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Calcium in PDB 4odq: Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide

Enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide

All present enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide:
5.2.1.8;

Protein crystallography data

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide, PDB code: 4odq was solved by E.M.Quistgaard, C.Low, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.20 / 2.00
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 93.560, 93.560, 93.560, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.3

Other elements in 4odq:

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide (pdb code 4odq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide, PDB code: 4odq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4odq

Go back to Calcium Binding Sites List in 4odq
Calcium binding site 1 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:30.4
occ:1.00
 O A:HIS33 2.2 24.2 1.0
O A:HOH362 2.3 42.9 1.0
O A:HOH314 2.3 27.7 1.0
O A:HOH336 2.4 35.6 1.0
O A:HOH305 2.4 25.1 1.0
O A:HOH356 2.5 39.3 1.0
OD1 A:ASN35 2.5 21.4 1.0
C A:HIS33 3.5 23.6 1.0
CG A:ASN35 3.7 21.8 1.0
O A:ARG34 3.9 25.9 1.0
C A:ARG34 4.1 24.8 1.0
CB A:HIS33 4.2 21.6 1.0
ND2 A:ASN35 4.3 22.1 1.0
CB A:ARG34 4.4 36.1 1.0
CA A:HIS33 4.4 22.0 1.0
N A:ARG34 4.4 25.4 1.0
N A:ASN35 4.5 21.5 1.0
O A:GLY98 4.5 18.9 1.0
CA A:ARG34 4.5 28.5 1.0
CA A:ASN35 4.8 20.9 1.0
O A:HOH383 4.8 53.9 1.0
CB A:ASN35 4.8 19.8 1.0

Calcium binding site 2 out of 4 in 4odq

Go back to Calcium Binding Sites List in 4odq
Calcium binding site 2 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:47.6
occ:1.00
 O A:HOH326 2.3 35.9 1.0
OE2 A:GLU49 2.4 19.1 1.0
OE1 A:GLU49 2.5 27.2 1.0
O A:HOH313 2.5 33.1 1.0
CD A:GLU49 2.8 24.3 1.0
O A:VAL87 4.3 15.4 1.0
CG A:GLU49 4.3 23.3 1.0
O A:HOH382 4.4 52.1 1.0
CG A:LYS86 4.6 26.3 1.0
N A:VAL87 4.8 14.8 1.0
CB A:GLU49 5.0 21.3 1.0

Calcium binding site 3 out of 4 in 4odq

Go back to Calcium Binding Sites List in 4odq
Calcium binding site 3 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:53.9
occ:1.00
 O A:HOH347 2.3 41.4 1.0
O A:HOH352 2.4 53.4 1.0
O A:HOH368 2.4 49.3 1.0
O A:HOH370 2.4 61.8 1.0
O A:ALA52 2.4 23.5 1.0
C A:ALA52 3.6 22.5 1.0
N A:ALA52 4.1 18.7 1.0
CA A:ALA52 4.4 20.9 1.0
N A:PHE53 4.6 20.5 1.0
CA A:PHE53 4.7 21.7 1.0
CB A:ALA52 4.8 21.6 1.0
CB A:PHE53 4.8 22.1 1.0
O A:HOH311 4.9 30.9 1.0

Calcium binding site 4 out of 4 in 4odq

Go back to Calcium Binding Sites List in 4odq
Calcium binding site 4 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:49.0
occ:1.00
 O A:HOH328 2.4 35.8 1.0
O A:HOH322 2.4 53.3 1.0
OE1 A:GLN16 2.4 41.3 1.0
O A:HOH331 2.4 59.8 1.0
O A:HOH329 2.5 30.9 1.0
CD A:GLN16 3.5 39.6 1.0
NE2 A:GLN16 4.2 38.9 1.0
O A:HOH373 4.2 51.1 1.0
O A:HOH309 4.5 26.1 1.0
CG2 A:VAL21 4.6 42.7 1.0
CG A:GLN16 4.7 37.9 1.0
O A:HOH371 4.8 39.2 1.0
O A:GLY19 4.8 42.0 1.0

Reference:

E.M.Quistgaard, C.Low, P.Nordlund. Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S3 Peptide To Be Published.
Page generated: Sat Dec 12 05:02:09 2020

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