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Calcium in PDB 4k3l: E. Coli Sliding Clamp in Complex with Aclf Dipeptide

Enzymatic activity of E. Coli Sliding Clamp in Complex with Aclf Dipeptide

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

Protein crystallography data

The structure of E. Coli Sliding Clamp in Complex with Aclf Dipeptide, PDB code: 4k3l 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) 27.06 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.845, 67.464, 81.369, 90.00, 113.73, 90.00
R / Rfree (%) 21.7 / 25.5

Other elements in 4k3l:

The structure of E. Coli Sliding Clamp in Complex with Aclf Dipeptide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide (pdb code 4k3l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide, PDB code: 4k3l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 4k3l

Go back to Calcium Binding Sites List in 4k3l
Calcium binding site 1 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:29.5
occ:1.00
 O A:HOH560 2.9 16.4 1.0
ND1 A:HIS9 3.3 25.9 1.0
N A:GLU6 3.4 17.6 1.0
NE2 A:GLN61 3.5 22.5 1.0
CG2 A:VAL5 3.8 16.6 0.4
CE1 A:HIS9 3.8 25.4 1.0
CA A:VAL5 3.8 16.3 0.6
CA A:VAL5 3.9 16.5 0.4
CG A:GLU6 3.9 20.5 0.6
CB A:GLU6 4.0 19.3 0.6
C A:VAL5 4.1 16.6 1.0
CB A:GLU6 4.1 18.4 0.4
OE2 A:GLU6 4.1 23.1 0.6
CG2 A:VAL60 4.2 17.6 1.0
CB A:VAL5 4.2 16.4 0.6
CA A:GLU6 4.3 18.2 0.6
CA A:GLU6 4.3 17.9 0.4
O A:HOH546 4.4 16.4 1.0
CB A:VAL5 4.4 16.6 0.4
CG1 A:VAL5 4.5 16.1 0.6
CG A:HIS9 4.5 23.9 1.0
CD A:GLN61 4.5 21.2 1.0
CD A:GLU6 4.5 21.8 0.6
O A:THR4 4.6 17.0 1.0
CG A:GLN61 4.6 20.3 1.0
OE1 A:GLU87 4.8 26.4 1.0
CB A:HIS9 5.0 22.1 1.0
N A:VAL5 5.0 16.3 1.0

Calcium binding site 2 out of 12 in 4k3l

Go back to Calcium Binding Sites List in 4k3l
Calcium binding site 2 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:45.5
occ:1.00
 OG A:SER181 3.3 18.0 1.0
O A:HOH710 3.5 32.8 1.0
O A:SER356 3.5 17.2 1.0
CB A:SER181 3.7 16.0 1.0
O A:GLN355 3.7 21.1 1.0
C A:SER356 4.0 17.0 1.0
N A:SER181 4.1 14.1 1.0
O A:HOH779 4.1 42.6 1.0
O A:HOH680 4.3 26.3 1.0
CA A:SER356 4.5 18.7 1.0
CA A:SER181 4.5 15.3 1.0
C A:CYS180 4.7 13.2 1.0
CG2 A:VAL179 4.7 11.7 1.0
N A:ALA357 4.7 15.1 1.0
C A:GLN355 4.8 20.9 1.0
O A:VAL179 4.8 11.4 1.0
CA A:CYS180 4.8 12.9 1.0
CA A:ALA357 4.9 14.3 1.0

Calcium binding site 3 out of 12 in 4k3l

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Calcium binding site 3 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:57.6
occ:1.00
 O A:HOH621 3.9 21.8 1.0
NE B:ARG105 4.0 19.9 1.0
CB A:GLU303 4.1 16.6 1.0
CB B:ARG105 4.3 16.4 1.0
CB A:GLU301 4.3 17.7 1.0
O A:HOH614 4.4 28.3 1.0
O B:ARG105 4.4 14.9 1.0
O A:GLU301 4.5 14.9 1.0
OE1 A:GLU303 4.6 22.3 1.0
N A:GLU303 4.6 15.0 1.0
O B:HOH753 4.6 30.1 1.0
C B:ARG105 4.7 14.4 1.0
C A:ALA302 4.7 14.7 1.0
C A:GLU301 4.7 15.5 1.0
CD A:GLU303 4.9 19.7 1.0
OE2 A:GLU301 4.9 23.9 1.0
CA A:GLU303 5.0 15.3 1.0

Calcium binding site 4 out of 12 in 4k3l

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Calcium binding site 4 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:41.4
occ:1.00
 O A:HOH859 2.6 43.9 1.0
O A:HOH618 2.9 24.2 1.0
O A:HOH855 4.7 39.5 1.0

Calcium binding site 5 out of 12 in 4k3l

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Calcium binding site 5 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:15.8
occ:1.00
 OE1 B:GLU163 2.3 16.5 1.0
OE1 B:GLU166 2.3 16.5 1.0
O B:HOH617 2.3 21.1 1.0
O B:HOH588 2.4 20.3 1.0
O B:HOH792 2.5 17.0 1.0
CD B:GLU166 3.4 15.5 1.0
CD B:GLU163 3.4 15.9 1.0
CG B:GLU163 4.1 14.9 1.0
OE2 B:GLU166 4.1 15.1 1.0
CG B:GLU166 4.2 14.4 1.0
OE2 B:GLU163 4.3 18.1 1.0
NH2 B:ARG168 4.4 14.3 1.0
NH1 B:ARG168 4.5 13.8 1.0
CB B:GLU163 4.5 14.2 1.0
O B:HOH649 4.5 24.5 1.0
O B:GLU163 4.6 13.2 1.0
O B:HOH563 4.7 19.6 1.0
O B:HOH630 4.7 27.1 1.0
CZ B:ARG168 4.9 13.5 1.0

