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Calcium in PDB 4miv: Crystal Structure of Sulfamidase, Crystal Form L

Enzymatic activity of Crystal Structure of Sulfamidase, Crystal Form L

All present enzymatic activity of Crystal Structure of Sulfamidase, Crystal Form L:
3.10.1.1;

Protein crystallography data

The structure of Crystal Structure of Sulfamidase, Crystal Form L, PDB code: 4miv was solved by N.S.Sidhu, I.Uson, K.Schreiber, K.Proepper, S.Becker, G.M.Sheldrick, J.Gaertner, R.Kraetzner, R.Steinfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.85 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.930, 211.450, 108.350, 90.00, 102.69, 90.00
R / Rfree (%) 21.6 / 24.5

Other elements in 4miv:

The structure of Crystal Structure of Sulfamidase, Crystal Form L also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Sulfamidase, Crystal Form L (pdb code 4miv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Sulfamidase, Crystal Form L, PDB code: 4miv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4miv

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Calcium binding site 1 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:57.3
occ:1.00
 OD2 A:ASP273 2.2 41.7 1.0
OD1 A:ASP31 2.4 42.8 1.0
OD1 A:ASP32 2.4 37.8 1.0
OG2 A:FGP70 2.6 60.4 1.0
OD1 A:ASN274 2.8 36.7 1.0
CG A:ASP273 2.9 40.5 1.0
OD1 A:ASP273 2.9 50.4 1.0
O2P A:FGP70 2.9 0.9 1.0
P A:FGP70 3.4 0.2 1.0
CG A:ASN274 3.5 41.5 1.0
CG A:ASP32 3.6 38.4 1.0
CG A:ASP31 3.6 41.0 1.0
ND2 A:ASN274 3.6 42.5 1.0
CB A:FGP70 3.6 53.1 1.0
N A:ASP32 3.7 42.6 1.0
CA A:FGP70 3.9 42.2 1.0
OG1 A:FGP70 4.0 50.4 1.0
NH2 A:ARG74 4.1 47.9 1.0
O3P A:FGP70 4.2 70.2 1.0
CB A:ASP273 4.3 40.0 1.0
OD2 A:ASP32 4.3 36.6 1.0
C A:ASP31 4.4 41.0 1.0
CA A:ASP32 4.4 40.4 1.0
OD2 A:ASP31 4.4 40.0 1.0
N A:FGP70 4.4 36.2 1.0
CA A:ASP31 4.4 40.4 1.0
NZ A:LYS123 4.5 56.0 1.0
O1P A:FGP70 4.5 0.5 1.0
CB A:ASP32 4.5 39.3 1.0
CB A:ASP31 4.7 41.3 1.0
CD2 A:HIS181 4.7 42.1 1.0
NE A:ARG74 4.7 39.7 1.0
N A:ASN274 4.8 41.6 1.0
CB A:ASN274 4.8 41.0 1.0
CZ A:ARG74 4.9 41.7 1.0

Calcium binding site 2 out of 8 in 4miv

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Calcium binding site 2 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:52.5
occ:1.00
 OD1 B:ASP32 2.4 36.6 1.0
OD1 B:ASP31 2.4 39.2 1.0
OD2 B:ASP273 2.4 33.5 1.0
OG2 B:FGP70 2.6 49.8 1.0
OD1 B:ASN274 2.6 39.2 1.0
O1P B:FGP70 2.9 85.8 1.0
OD1 B:ASP273 2.9 35.4 1.0
CG B:ASP273 3.0 32.0 1.0
CG B:ASN274 3.3 36.7 1.0
P B:FGP70 3.4 0.2 1.0
ND2 B:ASN274 3.5 40.6 1.0
CG B:ASP32 3.5 33.2 1.0
CG B:ASP31 3.6 35.6 1.0
CB B:FGP70 3.7 38.1 1.0
N B:ASP32 3.8 33.4 1.0
CA B:FGP70 4.0 32.2 1.0
OG1 B:FGP70 4.0 34.8 1.0
O2P B:FGP70 4.1 73.4 1.0
OD2 B:ASP32 4.2 36.2 1.0
CA B:ASP32 4.3 34.9 1.0
OD2 B:ASP31 4.3 33.2 1.0
C B:ASP31 4.4 32.4 1.0
NH2 B:ARG74 4.4 36.7 1.0
CB B:ASP273 4.5 31.4 1.0
CB B:ASP32 4.5 34.0 1.0
CA B:ASP31 4.5 33.0 1.0
N B:FGP70 4.5 29.1 1.0
O3P B:FGP70 4.6 62.2 1.0
NZ B:LYS123 4.6 48.0 1.0
CD2 B:HIS181 4.6 39.9 1.0
CB B:ASP31 4.7 33.4 1.0
CB B:ASN274 4.7 30.9 1.0
CD B:ARG282 4.8 39.6 1.0
N B:ASN274 4.8 30.1 1.0
NE B:ARG74 5.0 37.7 1.0

