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Calcium in PDB 6l2j: Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.

Enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.

All present enzymatic activity of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution., PDB code: 6l2j was solved by V.Viswanathan, P.Sharma, C.Rani, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.84 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.850, 78.920, 67.750, 90.00, 92.95, 90.00
R / Rfree (%) 14.5 / 19.8

Other elements in 6l2j:

The structure of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. also contains other interesting chemical elements:

Iodine (I) 26 atoms
Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. (pdb code 6l2j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution., PDB code: 6l2j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6l2j

Go back to Calcium Binding Sites List in 6l2j
Calcium binding site 1 out of 5 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 at 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca654

b:24.8
occ:0.95
 O A:HOH1014 2.4 20.2 1.0
O A:HOH1109 2.8 26.0 1.0
O A:HOH720 3.2 19.0 1.0
N A:ALA225 3.5 13.0 1.0
O A:HOH823 3.7 18.4 1.0
CD2 A:LEU224 3.8 16.2 1.0
CB A:ALA225 3.9 13.0 1.0
CA A:LEU224 4.0 14.5 1.0
O A:HOH719 4.0 21.9 1.0
CG A:ARG271 4.0 12.6 1.0
C A:LEU224 4.2 13.3 1.0
CB A:LEU224 4.2 14.1 1.0
CA A:ALA225 4.3 12.7 1.0
CB A:ARG271 4.4 13.3 1.0
NH1 A:ARG278 4.4 32.6 1.0
CD A:ARG271 4.5 13.0 1.0
CA A:ARG271 4.6 12.6 1.0
CG A:LEU224 4.7 15.2 1.0
O A:HOH1239 4.8 28.3 1.0
O A:GLY223 4.9 17.4 1.0
NE A:ARG271 4.9 12.2 1.0
O A:ARG271 4.9 11.6 1.0

Calcium binding site 2 out of 5 in 6l2j

Go back to Calcium Binding Sites List in 6l2j
Calcium binding site 2 out of 5 in the Crystal Structure of Yak Lactoperoxidase at 1.93 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 at 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca655

b:38.8
occ:1.00
 OD1 A:ASP410 2.0 29.6 1.0
O A:HOH1099 2.7 27.6 1.0
CG A:ASP410 3.2 24.5 1.0
ND2 A:ASN473 3.5 16.1 1.0
OD1 A:ASN473 3.7 19.0 1.0
OD2 A:ASP410 3.9 35.9 1.0
CG A:ASN473 4.0 16.1 1.0
N A:LEU476 4.2 12.5 1.0
CB A:LEU476 4.2 12.4 1.0
O A:GLN409 4.2 13.4 1.0
CG2 A:ILE475 4.3 18.0 1.0
CB A:ASP410 4.3 20.0 1.0
CB A:ILE475 4.3 17.4 1.0
CA A:ASP410 4.3 16.8 1.0
O A:HOH849 4.4 12.0 1.0
C A:GLN409 4.4 13.2 1.0
N A:ASP410 4.5 14.6 1.0
CA A:LEU476 4.5 12.5 1.0
NZ A:LYS479 4.8 24.6 1.0
CB A:GLN409 4.8 13.2 1.0
C A:ILE475 4.8 12.9 1.0

Calcium binding site 3 out of 5 in 6l2j

Go back to Calcium Binding Sites List in 6l2j
Calcium binding site 3 out of 5 in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.


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 Yak Lactoperoxidase at 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca656

b:10.0
occ:1.00
 O A:PHE186 2.3 10.9 1.0
OD1 A:ASP110 2.3 10.4 1.0
O A:ASP110 2.3 8.2 1.0
OG A:SER190 2.4 9.3 1.0
OD1 A:ASP188 2.4 10.1 1.0
O A:THR184 2.4 8.0 1.0
OG1 A:THR184 2.5 8.3 1.0
C A:THR184 3.4 8.8 1.0
C A:ASP110 3.4 8.5 1.0
CG A:ASP188 3.4 10.0 1.0
CB A:SER190 3.4 10.3 1.0
CG A:ASP110 3.4 10.5 1.0
C A:PHE186 3.5 10.1 1.0
CB A:THR184 3.7 8.3 1.0
OD2 A:ASP188 3.8 10.3 1.0
CA A:THR184 3.8 8.6 1.0
N A:THR184 4.0 8.6 1.0
N A:ASP188 4.1 10.5 1.0
CA A:ASP110 4.1 9.1 1.0
N A:PHE186 4.2 9.6 1.0
N A:SER190 4.3 10.2 1.0
OD2 A:ASP110 4.3 12.7 1.0
CB A:ASP110 4.3 9.7 1.0
N A:LEU111 4.3 8.5 1.0
N A:SER185 4.4 9.0 1.0
CA A:PHE186 4.4 9.9 1.0
CA A:SER190 4.4 9.9 1.0
C A:SER185 4.5 9.9 1.0
CA A:LEU111 4.5 8.8 1.0
N A:LEU187 4.5 10.0 1.0
CB A:ASP188 4.5 10.3 1.0
CA A:LEU187 4.6 9.7 1.0
O A:HOH973 4.7 6.3 1.0
CG2 A:THR184 4.7 8.4 1.0
CA A:ASP188 4.8 10.4 1.0
CD2 A:LEU111 4.8 8.3 1.0
C A:LEU187 4.9 10.7 1.0
CA A:SER185 4.9 9.2 1.0
O A:SER185 4.9 9.7 1.0
N A:ALA189 5.0 10.5 1.0
C A:VAL183 5.0 8.4 1.0

