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Calcium in PDB 3gqf: Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q

Enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q

All present enzymatic activity of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q:
1.15.1.1;

Protein crystallography data

The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf was solved by D.D.Winkler, J.P.Schuermann, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.07 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 112.576, 194.331, 143.179, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 3gqf:

The structure of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q (pdb code 3gqf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q, PDB code: 3gqf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3gqf

Go back to Calcium Binding Sites List in 3gqf
Calcium binding site 1 out of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca154

b:63.6
occ:1.00
 O A:SER102 2.4 31.3 1.0
O A:HOH493 2.4 60.2 1.0
O A:HOH484 2.4 46.1 1.0
OD1 A:ASN26 2.4 52.3 1.0
O A:HOH483 2.6 30.0 1.0
O A:HOH492 2.6 54.6 1.0
O A:ASN26 2.7 44.8 1.0
CG A:ASN26 3.4 49.4 1.0
C A:SER102 3.5 31.3 1.0
C A:ASN26 3.5 44.5 1.0
CA A:ASN26 4.0 45.8 1.0
O A:GLY27 4.1 39.5 1.0
CA A:SER102 4.2 31.8 1.0
ND2 A:ASN26 4.3 51.5 1.0
CB A:ASN26 4.3 46.7 1.0
O A:ILE104 4.3 28.6 1.0
N A:VAL103 4.5 30.8 1.0
CB A:SER102 4.5 32.4 1.0
O A:VAL103 4.5 30.3 1.0
N A:GLY27 4.6 42.9 1.0
CA A:VAL103 4.6 29.9 1.0
C A:GLY27 4.7 39.8 1.0
C A:VAL103 4.7 30.0 1.0

Calcium binding site 2 out of 5 in 3gqf

Go back to Calcium Binding Sites List in 3gqf
Calcium binding site 2 out of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca154

b:51.6
occ:1.00
 O B:HOH491 2.2 42.9 1.0
O B:HOH485 2.4 28.9 1.0
O B:SER102 2.5 30.7 1.0
O B:HOH490 2.5 52.9 1.0
O B:HOH486 2.6 33.8 1.0
O B:ASN26 2.8 44.7 1.0
OD1 B:ASN26 3.1 52.6 1.0
C B:ASN26 3.5 44.4 1.0
C B:SER102 3.6 30.3 1.0
CA B:ASN26 3.8 45.7 1.0
CG B:ASN26 3.9 49.4 1.0
CB B:ASN26 4.0 46.4 1.0
O B:GLY27 4.2 39.1 1.0
CA B:SER102 4.3 31.4 1.0
O B:ILE104 4.4 27.6 1.0
CB B:SER102 4.5 31.5 1.0
N B:GLY27 4.6 42.7 1.0
N B:VAL103 4.6 29.3 1.0
O B:VAL103 4.6 28.3 1.0
CA B:VAL103 4.7 28.2 1.0
C B:GLY27 4.8 39.2 1.0
C B:VAL103 4.9 28.2 1.0

Calcium binding site 3 out of 5 in 3gqf

Go back to Calcium Binding Sites List in 3gqf
Calcium binding site 3 out of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca154

b:62.3
occ:1.00
 O C:HOH496 2.4 45.9 1.0
O C:SER102 2.5 32.1 1.0
O C:HOH494 2.6 42.3 1.0
OD1 C:ASN26 2.9 49.4 1.0
O C:HOH495 2.9 43.0 1.0
O C:HOH488 3.1 43.6 1.0
O C:ASN26 3.2 44.9 1.0
C C:SER102 3.7 31.8 1.0
CG C:ASN26 4.0 49.3 1.0
C C:ASN26 4.0 45.1 1.0
CA C:ASN26 4.2 46.4 1.0
CB C:ASN26 4.4 47.2 1.0
CA C:SER102 4.5 32.5 1.0
CA C:VAL103 4.6 31.0 1.0
N C:VAL103 4.6 31.3 1.0
O C:ILE104 4.6 29.9 1.0
O C:VAL103 4.6 31.7 1.0
O C:GLY27 4.7 40.9 1.0
CB C:SER102 4.7 33.0 1.0
C C:VAL103 4.7 31.3 1.0

Calcium binding site 4 out of 5 in 3gqf

Go back to Calcium Binding Sites List in 3gqf
Calcium binding site 4 out of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca154

b:62.6
occ:1.00
 OD1 D:ASN26 2.3 51.8 1.0
O D:HOH497 2.3 51.8 1.0
O D:HOH498 2.5 44.1 1.0
O D:SER102 2.5 32.3 1.0
O D:HOH489 2.5 38.1 1.0
O D:ASN26 2.7 46.1 1.0
CG D:ASN26 3.4 49.8 1.0
C D:SER102 3.6 31.9 1.0
C D:ASN26 3.7 45.7 1.0
CA D:ASN26 4.0 46.7 1.0
ND2 D:ASN26 4.2 50.5 1.0
O D:GLY27 4.3 41.0 1.0
CB D:ASN26 4.3 47.5 1.0
CA D:SER102 4.4 32.7 1.0
O D:ILE104 4.5 30.2 1.0
N D:VAL103 4.6 31.3 1.0
CB D:SER102 4.6 33.1 1.0
O D:VAL103 4.7 30.4 1.0
CA D:VAL103 4.7 30.6 1.0
C D:VAL103 4.8 30.7 1.0
N D:GLY27 4.8 44.2 1.0
C D:GLY27 4.9 41.4 1.0

Calcium binding site 5 out of 5 in 3gqf

Go back to Calcium Binding Sites List in 3gqf
Calcium binding site 5 out of 5 in the Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca154

b:56.0
occ:1.00
 O F:SER102 2.4 29.8 1.0
O F:HOH170 2.6 24.3 1.0
O F:HOH460 2.6 46.7 1.0
OD1 F:ASN26 2.7 48.5 1.0
O F:ASN26 2.9 43.1 1.0
O F:HOH424 2.9 40.4 0.5
O F:HOH181 3.2 42.0 1.0
CG F:ASN26 3.4 46.5 1.0
C F:SER102 3.6 29.3 1.0
C F:ASN26 3.7 42.7 1.0
ND2 F:ASN26 4.0 47.3 1.0
CA F:ASN26 4.1 43.9 1.0
CB F:ASN26 4.3 44.2 1.0
CA F:SER102 4.4 29.9 1.0
O F:GLY27 4.4 37.6 1.0
O F:ILE104 4.5 26.4 1.0
N F:VAL103 4.5 28.1 1.0
CA F:VAL103 4.6 27.5 1.0
CB F:SER102 4.7 30.2 1.0
O F:VAL103 4.7 27.5 1.0
N F:GLY27 4.8 41.3 1.0
C F:VAL103 4.8 27.8 1.0
C F:GLY27 4.9 38.2 1.0
O F:HOH399 5.0 48.2 1.0

Reference:

D.D.Winkler, J.P.Schuermann, X.Cao, S.P.Holloway, D.R.Borchelt, M.C.Carroll, J.B.Proescher, V.C.Culotta, P.J.Hart. Structural and Biophysical Properties of the Pathogenic SOD1 Variant H46R/H48Q. Biochemistry V. 48 3436 2009.
ISSN: ISSN 0006-2960
PubMed: 19227972
DOI: 10.1021/BI8021735
Page generated: Sat Jul 13 10:46:22 2024

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