Calcium binding site 3 out of 8 in 4miv

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Calcium binding site 3 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:50.7
occ:1.00
 OD2 C:ASP273 2.4 35.6 1.0
OD1 C:ASP32 2.4 42.7 1.0
OG2 C:FGP70 2.5 50.6 1.0
OD1 C:ASP31 2.5 42.1 1.0
OD1 C:ASN274 2.6 38.6 1.0
CG C:ASP273 3.0 35.9 1.0
OD1 C:ASP273 3.0 35.3 1.0
O2P C:FGP70 3.1 91.7 1.0
P C:FGP70 3.4 0.4 1.0
CG C:ASN274 3.4 41.1 1.0
CG C:ASP32 3.5 44.1 1.0
ND2 C:ASN274 3.6 39.2 1.0
CB C:FGP70 3.6 43.9 1.0
CG C:ASP31 3.7 38.9 1.0
CA C:FGP70 3.9 36.2 1.0
O3P C:FGP70 3.9 72.7 1.0
N C:ASP32 3.9 39.6 1.0
OG1 C:FGP70 4.0 40.9 1.0
OD2 C:ASP32 4.2 41.0 1.0
NH2 C:ARG74 4.3 34.8 1.0
N C:FGP70 4.3 34.3 1.0
OD2 C:ASP31 4.4 37.9 1.0
CB C:ASP273 4.4 35.4 1.0
CA C:ASP32 4.5 40.3 1.0
NZ C:LYS123 4.5 51.8 1.0
C C:ASP31 4.5 37.1 1.0
CB C:ASP32 4.6 43.6 1.0
CA C:ASP31 4.6 37.4 1.0
O1P C:FGP70 4.7 68.7 1.0
CD2 C:HIS181 4.7 36.9 1.0
CB C:ASN274 4.7 39.6 1.0
CB C:ASP31 4.8 37.6 1.0
NE C:ARG74 4.8 31.6 1.0
N C:ASN274 4.9 36.5 1.0
CD C:ARG282 4.9 47.0 1.0

Calcium binding site 4 out of 8 in 4miv

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Calcium binding site 4 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:43.1
occ:1.00
 OD2 D:ASP273 2.2 35.2 1.0
OD1 D:ASP31 2.3 36.6 1.0
OD1 D:ASP32 2.4 40.1 1.0
OG2 D:FGP70 2.7 51.1 1.0
OD1 D:ASP273 2.8 37.2 1.0
CG D:ASP273 2.9 34.0 1.0
O2P D:FGP70 2.9 93.3 1.0
ND2 D:ASN274 3.0 39.5 1.0
OD1 D:ASN274 3.4 54.8 1.0
P D:FGP70 3.5 95.1 1.0
CG D:ASP32 3.5 44.0 1.0
CG D:ASN274 3.5 37.0 1.0
CG D:ASP31 3.5 36.5 1.0
N D:ASP32 3.6 38.7 1.0
CB D:FGP70 3.8 40.7 1.0
NH2 D:ARG74 4.1 49.4 1.0
CA D:FGP70 4.1 34.5 1.0
OG1 D:FGP70 4.1 42.2 1.0
C D:ASP31 4.2 36.6 1.0
CA D:ASP32 4.2 37.0 1.0
OD2 D:ASP32 4.2 52.4 1.0
OD2 D:ASP31 4.3 40.1 1.0
CA D:ASP31 4.3 35.3 1.0
CB D:ASP273 4.3 31.4 1.0
CB D:ASP32 4.4 39.9 1.0
O3P D:FGP70 4.4 70.9 1.0
NZ D:LYS123 4.5 44.1 1.0
O1P D:FGP70 4.5 65.4 1.0
CB D:ASP31 4.5 35.4 1.0
CD2 D:HIS181 4.6 37.7 1.0
N D:FGP70 4.6 32.5 1.0
NE D:ARG74 4.7 39.9 1.0
N D:ASN274 4.8 32.7 1.0
CB D:ASN274 4.8 32.3 1.0
CZ D:ARG74 4.9 43.3 1.0

