Calcium in PDB 7c73: Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution

Protein crystallography data

The structure of Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution, PDB code: 7c73 was solved by P.K.Singh, S.N.Pandey, C.Rani, N.Ahmad, V.Viswanathan, P.Sharma, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.58 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.880, 79.930, 75.050, 90.00, 101.35, 90.00
R / Rfree (%) 21.8 / 30.6

Other elements in 7c73:

The structure of Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution (pdb code 7c73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution, PDB code: 7c73:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7c73

Go back to Calcium Binding Sites List in 7c73
Calcium binding site 1 out of 2 in the Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution


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 Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:20.2
occ:1.00
O A:ASP110 2.2 18.9 1.0
O A:PHE186 2.3 21.3 1.0
OG A:SER190 2.5 20.1 1.0
OG1 A:THR184 2.5 20.1 1.0
O A:THR184 2.5 21.1 1.0
OD1 A:ASP110 2.6 19.0 1.0
OD1 A:ASP188 2.6 20.4 1.0
C A:ASP110 3.3 19.1 1.0
CG A:ASP188 3.4 20.6 1.0
CB A:SER190 3.4 20.2 1.0
C A:PHE186 3.4 21.9 1.0
C A:THR184 3.5 21.1 1.0
OD2 A:ASP188 3.6 20.1 1.0
CG A:ASP110 3.7 18.8 1.0
CB A:THR184 3.7 20.2 1.0
CA A:THR184 4.0 20.9 1.0
N A:PHE186 4.0 20.8 1.0
N A:THR184 4.0 21.5 1.0
CA A:ASP110 4.1 19.1 1.0
N A:LEU111 4.2 19.7 1.0
CA A:PHE186 4.2 21.4 1.0
N A:ASP188 4.3 21.1 1.0
CB A:ASP110 4.3 18.9 1.0
N A:SER190 4.3 20.1 1.0
C A:SER185 4.3 20.6 1.0
CA A:LEU111 4.4 20.3 1.0
N A:LEU187 4.4 21.8 1.0
CA A:SER190 4.5 20.3 1.0
N A:SER185 4.5 21.1 1.0
OD2 A:ASP110 4.6 18.5 1.0
CB A:ASP188 4.7 20.9 1.0
CA A:LEU187 4.7 22.2 1.0
O A:SER185 4.7 20.5 1.0
O A:HOH791 4.7 34.7 1.0
CG2 A:THR184 4.9 20.3 1.0
CA A:SER185 4.9 21.1 1.0
CB A:PHE186 4.9 20.6 1.0
CA A:ASP188 4.9 21.2 1.0
O A:LEU111 5.0 23.2 1.0
CD2 A:LEU111 5.0 19.3 1.0
C A:VAL183 5.0 23.0 1.0

Calcium binding site 2 out of 2 in 7c73

Go back to Calcium Binding Sites List in 7c73
Calcium binding site 2 out of 2 in the Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution


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 Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:23.1
occ:1.00
N A:TRP46 3.0 20.8 1.0
N A:VAL342 3.4 17.2 1.0
O A:HOH738 3.4 9.4 1.0
N A:ASN341 3.6 17.5 1.0
CH2 A:TRP452 3.6 16.5 1.0
CA A:ARG45 3.7 22.0 1.0
CB A:ASN341 3.7 17.1 1.0
O A:ALA44 3.8 21.1 1.0
CB A:TRP46 3.8 19.6 1.0
C A:ARG45 3.8 21.9 1.0
CB A:VAL342 3.9 17.1 1.0
CA A:TRP46 3.9 20.0 1.0
CG1 A:VAL342 4.0 17.2 1.0
CA A:ASN341 4.0 17.2 1.0
N A:LEU47 4.0 19.6 1.0
CZ2 A:TRP452 4.1 16.4 1.0
C A:ASN341 4.1 17.5 1.0
CA A:VAL342 4.2 16.8 1.0
CB A:SER340 4.2 18.6 1.0
CD A:ARG45 4.2 22.1 1.0
CE A:MET446 4.2 18.9 1.0
O A:LEU47 4.3 20.5 1.0
CG A:TRP46 4.5 19.4 1.0
C A:SER340 4.5 17.7 1.0
C A:TRP46 4.5 19.8 1.0
CB A:ARG45 4.6 21.9 1.0
C A:ALA44 4.6 21.9 1.0
N A:ARG45 4.6 21.8 1.0
OG A:SER340 4.6 18.3 1.0
CA A:SER340 4.7 18.7 1.0
CZ3 A:TRP452 4.7 16.5 1.0
CG A:ARG45 4.9 21.9 1.0
NH1 A:ARG45 5.0 21.8 1.0

Reference:

P.K.Singh, S.N.Pandey, C.Rani, N.Ahmad, V.Viswanathan, P.Sharma, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase Using Data Obtained From Crystals Soaked in MGCL2 at 2.70 A Resolution To Be Published.
Page generated: Sat Dec 12 08:03:56 2020

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