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Calcium in PDB 4wiw: Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2

Protein crystallography data

The structure of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2, PDB code: 4wiw was solved by C.Chang, C.Tesar, M.Endres, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.14 / 2.64
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.933, 346.625, 193.442, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.6

Other elements in 4wiw:

The structure of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 (pdb code 4wiw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2, PDB code: 4wiw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4wiw

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Calcium binding site 1 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


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 C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:60.0
occ:1.00
 O A:HOH821 3.5 36.0 1.0
O A:SER507 4.0 46.0 1.0
O A:LYS469 4.3 48.8 1.0
OD2 A:ASP513 4.3 38.7 1.0
O A:VAL468 4.4 37.7 1.0
CB A:PRO471 4.5 27.8 1.0

Calcium binding site 2 out of 10 in 4wiw

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Calcium binding site 2 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


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 C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:30.9
occ:1.00
 O A:TYR465 2.2 37.7 1.0
O A:ASP470 2.2 38.7 1.0
O A:ASP467 2.3 41.7 1.0
OD1 A:ASP473 2.3 42.8 1.0
O A:HOH850 2.5 25.7 1.0
O A:HOH849 2.5 36.5 1.0
CG A:ASP473 3.4 39.9 1.0
C A:TYR465 3.4 36.4 1.0
C A:ASP470 3.5 39.2 1.0
C A:ASP467 3.5 28.7 1.0
O A:ASP473 3.9 27.0 1.0
OD2 A:ASP473 3.9 37.9 1.0
N A:ASP467 3.9 41.6 1.0
C A:GLY466 4.1 42.7 1.0
CA A:PRO471 4.3 35.0 1.0
CA A:ASP467 4.3 40.8 1.0
CA A:TYR465 4.3 36.4 1.0
N A:PRO471 4.3 34.5 1.0
N A:GLY466 4.3 33.4 1.0
N A:ASP473 4.4 38.2 1.0
O A:VAL468 4.4 37.7 1.0
C A:ASP473 4.4 37.1 1.0
CA A:GLY466 4.4 28.2 1.0
CA A:ASP470 4.4 39.6 1.0
CB A:TYR465 4.4 24.8 1.0
C A:PRO471 4.4 43.9 1.0
CB A:ASP470 4.4 30.6 1.0
N A:VAL468 4.5 28.9 1.0
OD2 A:ASP513 4.5 38.7 1.0
C A:VAL468 4.5 32.9 1.0
CA A:VAL468 4.6 28.2 1.0
O A:GLY466 4.6 36.1 1.0
CB A:ASP473 4.6 29.8 1.0
N A:TYR472 4.6 28.2 1.0
N A:ASP470 4.7 39.2 1.0
CA A:ASP473 4.7 38.4 1.0
CB A:ASP513 4.8 37.6 1.0
CD2 A:TYR465 4.9 29.2 1.0
O A:PRO471 4.9 36.5 1.0

Calcium binding site 3 out of 10 in 4wiw

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Calcium binding site 3 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


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 C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:57.7
occ:1.00
 OD1 A:ASN588 2.4 32.7 1.0
CG A:ASN588 3.4 19.6 1.0
O A:ASN586 3.8 36.2 1.0
ND2 A:ASN588 4.0 19.4 1.0
N A:ASN588 4.6 17.5 1.0
CA A:ASN588 4.6 32.1 1.0
CB A:ASN588 4.6 16.8 1.0
C A:GLY587 4.7 22.4 1.0
O A:GLY587 4.8 24.0 1.0
C A:ASN586 4.9 23.2 1.0

Calcium binding site 4 out of 10 in 4wiw

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Calcium binding site 4 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


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 C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:66.3
occ:1.00
 OE2 A:GLU460 2.4 50.4 1.0
CD A:GLU460 3.3 51.5 1.0
OE1 A:GLU460 3.5 66.1 1.0
O A:HOH817 3.6 23.7 1.0
OD2 A:ASP458 4.1 43.4 1.0
SE A:MSE530 4.4 52.1 1.0
CG A:GLU460 4.7 40.0 1.0
OD1 A:ASP458 5.0 39.2 1.0
CG A:ASP458 5.0 39.7 1.0

