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Calcium in PDB 4odp: Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide

Enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide

All present enzymatic activity of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide:
5.2.1.8;

Protein crystallography data

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide, PDB code: 4odp 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) 29.63 / 1.75
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 93.690, 93.690, 93.690, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.2

Other elements in 4odp:

The structure of Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A 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 S2-W23A Peptide (pdb code 4odp). 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 S2-W23A Peptide, PDB code: 4odp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4odp

Go back to Calcium Binding Sites List in 4odp
Calcium binding site 1 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A 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 S2-W23A Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:41.6
occ:1.00
 O A:HOH370 2.3 43.7 1.0
OE2 A:GLU49 2.4 30.6 1.0
O A:HOH388 2.4 60.2 0.3
O A:HOH363 2.4 48.3 1.0
OE1 A:GLU49 2.5 46.5 1.0
O A:HOH320 2.5 37.3 1.0
CD A:GLU49 2.8 55.9 1.0
O A:HOH346 4.3 45.8 1.0
CG A:GLU49 4.3 36.3 1.0
O A:VAL87 4.4 23.2 1.0
CG A:LYS86 4.9 28.6 1.0

Calcium binding site 2 out of 4 in 4odp

Go back to Calcium Binding Sites List in 4odp
Calcium binding site 2 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A 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 S2-W23A Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:37.2
occ:1.00
 O A:HOH308 2.3 41.5 1.0
O A:HOH378 2.3 44.6 1.0
O A:HOH391 2.4 51.0 1.0
O A:ALA52 2.4 30.7 1.0
O A:HOH350 2.4 48.7 1.0
C A:ALA52 3.6 31.0 1.0
N A:ALA52 4.1 24.7 1.0
CG A:GLU51 4.4 60.2 1.0
CA A:ALA52 4.4 24.1 1.0
N A:PHE53 4.6 25.7 1.0
CA A:PHE53 4.6 24.1 1.0
CB A:PHE53 4.7 26.6 1.0
CB A:ALA52 4.7 28.5 1.0
O A:HOH318 4.7 45.2 1.0
OE2 A:GLU51 4.9 48.4 1.0

Calcium binding site 3 out of 4 in 4odp

Go back to Calcium Binding Sites List in 4odp
Calcium binding site 3 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A 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 S2-W23A Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:38.1
occ:1.00
 O A:HIS33 2.3 34.4 1.0
O A:HOH384 2.3 46.4 1.0
O A:HOH321 2.4 40.4 1.0
O A:HOH353 2.4 47.6 1.0
O A:HOH375 2.5 43.1 1.0
OD1 A:ASN35 2.6 43.5 1.0
C A:HIS33 3.5 33.2 1.0
CG A:ASN35 3.8 35.9 1.0
O A:ARG34 4.0 41.8 1.0
C A:ARG34 4.1 36.9 1.0
CB A:ARG34 4.2 35.0 1.0
CB A:HIS33 4.3 25.4 1.0
O A:HOH333 4.4 54.7 1.0
N A:ARG34 4.4 30.6 1.0
ND2 A:ASN35 4.4 34.5 1.0
CA A:HIS33 4.4 26.5 1.0
CA A:ARG34 4.4 29.9 1.0
O A:GLY98 4.5 26.6 1.0
N A:ASN35 4.5 28.6 1.0
CA A:ASN35 4.8 26.1 1.0
CB A:ASN35 4.9 33.6 1.0

Calcium binding site 4 out of 4 in 4odp

Go back to Calcium Binding Sites List in 4odp
Calcium binding site 4 out of 4 in the Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A 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 S2-W23A Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:48.1
occ:1.00
 OE1 A:GLN16 2.2 51.3 1.0
O A:HOH376 2.4 39.8 1.0
O A:HOH374 2.4 46.6 1.0
O A:HOH331 2.4 51.6 1.0
O A:HOH387 2.5 58.3 1.0
O A:HOH398 2.5 62.2 1.0
CD A:GLN16 3.4 40.5 1.0
NE2 A:GLN16 4.1 44.3 1.0
O A:GLY19 4.4 37.4 1.0
O A:HOH355 4.5 53.9 1.0
CG A:GLN16 4.5 38.2 1.0
O A:HOH314 4.6 33.9 1.0
CG2 A:VAL21 4.6 41.7 1.0

Reference:

E.M.Quistgaard, C.Low, P.Nordlund. Structure of Slyd Delta-if From Thermus Thermophilus in Complex with S2-W23A Peptide To Be Published.
Page generated: Wed Jul 9 01:02:31 2025

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