Calcium binding site 6 out of 12 in 4k3l

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Calcium binding site 6 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:33.0
occ:1.00
 O B:SER346 2.7 13.7 1.0
OG1 B:THR341 2.8 19.1 1.0
O B:MET339 2.9 17.7 1.0
N B:THR341 3.4 17.8 1.0
C B:LEU340 3.5 17.8 1.0
O B:HOH547 3.5 12.6 1.0
CA B:LEU340 3.6 18.4 1.0
CB B:PRO249 3.6 22.1 1.0
CB B:PRO252 3.6 22.1 1.0
CB B:THR341 3.6 18.9 1.0
CG B:PRO249 3.6 21.6 1.0
C B:MET339 3.7 19.0 1.0
CG B:PRO252 3.7 22.2 1.0
C B:SER346 3.8 14.2 1.0
N B:LEU340 3.9 18.4 1.0
CA B:VAL347 4.0 14.8 1.0
O B:LEU340 4.1 17.7 1.0
CA B:THR341 4.1 18.4 1.0
O B:HOH554 4.3 22.5 1.0
N B:VAL347 4.3 14.2 1.0
N B:GLN348 4.4 15.3 1.0
CA B:PRO252 4.5 22.4 1.0
C B:VAL347 4.6 15.1 1.0
CA B:MET339 5.0 19.9 1.0
CB B:SER345 5.0 15.4 1.0
CA B:SER346 5.0 14.3 1.0
CB B:LEU340 5.0 18.9 1.0

Calcium binding site 7 out of 12 in 4k3l

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Calcium binding site 7 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


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 Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:54.3
occ:1.00
 CB A:ARG105 4.1 18.2 1.0
O B:HOH548 4.2 20.2 1.0
CB B:GLU303 4.2 15.2 1.0
NE A:ARG105 4.3 24.9 1.0
O A:ARG105 4.4 15.2 1.0
O B:HOH700 4.5 28.5 1.0
O A:HOH699 4.5 31.2 1.0
CB B:GLU301 4.5 16.9 1.0
O B:GLU301 4.6 13.9 1.0
C A:ARG105 4.6 15.3 1.0
OE1 B:GLU303 4.6 20.8 1.0
N B:GLU303 4.8 13.5 1.0
CD A:ARG105 4.8 22.4 1.0
C B:GLU301 4.9 14.2 1.0
C B:ALA302 4.9 13.5 1.0
N A:PHE106 4.9 14.2 1.0
CD B:GLU303 5.0 17.7 1.0

Calcium binding site 8 out of 12 in 4k3l

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Calcium binding site 8 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of E. Coli Sliding Clamp in Complex with Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:27.1
occ:1.00
 O B:GLY46 3.4 12.9 1.0
C B:GLY46 3.5 13.8 1.0
OE2 B:GLU202 3.6 17.4 1.0
OE1 B:GLU202 3.6 19.1 1.0
N B:THR47 3.7 14.4 1.0
CA B:THR47 3.7 15.1 1.0
CD B:GLU202 4.0 17.0 1.0
O B:MET51 4.1 14.2 1.0
C B:THR47 4.2 15.5 1.0
N B:MET53 4.2 12.8 1.0
O B:VAL17 4.3 17.9 1.0
CA B:GLU52 4.3 14.0 1.0
CA B:GLY46 4.3 12.9 1.0
N B:ASP48 4.3 16.1 1.0
C B:GLU52 4.5 13.3 1.0
C B:MET51 4.6 14.3 1.0
CG B:MET51 4.6 16.3 1.0
N B:GLU52 4.6 13.6 1.0
O B:HOH531 4.7 25.0 1.0
CB B:MET53 4.7 13.0 1.0
O B:HOH807 4.8 38.1 1.0
O B:THR47 4.8 15.4 1.0
C B:VAL17 5.0 17.5 1.0

Calcium binding site 9 out of 12 in 4k3l

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Calcium binding site 9 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of E. Coli Sliding Clamp in Complex with Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca411

b:31.7
occ:0.90
 CG1 B:VAL344 3.9 14.7 1.0
O B:HOH900 4.2 30.3 1.0
CG2 B:VAL344 4.3 15.0 1.0
CB B:VAL344 4.5 14.7 1.0

Calcium binding site 10 out of 12 in 4k3l

Go back to Calcium Binding Sites List in 4k3l
Calcium binding site 10 out of 12 in the E. Coli Sliding Clamp in Complex with Aclf Dipeptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of E. Coli Sliding Clamp in Complex with Aclf Dipeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca412

b:32.2
occ:1.00
 O B:HOH790 2.7 34.6 1.0
O B:HOH616 2.9 19.6 1.0
N B:GLU127 3.1 12.3 1.0
O B:GLU127 3.4 12.6 1.0
O B:HOH778 3.5 32.2 1.0
CA B:VAL126 3.6 13.5 1.0
CD B:PRO189 3.8 15.3 1.0
C B:VAL126 3.9 12.7 1.0
CG1 B:VAL126 3.9 14.8 1.0
CA B:GLU127 4.1 12.2 1.0
C B:GLU127 4.2 12.2 1.0
CG B:PRO189 4.2 15.8 1.0
CB B:VAL126 4.3 13.8 1.0
O B:GLU125 4.5 15.0 1.0
O B:HOH795 4.5 17.1 1.0
CB B:GLU127 4.7 12.5 1.0
N B:VAL126 4.8 13.8 1.0
CG2 B:VAL126 4.8 13.8 1.0
O B:HOH661 4.8 28.2 1.0
O2 B:PEG410 5.0 45.6 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 08:47:37 2024

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