Calcium binding site 5 out of 10 in 4wiw

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Calcium binding site 5 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


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 C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:59.0
occ:1.00
 O B:TYR465 2.2 57.7 1.0
O B:ASP467 2.3 58.7 1.0
O B:ASP470 2.3 41.9 1.0
OD1 B:ASP473 2.4 51.5 1.0
O B:HOH859 2.4 35.3 1.0
O B:HOH853 2.6 33.8 1.0
C B:TYR465 3.3 49.9 1.0
C B:ASP467 3.4 54.6 1.0
CG B:ASP473 3.5 54.0 1.0
C B:ASP470 3.5 47.1 1.0
N B:ASP467 3.8 42.1 1.0
OD2 B:ASP473 3.9 53.0 1.0
CB B:TYR465 4.1 37.4 1.0
C B:GLY466 4.1 44.8 1.0
CA B:TYR465 4.1 48.1 1.0
CA B:ASP467 4.2 42.9 1.0
O B:ASP473 4.2 38.0 1.0
N B:GLY466 4.3 47.2 1.0
OD2 B:ASP513 4.3 51.2 1.0
CD2 B:TYR465 4.3 39.9 1.0
CA B:ASP470 4.4 44.1 1.0
N B:PRO471 4.4 49.3 1.0
CA B:PRO471 4.5 48.0 1.0
CA B:GLY466 4.5 40.2 1.0
CB B:ASP470 4.5 45.3 1.0
N B:VAL468 4.5 46.1 1.0
O B:VAL468 4.5 51.8 1.0
N B:ASP470 4.5 54.1 1.0
C B:PRO471 4.6 52.2 1.0
O B:GLY466 4.6 41.4 1.0
C B:VAL468 4.6 49.5 1.0
CB B:ASP513 4.7 36.9 1.0
CA B:VAL468 4.7 45.3 1.0
C B:ASP473 4.7 47.5 1.0
O B:PRO471 4.7 43.0 1.0
N B:ASP473 4.7 41.6 1.0
CB B:ASP467 4.7 45.1 1.0
CG B:TYR465 4.7 33.8 1.0
CB B:ASP473 4.8 43.8 1.0
CA B:ASP473 5.0 42.2 1.0
CG B:ASP513 5.0 45.4 1.0

Calcium binding site 6 out of 10 in 4wiw

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Calcium binding site 6 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:47.6
occ:1.00
 O C:TYR465 2.3 72.0 1.0
O C:ASP470 2.3 59.8 1.0
OD1 C:ASP473 2.4 56.1 1.0
O C:ASP467 2.4 54.9 1.0
C C:ASP470 3.5 59.2 1.0
C C:TYR465 3.5 64.4 1.0
CG C:ASP473 3.6 57.1 1.0
C C:ASP467 3.6 55.3 1.0
OD2 C:ASP513 3.7 66.0 1.0
O C:ASP473 3.9 58.3 1.0
CA C:PRO471 4.1 65.2 1.0
N C:ASP467 4.1 57.5 1.0
OD2 C:ASP473 4.2 57.4 1.0
C C:PRO471 4.2 70.1 1.0
N C:PRO471 4.2 68.8 1.0
CB C:TYR465 4.2 52.0 1.0
CA C:TYR465 4.3 62.5 1.0
CB C:ASP513 4.3 64.0 1.0
O C:VAL468 4.3 53.8 1.0
C C:GLY466 4.4 64.3 1.0
O C:PRO471 4.4 55.0 1.0
CG C:ASP513 4.4 70.2 1.0
CA C:ASP467 4.5 56.3 1.0
N C:ASP473 4.5 61.4 1.0
C C:VAL468 4.5 54.4 1.0
N C:GLY466 4.5 54.6 1.0
CA C:ASP470 4.5 57.3 1.0
CD2 C:TYR465 4.6 54.5 1.0
C C:ASP473 4.6 64.3 1.0
N C:VAL468 4.6 55.0 1.0
N C:ASP470 4.6 56.8 1.0
CA C:GLY466 4.7 55.6 1.0
CA C:VAL468 4.7 54.2 1.0
N C:TYR472 4.8 67.0 1.0
CB C:ASP473 4.8 58.1 1.0
O C:GLY466 4.8 68.8 1.0
CA C:ASP473 4.9 64.1 1.0
CB C:ASP470 4.9 58.2 1.0
CG C:TYR465 4.9 56.4 1.0

Calcium binding site 7 out of 10 in 4wiw

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Calcium binding site 7 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:0.4
occ:1.00
 O D:ASP470 2.2 43.3 1.0
O D:TYR465 2.2 51.4 1.0
OD1 D:ASP473 2.3 53.6 1.0
O D:HOH829 2.4 33.0 1.0
O D:ASP467 2.4 43.6 1.0
O D:HOH828 2.5 41.5 1.0
C D:TYR465 3.3 41.5 1.0
CG D:ASP473 3.4 49.8 1.0
C D:ASP470 3.4 54.4 1.0
C D:ASP467 3.6 43.4 1.0
N D:ASP467 3.8 45.4 1.0
OD2 D:ASP473 3.9 47.4 1.0
C D:GLY466 3.9 49.2 1.0
O D:ASP473 4.0 43.9 1.0
CA D:GLY466 4.1 51.2 1.0
N D:GLY466 4.1 42.9 1.0
CA D:ASP470 4.3 46.1 1.0
CB D:ASP470 4.3 55.7 1.0
CA D:ASP467 4.3 48.2 1.0
CA D:TYR465 4.3 44.0 1.0
N D:ASP473 4.4 46.5 1.0
O D:GLY466 4.4 43.8 1.0
N D:PRO471 4.4 51.9 1.0
N D:ASP470 4.4 45.1 1.0
C D:ASP473 4.4 46.4 1.0
CA D:PRO471 4.5 53.4 1.0
O D:VAL468 4.5 53.0 1.0
OD2 D:ASP513 4.5 57.4 1.0
CB D:TYR465 4.5 41.7 1.0
CB D:ASP473 4.6 48.3 1.0
N D:VAL468 4.6 42.8 1.0
C D:PRO471 4.6 52.1 1.0
C D:VAL468 4.7 42.8 1.0
CA D:ASP473 4.7 47.2 1.0
N D:TYR472 4.8 50.0 1.0
CB D:ASP513 4.8 43.1 1.0
CD2 D:TYR465 4.8 39.0 1.0
CA D:VAL468 4.9 41.3 1.0
CB D:ASP467 5.0 62.1 1.0

Calcium binding site 8 out of 10 in 4wiw

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Calcium binding site 8 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:59.9
occ:0.50
 OE2 D:GLU518 2.4 57.3 1.0
O D:HOH806 2.4 30.9 1.0
CD D:GLU518 3.1 54.8 1.0
OE1 D:GLU518 3.7 67.4 1.0
CG D:GLU518 4.0 46.2 1.0
CB D:GLU518 4.2 45.9 1.0
OD1 D:ASP516 5.0 63.1 1.0

Calcium binding site 9 out of 10 in 4wiw

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Calcium binding site 9 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:57.4
occ:1.00
 O E:ASP470 2.2 73.5 1.0
O E:TYR465 2.3 59.0 1.0
OD1 E:ASP473 2.5 61.8 1.0
O E:ASP467 2.5 81.5 1.0
C E:ASP470 3.4 74.8 1.0
C E:TYR465 3.5 63.5 1.0
CG E:ASP473 3.6 63.9 1.0
C E:ASP467 3.7 81.4 1.0
OD2 E:ASP513 3.8 67.9 1.0
CA E:PRO471 4.1 66.0 1.0
CB E:TYR465 4.1 55.2 1.0
O E:PRO471 4.1 58.8 1.0
OD2 E:ASP473 4.1 65.2 1.0
C E:PRO471 4.2 64.1 1.0
CA E:TYR465 4.2 64.4 1.0
CB E:ASP513 4.2 64.9 1.0
N E:PRO471 4.2 72.2 1.0
N E:ASP467 4.3 70.0 1.0
O E:ASP473 4.3 70.0 1.0
C E:GLY466 4.4 69.1 1.0
O E:VAL468 4.5 60.5 1.0
CG E:ASP513 4.5 69.6 1.0
CA E:ASP470 4.5 69.7 1.0
N E:GLY466 4.5 69.2 1.0
CD2 E:TYR465 4.6 57.4 1.0
CA E:ASP467 4.6 65.7 1.0
N E:ASP470 4.6 65.2 1.0
C E:VAL468 4.6 62.1 1.0
N E:ASP473 4.7 69.4 1.0
N E:VAL468 4.7 63.8 1.0
CA E:GLY466 4.8 69.7 1.0
CA E:VAL468 4.8 62.1 1.0
O E:GLY466 4.8 62.6 1.0
CB E:ASP470 4.8 67.0 1.0
C E:ASP473 4.8 68.2 1.0
CG E:TYR465 4.8 55.8 1.0
CB E:ASP473 4.9 67.3 1.0
N E:TYR472 4.9 67.9 1.0
O E:TYR510 5.0 54.3 1.0

Calcium binding site 10 out of 10 in 4wiw

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Calcium binding site 10 out of 10 in the Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca701

b:40.5
occ:1.00
 O F:ASP470 2.2 40.2 1.0
O F:TYR465 2.2 35.6 1.0
OD1 F:ASP473 2.3 33.1 1.0
O F:ASP467 2.3 39.8 1.0
O F:HOH890 2.5 57.0 1.0
O F:HOH889 2.5 25.2 1.0
C F:TYR465 3.4 34.4 1.0
C F:ASP470 3.4 38.8 1.0
CG F:ASP473 3.5 39.8 1.0
C F:ASP467 3.5 45.7 1.0
O F:ASP473 3.8 30.2 1.0
N F:ASP467 4.0 28.9 1.0
OD2 F:ASP473 4.0 38.7 1.0
OD2 F:ASP513 4.1 44.8 1.0
C F:GLY466 4.2 33.3 1.0
CA F:TYR465 4.3 39.1 1.0
C F:PRO471 4.3 27.4 1.0
CA F:PRO471 4.3 28.0 1.0
CB F:TYR465 4.3 23.8 1.0
N F:PRO471 4.3 41.5 1.0
N F:ASP473 4.3 28.0 1.0
CA F:ASP467 4.4 39.1 1.0
N F:GLY466 4.4 26.1 1.0
CA F:ASP470 4.4 38.8 1.0
N F:VAL468 4.4 49.3 1.0
C F:ASP473 4.5 29.6 1.0
CB F:ASP513 4.5 34.0 1.0
O F:VAL468 4.5 53.5 1.0
O F:PRO471 4.5 33.3 1.0
CB F:ASP470 4.5 43.1 1.0
CA F:VAL468 4.5 41.4 1.0
CA F:GLY466 4.5 33.3 1.0
N F:TYR472 4.6 28.2 1.0
N F:ASP470 4.6 46.8 1.0
C F:VAL468 4.7 41.6 1.0
CB F:ASP473 4.7 38.3 1.0
CA F:ASP473 4.7 28.1 1.0
CG F:ASP513 4.7 41.6 1.0
O F:GLY466 4.8 41.3 1.0
CD2 F:TYR465 4.8 29.5 1.0

Reference:

C.Chang, C.Tesar, M.Endres, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of C-Terminal Domain of Putative Chitinase From Desulfitobacterium Hafniense Dcb-2 To Be Published.
Page generated: Sun Jul 14 14:07:34 2024

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