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Calcium in PDB 4k3m: E.Coli Sliding Clamp in Complex with Acaldlf Peptide

Enzymatic activity of E.Coli Sliding Clamp in Complex with Acaldlf Peptide

All present enzymatic activity of E.Coli Sliding Clamp in Complex with Acaldlf Peptide:
2.7.7.7;

Protein crystallography data

The structure of E.Coli Sliding Clamp in Complex with Acaldlf Peptide, PDB code: 4k3m was solved by Z.Yin, A.J.Oakley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.65 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.853, 67.290, 81.190, 90.00, 113.76, 90.00
R / Rfree (%) 20.2 / 25.8

Calcium Binding Sites:

The binding sites of Calcium atom in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide (pdb code 4k3m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide, PDB code: 4k3m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4k3m

Go back to Calcium Binding Sites List in 4k3m
Calcium binding site 1 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:57.9
occ:1.00
 O A:HOH707 2.4 42.0 1.0
OG A:SER107 3.6 13.2 0.4
O B:GLU301 4.0 13.9 1.0
CB A:ARG105 4.2 17.2 1.0
O A:ARG105 4.3 13.7 1.0
CB B:GLU301 4.3 17.4 1.0
O B:HOH554 4.3 14.0 1.0
C A:ARG105 4.4 14.5 1.0
CB B:GLU303 4.5 13.9 1.0
C B:GLU301 4.5 14.8 1.0
CB A:SER107 4.5 13.3 0.4
CB A:SER107 4.5 13.7 0.6
NE A:ARG105 4.6 25.7 1.0
N A:SER107 4.7 13.1 1.0
N A:PHE106 4.7 13.5 1.0
N B:GLU303 4.7 12.7 1.0
C A:PHE106 4.8 13.1 1.0
O B:HOH745 4.8 26.6 1.0
C B:ALA302 4.9 13.0 1.0
CA A:PHE106 4.9 13.1 1.0
N B:ALA302 5.0 13.7 1.0

Calcium binding site 2 out of 7 in 4k3m

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Calcium binding site 2 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:40.0
occ:1.00
 O A:GLY280 2.9 14.5 1.0
O A:HOH573 3.0 23.4 1.0
N A:ASN295 3.1 16.8 1.0
O A:HOH549 3.3 19.6 1.0
CA A:ALA294 3.4 14.6 1.0
O A:ASN295 3.6 18.8 1.0
C A:ALA294 3.7 15.6 1.0
C A:GLY280 3.7 14.4 1.0
OD1 A:ASN295 3.9 24.7 1.0
O A:THR293 4.1 12.7 1.0
CA A:VAL281 4.1 13.9 1.0
CG A:ASN295 4.1 21.8 1.0
CA A:ASN295 4.1 18.6 1.0
CB A:ALA294 4.2 14.1 1.0
NH2 A:ARG282 4.3 17.6 0.4
N A:VAL281 4.3 14.1 1.0
C A:ASN295 4.3 19.2 1.0
N A:ALA294 4.4 13.8 1.0
ND2 A:ASN295 4.5 21.6 1.0
C A:THR293 4.6 13.5 1.0
CZ A:ARG282 4.6 17.3 0.4
C A:VAL281 4.7 14.5 1.0
CG A:ARG282 4.7 18.8 0.6
CB A:ASN295 4.7 20.2 1.0
CA A:GLY280 4.7 15.1 1.0
N A:ARG282 4.7 14.9 1.0
CG A:ARG282 4.8 16.1 0.4
O A:ALA294 4.9 15.3 1.0
NH1 A:ARG282 4.9 17.2 0.4

Calcium binding site 3 out of 7 in 4k3m

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Calcium binding site 3 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:49.3
occ:1.00
 O A:HOH768 3.4 36.9 1.0
OG A:SER181 3.5 15.1 1.0
O A:SER356 3.7 15.2 1.0
CB A:SER181 3.8 14.3 1.0
O A:GLN355 3.9 19.8 1.0
N A:SER181 4.1 12.9 1.0
C A:SER356 4.3 15.9 1.0
O A:HOH693 4.3 31.5 1.0
O A:HOH744 4.4 46.1 1.0
CG2 A:VAL179 4.4 10.1 1.0
CA A:SER181 4.6 14.2 1.0
O A:VAL179 4.6 11.2 1.0
C A:CYS180 4.7 12.3 1.0
CG1 A:VAL179 4.8 10.4 1.0
CA A:CYS180 4.8 11.7 1.0
CA A:SER356 4.9 16.6 0.5
C A:VAL179 4.9 10.8 1.0
N A:ALA357 4.9 14.5 1.0
CA A:SER356 4.9 16.7 0.5
CA A:ALA357 5.0 13.5 1.0

Calcium binding site 4 out of 7 in 4k3m

Go back to Calcium Binding Sites List in 4k3m
Calcium binding site 4 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:36.0
occ:1.00
 OD2 B:ASP211 2.5 15.9 1.0
CG B:ASP211 3.5 17.1 1.0
CB B:ASP211 3.7 17.2 1.0
OD1 B:ASP211 4.7 17.2 1.0

Calcium binding site 5 out of 7 in 4k3m

Go back to Calcium Binding Sites List in 4k3m
Calcium binding site 5 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:43.2
occ:1.00
 O B:HOH736 2.4 27.1 1.0
OE2 B:GLU161 2.7 17.9 1.0
O B:THR162 2.9 13.6 1.0
CG B:GLU161 3.3 15.4 1.0
CD B:GLU161 3.4 16.6 1.0
N B:HIS191 3.6 17.4 1.0
CB B:SER190 3.6 18.8 1.0
CA B:SER190 3.8 18.5 1.0
CB B:GLU163 3.9 17.2 1.0
C B:THR162 3.9 13.6 1.0
C B:SER190 3.9 18.4 1.0
O B:HIS191 4.0 15.6 1.0
CG B:GLU163 4.1 19.1 1.0
OG B:SER190 4.2 19.5 1.0
CA B:GLU163 4.3 15.9 1.0
C B:HIS191 4.4 16.6 1.0
CA B:HIS191 4.5 17.4 1.0
N B:GLU163 4.5 14.5 1.0
CD B:GLU163 4.6 20.5 1.0
OE2 B:GLU163 4.6 21.8 1.0
OE1 B:GLU161 4.6 16.9 1.0
N B:THR162 4.7 13.2 1.0
NH2 B:ARG245 4.8 25.6 1.0
CB B:GLU161 4.8 14.5 1.0
O B:SER190 4.9 18.3 1.0
CA B:THR162 5.0 13.1 1.0

Calcium binding site 6 out of 7 in 4k3m

Go back to Calcium Binding Sites List in 4k3m
Calcium binding site 6 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:51.0
occ:1.00
 O B:HOH806 2.5 17.4 1.0
O B:HOH767 3.0 25.1 1.0
O B:GLU84 3.7 18.9 1.0
CA B:GLY85 4.0 20.0 1.0
C B:GLU84 4.0 19.2 1.0
O B:HOH763 4.1 30.9 1.0
N B:GLY85 4.1 19.5 1.0
O B:HOH616 4.2 27.9 1.0
CB B:GLU84 4.6 19.1 1.0
O B:HOH723 4.9 26.4 1.0
CA B:GLU84 5.0 18.6 1.0
C B:GLY85 5.0 19.7 1.0

Calcium binding site 7 out of 7 in 4k3m

Go back to Calcium Binding Sites List in 4k3m
Calcium binding site 7 out of 7 in the E.Coli Sliding Clamp in Complex with Acaldlf Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of E.Coli Sliding Clamp in Complex with Acaldlf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:29.3
occ:1.00
 O B:HOH823 2.4 22.2 1.0
OE1 B:GLU163 2.5 21.8 1.0
O B:HOH814 2.6 19.0 1.0
CD B:GLU163 3.4 20.5 1.0
OE2 B:GLU166 3.8 20.7 1.0
CG B:GLU163 4.0 19.1 1.0
OE2 B:GLU163 4.3 21.8 1.0
NH2 B:ARG168 4.3 18.6 1.0
CD B:GLU166 4.4 21.2 1.0
CB B:GLU163 4.4 17.2 1.0
NH1 B:ARG168 4.5 17.8 1.0
CG B:GLU166 4.5 19.6 1.0
O B:HOH702 4.5 31.5 1.0
O B:GLU163 4.6 15.9 1.0
O B:HOH625 4.7 25.8 1.0
CZ B:ARG168 4.9 17.3 1.0
C B:GLU163 5.0 15.8 1.0

Reference:

Z.Yin, M.J.Kelso, J.L.Beck, A.J.Oakley. Structural and Thermodynamic Dissection of Linear Motif Recognition By the E. Coli Sliding Clamp J.Med.Chem. V. 56 8665 2013.
ISSN: ISSN 0022-2623
PubMed: 24090409
DOI: 10.1021/JM401118F
Page generated: Sun Jul 14 08:47:45 2024

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