Atomistry » Calcium » PDB 1pig-1px2 » 1pob
Atomistry »
  Calcium »
    PDB 1pig-1px2 »
      1pob »

Calcium in PDB 1pob: Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue

Enzymatic activity of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue

All present enzymatic activity of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue, PDB code: 1pob was solved by S.P.White, D.L.Scott, Z.Otwinowski, P.B.Sigler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 34.600, 73.500, 181.600, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue (pdb code 1pob). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue, PDB code: 1pob:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1pob

Go back to Calcium Binding Sites List in 1pob
Calcium binding site 1 out of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:14.6
occ:1.00
O A:TYR27 2.2 11.6 1.0
OD2 A:ASP48 2.3 12.0 1.0
O2P A:GEL930 2.4 15.8 1.0
OD1 A:ASP48 2.5 11.3 1.0
O4P A:GEL930 2.5 16.4 1.0
O A:GLY31 2.5 15.9 1.0
O A:GLY29 2.6 14.0 1.0
CG A:ASP48 2.7 11.2 1.0
C A:TYR27 3.4 11.7 1.0
C A:GLY31 3.6 16.2 1.0
C A:GLY29 3.8 13.9 1.0
P2 A:GEL930 3.8 15.8 1.0
P3 A:GEL930 3.8 16.4 1.0
C3 A:GEL930 3.9 16.8 1.0
N A:GLY29 3.9 12.8 1.0
N A:GLY31 4.0 15.5 1.0
C2 A:GEL930 4.0 17.0 1.0
CB A:ASP48 4.3 9.8 1.0
CA A:TYR27 4.3 11.6 1.0
O1P A:GEL930 4.3 16.1 1.0
CA A:GLY31 4.3 15.9 1.0
O3 A:GEL930 4.4 16.6 1.0
O A:HOH709 4.4 34.9 1.0
O2 A:GEL930 4.4 16.6 1.0
N A:CYS28 4.4 11.6 1.0
O5P A:GEL930 4.4 16.8 1.0
CA A:CYS28 4.4 11.9 1.0
C A:ARG30 4.5 15.3 1.0
CA A:GLY29 4.6 13.4 1.0
C A:CYS28 4.6 12.3 1.0
O A:CYS44 4.6 6.8 1.0
CB A:TYR27 4.7 10.6 1.0
N A:GLY32 4.7 16.5 1.0
N A:ARG30 4.8 14.6 1.0
O A:HOH402 4.8 23.7 1.0
CA A:ARG30 4.8 15.2 1.0
CB A:CYS44 4.9 8.8 1.0
CA A:GLY32 5.0 17.3 1.0

Calcium binding site 2 out of 4 in 1pob

Go back to Calcium Binding Sites List in 1pob
Calcium binding site 2 out of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:28.3
occ:1.00
O A:HOH429 2.5 24.4 1.0
O A:CYS28 2.8 11.8 1.0
O A:GLY25 2.9 11.4 1.0
O A:HOH709 3.1 34.9 1.0
O A:TYR24 3.3 10.6 1.0
O A:HOH442 3.6 16.4 1.0
C A:CYS28 3.6 12.3 1.0
C A:GLY25 3.7 11.1 1.0
C A:TYR24 3.8 10.8 1.0
N A:TYR24 3.8 11.0 1.0
N A:CYS28 3.9 11.6 1.0
N A:TYR27 3.9 11.5 1.0
C A:CYS26 3.9 11.6 1.0
OD1 A:ASP23 4.1 17.0 1.0
CA A:CYS26 4.2 11.7 1.0
C A:TYR27 4.3 11.7 1.0
N A:CYS26 4.3 11.2 1.0
O A:CYS26 4.3 11.4 1.0
N A:GLY25 4.3 10.7 1.0
CD2 A:LEU114 4.4 20.5 1.0
CA A:TYR24 4.4 10.8 1.0
CA A:CYS28 4.4 11.9 1.0
C A:ASP23 4.4 10.8 1.0
N A:GLY29 4.5 12.8 1.0
CD1 A:LEU114 4.5 18.2 1.0
CA A:TYR27 4.5 11.6 1.0
CA A:ASP23 4.6 11.1 1.0
CA A:GLY25 4.7 11.0 1.0
CA A:GLY29 4.7 13.4 1.0
CG A:LEU114 4.9 19.4 1.0
O A:TYR27 4.9 11.6 1.0