Calcium binding site 4 out of 5 in 6l2j

Go back to Calcium Binding Sites List in 6l2j
Calcium binding site 4 out of 5 in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.


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 Yak Lactoperoxidase at 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca657

b:31.7
occ:1.00
 O A:HOH947 2.7 9.7 1.0
O A:HOH1250 2.9 23.1 1.0
NE A:ARG41 3.0 18.6 0.5
O A:HOH1019 3.1 10.6 1.0
O A:ALA35 3.4 14.7 1.0
CD A:ARG41 3.5 17.9 0.5
CD A:ARG41 3.5 19.2 0.5
CD A:ARG338 3.7 12.6 1.0
CB A:ARG41 3.8 15.3 0.5
CB A:ARG41 3.9 15.9 0.5
O A:HOH1225 3.9 36.4 1.0
C A:ALA35 4.0 14.6 1.0
CZ A:ARG41 4.0 20.6 0.5
CG A:ARG41 4.2 16.4 0.5
CG A:ARG41 4.2 17.3 0.5
NH1 A:ARG41 4.3 20.8 0.5
CB A:ALA35 4.3 15.0 1.0
CA A:LEU36 4.3 15.5 1.0
CD1 A:LEU36 4.3 23.5 1.0
N A:LEU36 4.4 15.4 1.0
CG A:ARG338 4.4 12.1 1.0
O A:HOH1004 4.6 11.0 1.0
N A:GLY37 4.7 14.0 1.0
NE A:ARG41 4.7 20.7 0.5
NH1 A:ARG338 4.7 17.8 1.0
CA A:ALA35 4.8 14.8 1.0
NE A:ARG338 4.8 13.4 1.0
O A:ALA42 5.0 8.8 1.0

Calcium binding site 5 out of 5 in 6l2j

Go back to Calcium Binding Sites List in 6l2j
Calcium binding site 5 out of 5 in the Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca658

b:34.7
occ:1.00
 O A:HOH1073 2.8 22.7 1.0
NE A:ARG385 3.1 18.3 1.0
OG1 A:THR378 3.3 10.3 1.0
O A:HOH769 3.4 31.9 1.0
NH2 A:ARG385 3.5 20.3 1.0
CB A:THR378 3.5 9.7 1.0
O A:THR378 3.7 10.6 1.0
ND2 A:ASN382 3.7 10.9 1.0
CZ A:ARG385 3.7 18.9 1.0
CG A:ARG385 4.0 15.9 1.0
CD2 A:LEU379 4.0 9.5 1.0
CZ2 A:TRP384 4.1 14.2 1.0
CD A:ARG385 4.1 17.7 1.0
CD1 A:LEU374 4.1 12.5 1.0
C A:THR378 4.3 9.9 1.0
CA A:THR378 4.5 10.1 1.0
CG2 A:THR378 4.6 10.3 1.0
CH2 A:TRP384 4.6 14.5 1.0
CD2 A:LEU374 4.6 12.5 1.0
O A:HOH776 4.8 17.5 1.0
O A:HOH939 4.8 17.1 1.0
CG A:LEU374 4.8 12.6 1.0
CE2 A:TRP384 4.9 14.2 1.0
CG A:ASN382 4.9 11.7 1.0
CG A:LEU379 5.0 9.5 1.0

Reference:

V.Viswanathan, P.Sharma, C.Rani, S.Sharma, T.P.Singh. Crystal Structure of Yak Lactoperoxidase at 1.93 A Resolution. To Be Published.
Page generated: Wed Jul 9 15:43:23 2025

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