Calcium binding site 5 out of 8 in 4miv

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Calcium binding site 5 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca600

b:69.0
occ:1.00
 OD2 E:ASP273 2.2 63.6 1.0
OD1 E:ASP31 2.4 62.5 1.0
OD1 E:ASN274 2.5 66.4 1.0
OG2 E:FGP70 2.6 0.1 1.0
OD1 E:ASP32 2.6 65.0 1.0
CG E:ASP273 2.9 63.3 1.0
OD1 E:ASP273 2.9 62.3 1.0
O2P E:FGP70 3.2 0.8 1.0
CG E:ASN274 3.3 67.8 1.0
P E:FGP70 3.4 0.6 1.0
ND2 E:ASN274 3.5 69.3 1.0
CG E:ASP31 3.6 62.6 1.0
CB E:FGP70 3.7 84.0 1.0
CG E:ASP32 3.7 64.3 1.0
O3P E:FGP70 3.8 0.9 1.0
CA E:FGP70 3.9 77.3 1.0
N E:ASP32 3.9 66.9 1.0
OG1 E:FGP70 4.1 80.5 1.0
NH2 E:ARG74 4.2 68.4 1.0
CB E:ASP273 4.3 64.0 1.0
OD2 E:ASP31 4.3 63.1 1.0
OD2 E:ASP32 4.3 63.2 1.0
N E:FGP70 4.4 74.5 1.0
C E:ASP31 4.5 65.8 1.0
CA E:ASP31 4.5 64.5 1.0
CA E:ASP32 4.5 67.2 1.0
NZ E:LYS123 4.6 75.8 1.0
CB E:ASN274 4.6 68.1 1.0
CB E:ASP31 4.7 63.3 1.0
CB E:ASP32 4.7 66.4 1.0
N E:ASN274 4.7 67.7 1.0
O1P E:FGP70 4.8 1.0 1.0
NE E:ARG74 4.8 64.8 1.0
CD2 E:HIS181 4.9 66.4 1.0

Calcium binding site 6 out of 8 in 4miv

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Calcium binding site 6 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:73.8
occ:1.00
 OD2 F:ASP273 2.3 64.9 1.0
OD1 F:ASP31 2.4 64.6 1.0
OD1 F:ASP32 2.5 67.9 1.0
OG2 F:FGP70 2.6 88.6 1.0
OD1 F:ASN274 2.8 59.3 1.0
CG F:ASP273 2.9 66.1 1.0
OD1 F:ASP273 3.0 72.2 1.0
O2P F:FGP70 3.1 0.6 1.0
P F:FGP70 3.5 0.3 1.0
CG F:ASN274 3.5 62.1 1.0
CG F:ASP32 3.6 70.1 1.0
CG F:ASP31 3.6 63.3 1.0
ND2 F:ASN274 3.7 64.1 1.0
CB F:FGP70 3.7 75.0 1.0
CA F:FGP70 3.9 68.6 1.0
N F:ASP32 3.9 66.1 1.0
NH2 F:ARG74 4.1 62.8 1.0
O3P F:FGP70 4.2 0.6 1.0
OD2 F:ASP32 4.2 74.0 1.0
OG1 F:FGP70 4.2 72.3 1.0
OD2 F:ASP31 4.3 63.8 1.0
NZ F:LYS123 4.4 73.6 1.0
CB F:ASP273 4.4 64.3 1.0
N F:FGP70 4.4 65.6 1.0
C F:ASP31 4.5 65.9 1.0
CA F:ASP31 4.5 64.0 1.0
CA F:ASP32 4.5 66.6 1.0
CB F:ASP32 4.6 69.0 1.0
CB F:ASP31 4.7 63.7 1.0
CD2 F:HIS181 4.7 74.2 1.0
O1P F:FGP70 4.7 0.4 1.0
NE F:ARG74 4.7 60.2 1.0
CB F:ASN274 4.9 63.8 1.0
CZ F:ARG74 4.9 61.3 1.0
N F:ASN274 4.9 62.6 1.0

