Atomistry » Calcium » PDB 6kzo-6lje » 6l2j
Atomistry »
  Calcium »
    PDB 6kzo-6lje »
      6l2j »

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: Tue Jul 16 10:43:43 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