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Calcium in PDB 2bd1: A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2

Enzymatic activity of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2

All present enzymatic activity of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2:
3.1.1.4;

Protein crystallography data

The structure of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2, PDB code: 2bd1 was solved by K.Sekar, D.Velmurugan, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.69 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.580, 48.690, 67.550, 90.00, 102.30, 90.00
R / Rfree (%) 20.7 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2 (pdb code 2bd1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2, PDB code: 2bd1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2bd1

Go back to Calcium Binding Sites List in 2bd1
Calcium binding site 1 out of 4 in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca847

b:13.9
occ:1.00
 O A:TYR28 2.3 11.5 1.0
O A:GLY30 2.3 20.5 1.0
OD2 A:ASP49 2.4 15.6 1.0
O A:GLY32 2.4 17.4 1.0
O A:HOH202 2.5 10.1 1.0
O A:HOH208 2.5 14.5 1.0
OD1 A:ASP49 2.6 13.9 1.0
CG A:ASP49 2.8 15.3 1.0
C A:TYR28 3.5 10.2 1.0
C A:GLY32 3.5 19.4 1.0
C A:GLY30 3.6 18.0 1.0
N A:GLY30 3.8 13.5 1.0
N A:GLY32 3.8 20.1 1.0
O A:HOH320 4.1 37.3 1.0
O A:HOH231 4.2 16.0 1.0
O A:HOH319 4.2 33.4 1.0
CA A:TYR28 4.2 12.8 1.0
CA A:GLY32 4.2 19.9 1.0
CB A:ASP49 4.3 14.2 1.0
C A:LEU31 4.3 21.7 1.0
CA A:GLY30 4.4 16.3 1.0
O A:HOH351 4.4 44.3 1.0
O A:HOH204 4.4 17.8 1.0
N A:CYS29 4.5 11.8 1.0
O A:HOH250 4.5 17.9 1.0
N A:LEU31 4.5 19.9 1.0
N A:GLY33 4.5 19.9 1.0
CB A:TYR28 4.6 11.2 1.0
CA A:LEU31 4.6 22.9 1.0
O2 A:MPD723 4.6 35.7 1.0
C A:CYS29 4.7 13.0 1.0
CA A:CYS29 4.7 9.2 1.0
CA A:GLY33 4.7 20.6 1.0
O A:CYS45 4.8 11.2 1.0

Calcium binding site 2 out of 4 in 2bd1

Go back to Calcium Binding Sites List in 2bd1
Calcium binding site 2 out of 4 in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca848

b:19.0
occ:1.00
 O A:HOH226 2.3 20.1 1.0
O A:HOH239 2.4 19.9 1.0
O A:ASN72 2.4 16.7 1.0
OD1 A:ASN71 2.4 14.5 1.0
OE2 A:GLU92 2.4 16.5 1.0
O A:HOH238 2.7 16.1 1.0
CD A:GLU92 3.5 15.4 1.0
C A:ASN72 3.5 13.3 1.0
CG A:ASN71 3.6 15.2 1.0
N A:ASN72 3.6 11.8 1.0
CG A:GLU92 3.8 15.9 1.0
O A:HOH218 4.0 22.1 1.0
O A:HOH279 4.0 51.1 1.0
CA A:ASN72 4.0 12.5 1.0
C A:ASN71 4.2 12.8 1.0
O A:HOH283 4.3 41.7 1.0
ND2 A:ASN71 4.3 14.7 1.0
CB A:ASN72 4.5 13.4 1.0
CA A:ASN71 4.5 13.1 1.0
OE1 A:GLU92 4.6 13.5 1.0
O A:HOH307 4.6 17.6 1.0
N A:TYR73 4.6 13.5 1.0
CB A:ASN71 4.7 15.3 1.0
O A:ASN71 4.9 12.1 1.0
CA A:TYR73 5.0 13.9 1.0