Calcium binding site 7 out of 8 in 4miv

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Calcium binding site 7 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:0.7
occ:1.00
 OD1 G:ASP31 2.3 82.4 1.0
OD1 G:ASP32 2.4 90.3 1.0
OD2 G:ASP273 2.5 80.5 1.0
OD1 G:ASN274 2.7 80.1 1.0
OG2 G:FGP70 2.7 78.8 1.0
CG G:ASP273 3.2 75.5 1.0
OD1 G:ASP273 3.2 78.5 1.0
CG G:ASP32 3.4 84.7 1.0
CG G:ASN274 3.5 79.5 1.0
CG G:ASP31 3.5 83.0 1.0
CB G:FGP70 3.5 84.0 1.0
ND2 G:ASN274 3.6 87.7 1.0
OG1 G:FGP70 3.7 80.5 1.0
CA G:FGP70 3.7 76.2 1.0
N G:ASP32 4.0 78.5 1.0
OD2 G:ASP32 4.0 83.6 1.0
OD2 G:ASP31 4.1 83.7 1.0
N G:FGP70 4.3 72.8 1.0
NH2 G:ARG74 4.4 76.6 1.0
NZ G:LYS123 4.4 87.9 1.0
C G:ASP31 4.5 78.3 1.0
CB G:ASP32 4.5 83.5 1.0
CA G:ASP32 4.5 79.0 1.0
CD2 G:HIS181 4.6 91.0 1.0
CB G:ASP273 4.6 71.2 1.0
CA G:ASP31 4.6 76.6 1.0
CB G:ASP31 4.7 80.3 1.0
CD G:ARG282 4.7 86.7 1.0
CB G:ASN274 4.9 73.0 1.0
NE G:ARG74 4.9 74.6 1.0

Calcium binding site 8 out of 8 in 4miv

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Calcium binding site 8 out of 8 in the Crystal Structure of Sulfamidase, Crystal Form L


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 Sulfamidase, Crystal Form L within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:75.9
occ:1.00
 OG2 H:FGP70 2.4 75.8 1.0
OD2 H:ASP273 2.4 74.2 1.0
OD1 H:ASP32 2.5 74.4 1.0
OD1 H:ASP31 2.6 69.9 1.0
OD1 H:ASN274 2.9 73.6 1.0
OG1 H:FGP70 3.0 68.8 1.0
CB H:FGP70 3.1 70.0 1.0
CG H:ASP273 3.3 76.0 1.0
OD1 H:ASP273 3.5 76.4 1.0
CA H:FGP70 3.5 69.0 1.0
CG H:ASP32 3.6 75.2 1.0
CG H:ASN274 3.8 76.0 1.0
CG H:ASP31 3.8 69.7 1.0
N H:FGP70 3.9 70.7 1.0
ND2 H:ASN274 4.0 75.7 1.0
NZ H:LYS123 4.1 82.3 1.0
OD2 H:ASP32 4.1 76.6 1.0
N H:ASP32 4.2 74.0 1.0
NH2 H:ARG74 4.3 80.3 1.0
OD2 H:ASP31 4.4 66.6 1.0
CD2 H:HIS181 4.5 78.7 1.0
CB H:ASP273 4.7 76.5 1.0
NE H:ARG74 4.7 73.3 1.0
CB H:ASP32 4.7 75.7 1.0
CA H:ASP32 4.7 76.3 1.0
C H:ASP31 4.8 73.2 1.0
CA H:ASP31 4.8 72.3 1.0
C H:FGP70 4.9 68.3 1.0
CB H:ASP31 4.9 70.5 1.0
CZ H:ARG74 5.0 76.4 1.0

Reference:

N.S.Sidhu, K.Schreiber, K.Proepper, S.Becker, I.Uson, G.M.Sheldrick, J.Gaertner, R.Kraetzner, R.Steinfeld. Structure of Sulfamidase Provides Insight Into the Molecular Pathology of Mucopolysaccharidosis Iiia Acta Crystallogr.,Sect.D V. D70 1321.
ISSN: ISSN 0907-4449
Page generated: Sun Jul 14 10:23:36 2024

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