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Calcium in PDB 3qyo: Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate

Enzymatic activity of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate

All present enzymatic activity of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate:
1.5.1.3;

Protein crystallography data

The structure of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate, PDB code: 3qyo was solved by E.J.Collins, A.L.Lee, M.J.Carroll, R.V.Mauldin, A.V.Gromova, S.F.Singleton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.33 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.990, 45.110, 97.800, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate (pdb code 3qyo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate, PDB code: 3qyo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3qyo

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Calcium binding site 1 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca160

b:29.1
occ:1.00
 O A:HOH272 2.3 12.3 1.0
O A:HOH350 2.5 4.4 1.0
O A:HOH243 2.5 3.0 1.0
O A:ASP122 2.5 7.8 1.0
O A:HOH308 2.7 19.1 1.0
O A:HOH348 3.4 21.5 1.0
C A:ASP122 3.7 8.3 1.0
OG1 A:THR123 4.1 6.8 1.0
O A:HOH223 4.5 5.9 1.0
CA A:THR123 4.5 3.2 1.0
N A:THR123 4.5 3.7 1.0
OD1 A:ASP122 4.6 11.1 1.0
CB A:ASP122 4.6 7.3 1.0
O2N A:NDP1160 4.6 8.9 1.0
CA A:ASP122 4.7 6.1 1.0
CG A:ASP122 4.7 10.6 1.0
CB A:THR123 4.8 6.4 1.0
O A:HOH218 4.9 11.7 1.0

Calcium binding site 2 out of 8 in 3qyo

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Calcium binding site 2 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca162

b:5.5
occ:1.00
 O A:ARG159 2.2 5.9 1.0
O A:HOH244 2.4 3.0 1.0
O A:HOH196 2.5 3.6 1.0
C A:ARG159 3.4 6.1 1.0
CA A:ARG159 3.9 4.7 1.0
OXT A:ARG159 4.4 9.2 1.0
CB A:ARG159 4.6 5.4 1.0
O A:ARG158 4.7 6.4 1.0

Calcium binding site 3 out of 8 in 3qyo

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Calcium binding site 3 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca163

b:49.8
occ:1.00
 O3X A:NDP1160 2.5 7.4 1.0
O A:HOH299 2.7 10.2 1.0
O A:HOH274 3.6 50.5 1.0
NH2 A:ARG44 3.8 6.1 1.0
O3B A:NDP1160 3.8 3.0 1.0
P2B A:NDP1160 3.8 8.0 1.0
O1X A:NDP1160 4.3 6.8 1.0
O A:HOH341 4.3 13.6 1.0
O2X A:NDP1160 4.8 10.1 1.0
O2B A:NDP1160 4.8 3.0 1.0
O A:HOH319 4.9 12.3 1.0
NH2 A:ARG98 4.9 3.0 1.0
NE2 A:HIS45 4.9 8.3 1.0
CZ A:ARG44 5.0 14.2 1.0

Calcium binding site 4 out of 8 in 3qyo

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Calcium binding site 4 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca164

b:53.0
occ:1.00
 O A:HOH355 2.8 13.6 1.0
O A:HOH174 4.5 13.3 1.0
OE1 A:GLU17 4.7 30.4 1.0

Calcium binding site 5 out of 8 in 3qyo

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Calcium binding site 5 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca165

b:29.9
occ:1.00
 O A:HOH250 2.3 17.9 1.0
OE1 A:GLU129 4.5 16.5 1.0
OE2 A:GLU129 4.7 13.6 1.0
O A:HOH363 4.8 16.5 1.0
CG A:PRO130 4.8 15.4 1.0
CD A:PRO130 4.9 10.9 1.0

Calcium binding site 6 out of 8 in 3qyo

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Calcium binding site 6 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:

Calcium binding site 7 out of 8 in 3qyo

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Calcium binding site 7 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca167

b:41.0
occ:1.00
 O A:HOH169 4.2 23.2 1.0
O A:HOH248 4.3 21.1 1.0
O A:HOH231 4.4 26.0 1.0
O A:HOH245 4.4 12.2 1.0

Calcium binding site 8 out of 8 in 3qyo

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Calcium binding site 8 out of 8 in the Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Sensitivity of Receptor Internal Motions to Ligand Binding Affinity and Kinetic Off-Rate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca168

b:63.6
occ:1.00
 OD1 A:ASN23 2.1 16.4 0.3
CG A:ASN23 2.6 20.9 0.3
ND2 A:ASN23 2.7 3.1 0.3
O A:HOH344 2.8 18.4 1.0
O A:ASN23 3.1 22.4 1.0
N A:SER148 3.4 7.0 1.0
OG A:SER148 3.4 22.1 1.0
O A:GLN146 3.4 6.0 1.0
CB A:SER148 3.5 10.5 1.0
CB A:ASN23 3.9 24.1 0.7
O A:HOH322 3.9 19.4 1.0
CA A:SER148 4.0 7.3 1.0
CB A:ASN23 4.0 17.2 0.3
C A:ASN23 4.1 21.4 1.0
O A:HOH321 4.1 14.5 1.0
C A:GLN146 4.1 8.1 1.0
C A:ASN147 4.2 8.9 1.0
CA A:ASN147 4.2 4.9 1.0
OD1 A:ASN23 4.2 47.5 0.7
N A:ASN147 4.4 4.9 1.0
CA A:ASN23 4.5 18.3 0.7
CG A:ASN23 4.5 51.2 0.7
CA A:ASN23 4.5 17.4 0.3
N A:ASN23 4.9 17.5 1.0

Reference:

M.J.Carroll, R.V.Mauldin, A.V.Gromova, S.F.Singleton, E.J.Collins, A.L.Lee. Evidence For Dynamics in Proteins As A Mechanism For Ligand Dissociation. Nat.Chem.Biol. V. 8 246 2012.
ISSN: ISSN 1552-4450
PubMed: 22246400
DOI: 10.1038/NCHEMBIO.769
Page generated: Tue Jul 8 16:05:44 2025

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