HOH1078 4.4 15.8 1.0
CA A:GLY30 4.4 21.9 1.0
N A:CYS29 4.4 16.8 1.0
C A:CYS29 4.5 19.6 1.0
CA A:GLY33 4.5 32.1 1.0
CB A:TYR28 4.5 17.9 1.0
CA A:CYS29 4.6 18.4 1.0
N A:SER31 4.6 27.4 1.0
O A:HOH1080 4.8 30.7 1.0
O A:HOH1027 4.8 31.3 1.0
CA A:SER31 4.8 30.6 1.0
O A:CYS45 4.8 18.3 1.0
O A:SER31 4.8 31.6 1.0

Calcium binding site 2 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 2 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:40.7
occ:1.00
 OD1 B:ASP49 2.3 30.3 1.0
O B:GLY32 2.5 42.0 1.0
O B:GLY30 2.5 41.2 1.0
O B:HOH1164 2.6 30.7 1.0
O B:TYR28 2.7 31.9 1.0
O B:HOH1140 2.9 42.1 1.0
CG B:ASP49 3.1 31.8 1.0
OD2 B:ASP49 3.3 33.1 1.0
C B:GLY30 3.6 41.0 1.0
C B:TYR28 3.7 30.0 1.0
C B:GLY32 3.7 42.2 1.0
O B:HOH1016 3.8 22.5 1.0
N B:GLY30 3.8 34.7 1.0
CA B:GLY30 4.2 37.8 1.0
CA B:TYR28 4.3 30.4 1.0
N B:GLY32 4.4 43.7 1.0
CB B:ASP49 4.5 30.2 1.0
CA B:GLY32 4.6 43.2 1.0
C B:CYS29 4.6 32.2 1.0
N B:GLY33 4.7 41.5 1.0
N B:CYS29 4.7 30.1 1.0
C B:SER31 4.7 43.9 1.0
N B:SER31 4.8 42.9 1.0
CB B:TYR28 4.8 30.1 1.0
CA B:GLY33 4.8 40.2 1.0
O B:HOH1068 4.8 15.3 1.0
O B:HOH1133 4.8 33.9 1.0
CA B:CYS29 5.0 30.8 1.0

Calcium binding site 3 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 3 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1003

b:30.4
occ:1.00
 O C:GLY32 2.2 24.7 1.0
OD2 C:ASP49 2.4 24.4 1.0
OD1 C:ASP49 2.4 23.4 1.0
O C:TYR28 2.6 16.6 1.0
O C:GLY30 2.6 23.4 1.0
CG C:ASP49 2.7 22.6 1.0
O C:HOH1073 2.8 20.5 1.0
C C:GLY32 3.2 24.1 1.0
C C:TYR28 3.7 16.5 1.0
N C:GLY32 3.8 24.8 1.0
C C:GLY30 3.8 22.2 1.0
CA C:GLY32 4.0 23.9 1.0
O C:HOH1074 4.1 8.8 1.0
N C:GLY33 4.2 24.3 1.0
N C:GLY30 4.2 20.9 1.0
CA C:TYR28 4.2 17.1 1.0
CB C:ASP49 4.3 22.2 1.0
C C:SER31 4.3 25.1 1.0
CA C:GLY33 4.4 25.3 1.0
O C:HOH1075 4.6 26.8 1.0
O C:HOH1076 4.7 33.2 1.0
CA C:GLY30 4.7 21.3 1.0
N C:CYS29 4.7 17.5 1.0
CB C:TYR28 4.7 16.3 1.0
N C:SER31 4.8 22.0 1.0
C C:CYS29 4.8 20.3 1.0
CA C:SER31 4.8 23.8 1.0
O C:SER31 4.8 25.9 1.0
CA C:CYS29 4.9 19.3 1.0
O C:CYS45 4.9 16.1 1.0
CD1 C:TYR28 4.9 15.9 1.0

Calcium binding site 4 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 4 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1004

b:30.9
occ:1.00
 O D:TYR28 2.1 21.6 1.0
O D:GLY30 2.2 27.4 1.0
O D:HOH1025 2.4 22.6 1.0
O D:GLY32 2.5 31.3 1.0
OD2 D:ASP49 2.6 19.8 1.0
OD1 D:ASP49 2.8 22.2 1.0
CG D:ASP49 3.1 21.3 1.0
C D:GLY30 3.3 28.1 1.0
C D:TYR28 3.3 21.7 1.0
N D:GLY30 3.5 24.7 1.0
O1 D:HEZ1009 3.7 42.2 1.0
C D:GLY32 3.7 30.9 1.0
O D:HOH1031 4.0 7.1 1.0
CA D:GLY30 4.0 27.3 1.0
CA D:TYR28 4.1 21.2 1.0
N D:GLY32 4.1 31.1 1.0
C D:SER31 4.2 31.9 1.0
C D:CYS29 4.2 23.2 1.0
N D:CYS29 4.3 22.3 1.0
N D:SER31 4.3 29.8 1.0
CA D:CYS29 4.4 22.8 1.0
CA D:SER31 4.5 31.6 1.0
O D:HOH1092 4.5 27.6 1.0
CA D:GLY32 4.5 30.8 1.0
O D:SER31 4.5 33.9 1.0
CB D:ASP49 4.6 21.2 1.0
CB D:TYR28 4.6 21.4 1.0
N D:GLY33 4.8 30.7 1.0
O D:CYS45 4.8 21.8 1.0
O D:HOH1091 4.8 30.5 1.0
CA D:GLY33 4.9 29.8 1.0