Calcium binding site 3 out of 4 in 1pob

Go back to Calcium Binding Sites List in 1pob
Calcium binding site 3 out of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:13.1
occ:1.00
O B:TYR27 2.3 13.5 1.0
OD2 B:ASP48 2.4 13.4 1.0
O2P B:GEL935 2.4 17.3 1.0
O B:GLY29 2.4 16.0 1.0
OD1 B:ASP48 2.4 9.6 1.0
O B:GLY31 2.4 18.2 1.0
O4P B:GEL935 2.4 20.4 1.0
CG B:ASP48 2.8 12.8 1.0
C B:TYR27 3.5 13.0 1.0
C B:GLY31 3.6 18.2 1.0
C B:GLY29 3.6 15.9 1.0
C2 B:GEL935 3.8 19.1 1.0
P2 B:GEL935 3.8 17.3 1.0
P3 B:GEL935 3.8 20.0 1.0
N B:GLY29 3.8 14.4 1.0
N B:GLY31 3.9 17.9 1.0
O1P B:GEL935 4.2 17.4 1.0
C3 B:GEL935 4.3 19.2 1.0
O2 B:GEL935 4.3 18.3 1.0
CA B:GLY31 4.3 18.2 1.0
CB B:ASP48 4.3 13.1 1.0
CA B:TYR27 4.4 12.9 1.0
C B:ARG30 4.4 17.8 1.0
CA B:GLY29 4.4 15.5 1.0
N B:CYS28 4.4 13.2 1.0
O5P B:GEL935 4.4 20.5 1.0
O3 B:GEL935 4.4 19.6 1.0
CA B:CYS28 4.5 13.4 1.0
N B:ARG30 4.6 16.6 1.0
C1 B:GEL935 4.6 19.9 1.0
C B:CYS28 4.6 14.0 1.0
N B:GLY32 4.6 18.5 1.0
O B:CYS44 4.6 12.1 1.0
CA B:ARG30 4.7 17.5 1.0
O B:HOH479 4.7 34.2 1.0
CB B:TYR27 4.8 12.5 1.0
O B:HOH636 4.9 50.7 1.0
O3P B:GEL935 4.9 20.2 1.0
CA B:GLY32 4.9 18.5 1.0
C31 B:GEL935 5.0 20.7 1.0

Calcium binding site 4 out of 4 in 1pob

Go back to Calcium Binding Sites List in 1pob
Calcium binding site 4 out of 4 in the Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:34.1
occ:1.00
O B:CYS28 2.7 13.4 1.0
O B:GLY25 2.9 12.7 1.0
O B:HOH481 3.0 38.7 1.0
O B:TYR24 3.2 12.6 1.0
C B:CYS28 3.4 14.0 1.0
N B:CYS28 3.5 13.2 1.0
O B:HOH636 3.5 50.7 1.0
C B:GLY25 3.7 12.8 1.0
O B:HOH555 3.7 16.2 1.0
C B:TYR24 3.8 12.8 1.0
C B:CYS26 3.8 12.7 1.0
N B:TYR24 3.9 13.4 1.0
N B:TYR27 3.9 12.8 1.0
CA B:CYS28 4.0 13.4 1.0
O B:CYS26 4.0 13.0 1.0
C B:TYR27 4.0 13.0 1.0
N B:GLY29 4.2 14.4 1.0
CA B:CYS26 4.2 12.8 1.0
N B:CYS26 4.2 12.6 1.0
OD1 B:ASP23 4.3 17.1 1.0
CD2 B:LEU114 4.3 15.7 1.0
CA B:TYR27 4.4 12.9 1.0
N B:GLY25 4.4 12.8 1.0
C B:ASP23 4.4 13.1 1.0
CA B:TYR24 4.5 12.9 1.0
O B:HOH516 4.5 41.1 1.0
CA B:ASP23 4.5 13.2 1.0
CA B:GLY29 4.6 15.5 1.0
CA B:GLY25 4.6 12.8 1.0
CB B:CYS28 4.7 9.8 1.0
O B:TYR27 4.8 13.5 1.0
O B:HOH480 4.9 33.0 1.0
CD1 B:LEU114 5.0 18.4 1.0

Reference:

S.P.White, D.L.Scott, Z.Otwinowski, M.H.Gelb, P.B.Sigler. Crystal Structure of Cobra-Venom Phospholipase A2 in A Complex with A Transition-State Analogue. Science V. 250 1560 1990.
ISSN: ISSN 0036-8075
PubMed: 2274787
Page generated: Thu Jul 11 13:49:58 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy