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Calcium in PDB 4m8d: Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate

Protein crystallography data

The structure of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate, PDB code: 4m8d was solved by K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.980, 51.820, 357.090, 90.00, 91.92, 90.00
R / Rfree (%) 15.2 / 19.2

Other elements in 4m8d:

The structure of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate also contains other interesting chemical elements:

Manganese (Mn) 12 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate (pdb code 4m8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate, PDB code: 4m8d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 4m8d

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Calcium binding site 1 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:36.2
occ:1.00
 O A:HOH716 2.4 44.2 1.0
O F:HOH517 2.5 31.3 1.0
O A:HOH690 3.2 64.7 1.0
O A:HOH564 4.3 43.1 1.0
O F:HOH461 4.3 30.5 1.0
O A:HOH499 4.4 24.0 1.0
O A:HOH461 4.6 25.9 1.0
OD2 A:ASP121 4.6 21.9 1.0
O F:HOH458 4.6 32.9 1.0
OD2 F:ASP121 4.7 23.4 1.0
OD1 F:ASP119 4.7 19.8 1.0
OD1 A:ASP119 4.7 25.2 1.0

Calcium binding site 2 out of 16 in 4m8d

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Calcium binding site 2 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:22.4
occ:1.00
 O A:HOH416 2.3 23.6 1.0
O A:HOH431 2.4 18.9 1.0
O A:HOH480 2.4 28.4 1.0
O B:HOH496 2.4 23.7 1.0
O A:HOH423 2.4 22.9 1.0
O A:HOH432 2.5 22.0 1.0
O B:HOH444 2.5 25.5 1.0
O B:HOH433 4.2 18.2 1.0
O B:HOH623 4.2 42.4 1.0
O A:HOH528 4.3 39.7 1.0
O B:HOH549 4.5 28.6 1.0
CB A:GLN101 4.5 12.0 1.0
CG A:GLN101 4.5 12.5 1.0
O A:HOH699 4.6 42.3 1.0
OD2 A:ASP99 4.6 16.9 1.0
OE1 A:GLN101 4.7 15.1 1.0
OD1 A:ASP99 4.7 15.8 1.0
CD A:GLN101 4.9 12.8 1.0

Calcium binding site 3 out of 16 in 4m8d

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Calcium binding site 3 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:52.1
occ:1.00
 OD1 A:ASN228 2.4 29.1 1.0
O A:HOH627 2.4 31.4 1.0
O A:HOH654 2.5 45.2 1.0
CG A:ASN228 3.6 28.6 1.0
O B:HOH516 4.1 31.5 1.0
O B:HOH603 4.1 34.1 1.0
ND2 A:ASN228 4.2 29.7 1.0
OD2 A:ASP152 4.5 20.0 1.0
OD1 A:ASP230 4.7 23.1 1.0
CA A:ASN228 4.7 14.1 1.0
CB A:ASN228 4.7 19.5 1.0
CE A:LYS231 4.9 40.8 1.0
OD2 A:ASP230 4.9 26.2 1.0
N A:ASN228 4.9 12.6 1.0
O A:HOH569 5.0 38.7 1.0

Calcium binding site 4 out of 16 in 4m8d

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Calcium binding site 4 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:34.7
occ:1.00
 O B:HOH653 2.3 45.1 1.0
O B:GLY156 2.4 19.2 1.0
O B:HOH570 2.4 37.8 1.0
O C:HOH632 2.4 42.7 1.0
O C:HOH521 2.4 26.0 1.0
O C:HOH543 2.5 38.0 1.0
C B:GLY156 3.5 20.4 1.0
O D:HOH529 4.0 28.8 1.0
CA B:GLY156 4.3 19.4 1.0
O C:HOH466 4.4 35.9 1.0
N B:ASP157 4.5 18.5 1.0
O B:HOH508 4.5 30.9 1.0
CA B:ASP157 4.6 19.3 1.0
OD1 C:ASP99 4.6 22.2 1.0
O D:HOH561 4.6 36.6 1.0
OD2 C:ASP99 4.6 21.9 1.0
O B:HOH543 4.9 28.3 1.0
CG C:ASP99 4.9 23.0 1.0
CB B:ASP157 5.0 20.1 1.0

Calcium binding site 5 out of 16 in 4m8d

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Calcium binding site 5 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:23.3
occ:1.00
 OE1 B:GLN201 2.3 24.3 1.0
O K:HOH439 2.3 31.7 1.0
O K:HOH411 2.3 19.8 1.0
OE1 K:GLN201 2.3 27.7 1.0
O B:HOH519 2.4 33.9 1.0
O B:HOH407 2.5 21.1 1.0
CD B:GLN201 3.4 22.7 1.0
CD K:GLN201 3.5 26.3 1.0
O B:HOH578 3.9 40.9 1.0
NE2 B:GLN201 4.2 22.5 1.0
NE2 K:GLN201 4.2 26.9 1.0
O K:THR167 4.3 27.6 1.0
O B:THR167 4.4 27.6 1.0
O B:GLN201 4.4 25.0 1.0
O B:HOH618 4.4 27.8 1.0
CB B:GLN201 4.4 21.6 1.0
CG B:GLN201 4.5 27.1 1.0
CB K:GLN201 4.5 26.7 1.0
O K:GLN201 4.5 23.9 1.0
CG K:GLN201 4.6 25.9 1.0
N B:GLY204 4.6 35.2 1.0
O B:HOH664 4.6 44.8 1.0
N K:GLY204 4.7 33.7 1.0
CA B:GLN201 4.7 23.3 1.0
CA B:GLY204 4.8 36.7 1.0
O B:HOH484 4.8 29.1 1.0
CA K:GLN201 4.9 26.0 1.0
CA K:GLY204 4.9 32.5 1.0
O K:HOH561 4.9 29.7 1.0
C B:GLN201 4.9 25.3 1.0

Calcium binding site 6 out of 16 in 4m8d

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Calcium binding site 6 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:43.3
occ:1.00
 O B:HOH720 2.2 29.6 1.0
O B:HOH717 2.4 38.1 1.0
OD1 B:ASN228 2.6 32.8 1.0
OD1 B:ASP230 2.6 21.6 1.0
OD2 B:ASP230 3.0 29.5 1.0
CG B:ASP230 3.2 25.3 1.0
CG B:ASN228 3.6 31.6 1.0
CE B:LYS231 3.8 36.8 1.0
CA B:ASN228 4.0 18.9 1.0
CB B:ASN228 4.1 23.6 1.0
CG B:LYS231 4.2 23.9 1.0
CD B:LYS231 4.2 30.5 1.0
NZ B:LYS231 4.5 39.4 1.0
CE B:LYS153 4.6 44.0 1.0
CB B:ASP230 4.7 21.1 1.0
ND2 B:ASN228 4.7 36.9 1.0
OE1 D:GLU18 4.8 37.2 1.0
OD2 B:ASP152 4.8 18.5 1.0
C B:ASN228 4.8 18.2 1.0
N B:ASN228 4.8 14.4 1.0

Calcium binding site 7 out of 16 in 4m8d

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Calcium binding site 7 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:31.6
occ:1.00
 OE1 C:GLN201 2.3 34.3 1.0
O C:HOH416 2.3 30.4 1.0
O C:HOH547 2.4 42.6 1.0
O C:HOH446 2.5 31.0 1.0
CD C:GLN201 3.4 33.0 1.0
NE2 C:GLN201 4.1 31.9 1.0
O C:THR167 4.3 36.8 1.0
O C:GLN201 4.4 36.8 1.0
CB C:GLN201 4.5 31.7 1.0
CG C:GLN201 4.5 34.9 1.0
O C:HOH519 4.6 39.3 1.0
N C:GLY204 4.7 46.8 1.0
CA C:GLN201 4.8 34.5 1.0
CA C:GLY204 4.9 47.9 1.0
C C:GLN201 5.0 37.6 1.0

Calcium binding site 8 out of 16 in 4m8d

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Calcium binding site 8 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:81.8
occ:1.00
 O C:HOH602 2.4 87.1 1.0
OD1 C:ASN228 2.4 32.8 1.0
O C:HOH474 2.5 42.7 1.0
OD1 C:ASP230 2.6 30.6 1.0
OD2 C:ASP230 3.2 33.6 1.0
CG C:ASP230 3.3 31.9 1.0
CE C:LYS231 3.4 42.7 1.0
CG C:ASN228 3.4 30.9 1.0
CA C:ASN228 3.8 24.3 1.0
CG C:LYS231 4.0 31.5 1.0
CB C:ASN228 4.1 25.5 1.0
NZ C:LYS231 4.2 45.6 1.0
CD C:LYS231 4.2 38.5 1.0
ND2 C:ASN228 4.4 30.0 1.0
OD2 C:ASP152 4.5 28.5 1.0
N C:ASN228 4.5 22.8 1.0
C C:ASN228 4.7 23.0 1.0
CB C:ASP230 4.8 30.0 1.0
O C:HOH435 4.8 22.8 1.0

Calcium binding site 9 out of 16 in 4m8d

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Calcium binding site 9 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:46.7
occ:1.00
 OD1 D:ASN228 2.4 27.0 1.0
O D:HOH616 2.4 32.0 1.0
O D:HOH484 2.4 32.5 1.0
O D:HOH592 2.5 33.0 1.0
CG D:ASN228 3.5 27.5 1.0
O C:HOH569 4.0 36.4 1.0
ND2 D:ASN228 4.1 31.6 1.0
OD2 D:ASP152 4.3 21.0 1.0
O D:HOH661 4.5 49.6 1.0
NZ D:LYS231 4.5 37.4 1.0
CA D:ASN228 4.7 15.1 1.0
CB D:ASN228 4.7 18.4 1.0
O D:HOH642 4.7 37.2 1.0
OD1 D:ASP230 4.8 23.9 1.0
N D:ASN228 4.8 14.2 1.0

Calcium binding site 10 out of 16 in 4m8d

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Calcium binding site 10 out of 16 in the Crystal Structure of An Isatin Hydrolase Bound to Product Analogue Thioisatinate


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 An Isatin Hydrolase Bound to Product Analogue Thioisatinate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca303

b:21.9
occ:1.00
 O F:HOH415 2.3 18.7 1.0
O F:HOH408 2.3 22.3 1.0
OE1 A:GLN201 2.3 27.8 1.0
OE1 F:GLN201 2.4 23.3 1.0
O A:HOH533 2.4 38.3 1.0
O F:HOH495 2.5 28.0 1.0
CD F:GLN201 3.5 21.8 1.0
CD A:GLN201 3.5 27.0 1.0
NE2 F:GLN201 4.2 20.4 1.0
NE2 A:GLN201 4.3 27.2 1.0
O A:HOH534 4.3 39.3 1.0
O A:THR167 4.3 23.8 1.0
O A:HOH600 4.3 30.1 1.0
O F:GLN201 4.4 18.2 1.0
O F:THR167 4.4 24.0 1.0
CB F:GLN201 4.5 18.9 1.0
N F:GLY204 4.5 29.4 1.0
O A:GLN201 4.5 29.0 1.0
CB A:GLN201 4.5 24.9 1.0
O F:HOH656 4.5 41.1 1.0
CG F:GLN201 4.5 20.6 1.0
CG A:GLN201 4.5 25.8 1.0
O F:HOH699 4.6 41.1 1.0
CA A:GLY204 4.7 32.5 1.0
CA F:GLY204 4.7 29.3 1.0
CA F:GLN201 4.7 20.1 1.0
N A:GLY204 4.8 34.1 1.0
O F:HOH535 4.8 27.8 1.0
CA A:GLN201 4.9 25.8 1.0
C F:GLN201 4.9 20.7 1.0

Reference:

K.Bjerregaard-Andersen, T.Sommer, J.K.Jensen, B.Jochimsen, M.Etzerodt, J.P.Morth. A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase. J.Biol.Chem. V. 289 21351 2014.
ISSN: ISSN 0021-9258
PubMed: 24917679
DOI: 10.1074/JBC.M114.568824
Page generated: Sun Jul 14 10:15:14 2024

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