Calcium binding site 5 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 5 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1005

b:41.2
occ:1.00
 O E:GLY32 2.2 25.8 1.0
OD2 E:ASP49 2.2 26.7 1.0
O E:HOH1036 2.3 23.6 1.0
O E:TYR28 2.3 20.2 1.0
O E:GLY30 2.5 27.4 1.0
OD1 E:ASP49 2.7 27.0 1.0
O E:HOH1103 2.7 17.8 1.0
CG E:ASP49 2.8 27.1 1.0
C E:GLY32 3.2 25.9 1.0
C E:TYR28 3.5 18.3 1.0
C E:GLY30 3.6 27.8 1.0
N E:GLY30 3.8 23.1 1.0
N E:GLY32 3.8 28.8 1.0
O E:HOH1104 3.9 27.3 1.0
CA E:GLY32 4.0 26.3 1.0
CA E:TYR28 4.2 17.8 1.0
N E:GLY33 4.2 26.0 1.0
O E:HOH1031 4.2 36.8 1.0
CB E:ASP49 4.3 25.4 1.0
C E:SER31 4.3 30.1 1.0
CA E:GLY30 4.3 25.9 1.0
CA E:GLY33 4.5 24.9 1.0
N E:CYS29 4.5 19.5 1.0
C E:CYS29 4.6 22.1 1.0
N E:SER31 4.7 29.3 1.0
CB E:TYR28 4.7 17.0 1.0
CA E:CYS29 4.7 21.0 1.0
O E:CYS45 4.8 25.6 1.0
CA E:SER31 4.9 31.0 1.0
O E:SER31 4.9 31.6 1.0
O E:HOH1015 4.9 10.4 1.0

Calcium binding site 6 out of 6 in 1m8t

Go back to Calcium Binding Sites List in 1m8t
Calcium binding site 6 out of 6 in the Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of An Acidic Phospholipase A2 From the Venom of Ophiophagus Hannah at 2.1 Resolution From A Hemihedrally Twinned Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1006

b:51.1
occ:1.00
 O F:GLY32 1.8 41.9 1.0
O F:GLY30 2.3 36.2 1.0
OD2 F:ASP49 2.5 25.1 1.0
O F:TYR28 2.6 26.4 1.0
OD1 F:ASP49 2.7 25.4 1.0
CG F:ASP49 2.9 24.9 1.0
C F:GLY32 3.0 42.5 1.0
O F:HOH1105 3.1 26.9 1.0
C F:TYR28 3.5 27.0 1.0
C F:GLY30 3.5 36.4 1.0
N F:GLY32 3.7 42.9 1.0
N F:GLY30 3.9 31.1 1.0
CA F:GLY32 3.9 42.7 1.0
N F:GLY33 4.0 43.0 1.0
CA F:TYR28 4.1 28.2 1.0
C F:SER31 4.1 42.3 1.0
CA F:GLY33 4.3 42.3 1.0
O F:HOH1081 4.3 26.4 1.0
CA F:GLY30 4.4 34.1 1.0
CB F:ASP49 4.4 26.7 1.0
N F:CYS29 4.5 27.4 1.0
N F:SER31 4.5 39.0 1.0
CA F:SER31 4.6 41.1 1.0
C F:CYS29 4.6 28.5 1.0
O F:SER31 4.6 42.6 1.0
CB F:TYR28 4.7 29.2 1.0
O F:HOH1035 4.7 11.8 1.0
CA F:CYS29 4.7 27.1 1.0
O F:CYS45 4.9 26.0 1.0

Reference:

S.Xu, L.Gu, Q.Wang, Y.Shu, S.Song, Z.Lin. Structure of A King Cobra Phospholipase A2 Determined From A Hemihedrally Twinned Crystal. Acta Crystallogr.,Sect.D V. 59 1574 2003.
ISSN: ISSN 0907-4449
PubMed: 12925787
DOI: 10.1107/S0907444903014598
Page generated: Sat Dec 12 03:06:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy