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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

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