Calcium binding site 3 out of 4 in 2bd1

Go back to Calcium Binding Sites List in 2bd1
Calcium binding site 3 out of 4 in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca849

b:12.5
occ:1.00
 O B:TYR28 2.3 12.7 1.0
OD2 B:ASP49 2.3 15.9 1.0
O B:GLY30 2.4 20.3 1.0
O B:GLY32 2.4 18.0 1.0
O B:HOH203 2.4 15.8 1.0
O B:HOH206 2.5 16.8 1.0
OD1 B:ASP49 2.6 12.6 1.0
CG B:ASP49 2.8 15.6 1.0
C B:TYR28 3.5 11.4 1.0
C B:GLY32 3.5 19.9 1.0
C B:GLY30 3.6 18.4 1.0
N B:GLY30 3.8 14.1 1.0
N B:GLY32 3.8 19.3 1.0
CA B:GLY32 4.2 20.3 1.0
O B:HOH365 4.2 34.3 1.0
O B:HOH322 4.2 35.6 1.0
CA B:TYR28 4.2 12.8 1.0
O B:HOH212 4.2 14.9 1.0
CB B:ASP49 4.3 12.5 1.0
C B:LEU31 4.3 21.4 1.0
CA B:GLY30 4.4 15.9 1.0
O B:HOH248 4.4 17.7 1.0
O B:HOH207 4.5 17.1 1.0
N B:CYS29 4.5 11.8 1.0
O B:HOH406 4.5 44.9 1.0
N B:GLY33 4.5 19.4 1.0
N B:LEU31 4.6 20.3 1.0
C B:CYS29 4.6 13.0 1.0
CA B:CYS29 4.6 9.8 1.0
O2 B:MPD724 4.6 42.8 1.0
CB B:TYR28 4.6 11.3 1.0
CA B:LEU31 4.6 22.0 1.0
CA B:GLY33 4.7 20.3 1.0
O B:CYS45 4.8 11.3 1.0
O B:LEU31 5.0 22.3 1.0

Calcium binding site 4 out of 4 in 2bd1

Go back to Calcium Binding Sites List in 2bd1
Calcium binding site 4 out of 4 in the A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Possible Role of the Second Calcium Ion in Interfacial Binding: Atomic and Medium Resolution Crystal Structures of the Quadruple Mutant of Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca850

b:21.1
occ:1.00
 O B:HOH254 2.2 21.3 1.0
OD1 B:ASN71 2.3 13.8 1.0
O B:HOH261 2.4 22.6 1.0
O B:ASN72 2.4 15.1 1.0
OE2 B:GLU92 2.4 15.3 1.0
O B:HOH245 2.9 18.4 1.0
CD B:GLU92 3.4 14.1 1.0
C B:ASN72 3.5 13.0 1.0
CG B:ASN71 3.5 14.9 1.0
N B:ASN72 3.6 11.8 1.0
O B:HOH295 3.7 44.5 1.0
CG B:GLU92 3.8 14.9 1.0
O B:HOH232 4.0 20.3 1.0
CA B:ASN72 4.0 12.7 1.0
C B:ASN71 4.1 12.6 1.0
ND2 B:ASN71 4.2 11.7 1.0
O B:HOH286 4.4 41.1 1.0
CA B:ASN71 4.5 12.6 1.0
CB B:ASN72 4.5 12.4 1.0
OE1 B:GLU92 4.6 12.3 1.0
CB B:ASN71 4.6 14.5 1.0
N B:TYR73 4.6 12.2 1.0
O B:HOH302 4.7 36.4 1.0
O B:ASN71 4.8 11.9 1.0
CA B:TYR73 5.0 12.6 1.0

Reference:

K.Sekar, M.Yogavel, S.P.Kanaujia, A.Sharma, D.Velmurugan, M.J.Poi, Z.Dauter, M.D.Tsai. Suggestive Evidence For the Involvement of the Second Calcium and Surface Loop in Interfacial Binding: Monoclinic and Trigonal Crystal Structures of A Quadruple Mutant of Phospholipase A(2). Acta Crystallogr.,Sect.D V. 62 717 2006.
ISSN: ISSN 0907-4449
PubMed: 16790927
DOI: 10.1107/S0907444906014855
Page generated: Fri Jul 12 08:58:57 2024

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