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Calcium in PDB 4n98: E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid

Enzymatic activity of E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid

All present enzymatic activity of E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid:
2.7.7.7;

Protein crystallography data

The structure of E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid, PDB code: 4n98 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) 30.17 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.900, 67.160, 81.060, 90.00, 114.11, 90.00
R / Rfree (%) 25.6 / 29.6

Other elements in 4n98:

The structure of E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid (pdb code 4n98). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid, PDB code: 4n98:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4n98

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Calcium binding site 1 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:34.1
occ:1.00
 O A:HOH727 2.5 14.7 0.5
OG A:SER345 4.1 19.2 1.0
O A:HOH501 4.2 16.5 0.5
CG2 A:VAL344 4.3 23.2 1.0
O A:VAL344 4.8 19.4 1.0
OD2 A:ASP342 4.8 19.2 1.0

Calcium binding site 2 out of 9 in 4n98

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Calcium binding site 2 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:39.7
occ:1.00
 OE2 A:GLU202 3.4 30.3 1.0
O A:GLY46 3.5 19.5 1.0
OE1 A:GLU202 3.6 29.4 1.0
C A:GLY46 3.8 20.8 1.0
CD A:GLU202 3.9 28.1 1.0
CA A:THR47 4.0 23.2 1.0
N A:THR47 4.0 21.9 1.0
N A:MET53 4.1 21.1 1.0
O A:MET51 4.1 20.8 1.0
CA A:GLU52 4.3 22.0 1.0
C A:THR47 4.3 23.7 1.0
C A:GLU52 4.4 21.4 1.0
O A:VAL17 4.5 26.0 1.0
CG A:MET51 4.5 23.9 1.0
CB A:MET53 4.5 22.3 1.0
N A:ASP48 4.5 23.8 1.0
C A:MET51 4.5 22.1 1.0
CA A:GLY46 4.6 20.9 1.0
N A:GLU52 4.6 21.4 1.0
CA A:MET53 4.9 20.7 1.0
O A:THR47 4.9 24.0 1.0
O A:HOH508 5.0 30.6 1.0

Calcium binding site 3 out of 9 in 4n98

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Calcium binding site 3 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:62.3
occ:1.00
 O A:HOH654 3.8 32.1 1.0
CB A:GLU303 3.9 21.4 1.0
O A:HOH623 4.2 32.6 1.0
CB B:ARG105 4.2 27.0 1.0
OE1 A:GLU303 4.4 25.3 1.0
CB A:GLU301 4.5 24.5 1.0
O B:ARG105 4.6 22.4 1.0
N A:GLU303 4.7 20.2 1.0
CD A:GLU303 4.7 24.2 1.0
O A:GLU301 4.8 20.9 1.0
C B:ARG105 4.8 22.6 1.0
O B:HOH692 4.9 37.1 1.0
C A:ALA302 4.9 19.8 1.0
CG A:GLU303 4.9 22.9 1.0
CA A:GLU303 5.0 20.1 1.0
CD B:ARG105 5.0 35.9 1.0
OE2 A:GLU301 5.0 31.3 1.0

Calcium binding site 4 out of 9 in 4n98

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Calcium binding site 4 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:51.6
occ:1.00
 O A:HOH706 3.6 37.6 1.0
OG A:SER181 3.6 23.5 1.0
O A:SER356 3.7 21.1 1.0
CB A:SER181 3.8 21.1 1.0
O A:GLN355 3.8 23.9 1.0
N A:SER181 4.0 18.1 1.0
C A:SER356 4.1 22.3 1.0
O A:HOH664 4.3 46.0 1.0
O A:HOH578 4.4 32.2 1.0
CA A:SER181 4.5 20.1 1.0
CG2 A:VAL179 4.5 15.2 1.0
C A:CYS180 4.6 18.1 1.0
O A:VAL179 4.7 17.0 1.0
CA A:SER356 4.7 24.7 1.0
CA A:CYS180 4.7 16.7 1.0
N A:ALA357 4.7 19.0 1.0
CG1 A:VAL179 4.7 15.5 1.0
CA A:ALA357 4.8 17.5 1.0
C A:GLN355 4.9 25.7 1.0
C A:VAL179 4.9 16.4 1.0
N A:CYS180 4.9 16.3 1.0

Calcium binding site 5 out of 9 in 4n98

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Calcium binding site 5 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:33.0
occ:1.00
 O A:HOH587 3.0 25.0 1.0
OE1 A:GLN61 3.3 23.9 1.0
N A:GLU6 3.3 21.1 1.0
ND1 A:HIS9 3.4 29.4 1.0
CA A:VAL5 3.8 20.1 0.5
CA A:VAL5 3.9 19.9 0.5
CB A:GLU6 3.9 25.7 1.0
CG1 A:VAL5 4.0 19.4 0.5
CE1 A:HIS9 4.0 29.3 1.0
C A:VAL5 4.1 19.8 1.0
CG2 A:VAL60 4.2 21.1 1.0
O A:HOH541 4.2 19.8 1.0
CD A:GLN61 4.2 20.4 1.0
CA A:GLU6 4.3 21.9 1.0
CB A:VAL5 4.3 19.9 0.5
CG A:GLN61 4.4 21.2 1.0
CB A:VAL5 4.5 19.7 0.5
CG1 A:VAL5 4.5 20.1 0.5
O A:THR4 4.5 20.8 1.0
CG A:HIS9 4.6 26.8 1.0
OE2 A:GLU87 4.7 24.4 1.0
CG2 A:VAL5 4.9 19.7 0.5
N A:VAL5 5.0 20.3 1.0

Calcium binding site 6 out of 9 in 4n98

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Calcium binding site 6 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:49.1
occ:1.00
 O B:HOH530 3.9 21.5 1.0
CB B:GLU303 4.0 18.4 1.0
O B:HOH603 4.0 31.2 1.0
CG A:ARG105 4.0 31.8 1.0
OE1 B:GLU303 4.4 22.7 1.0
CB A:ARG105 4.4 25.3 1.0
O A:ARG105 4.5 18.8 1.0
CB B:GLU301 4.5 19.9 1.0
NE A:ARG105 4.6 41.4 1.0
CD A:ARG105 4.6 35.5 1.0
N B:GLU303 4.7 15.7 1.0
O B:GLU301 4.7 16.9 1.0
CD B:GLU303 4.7 20.6 1.0
C A:ARG105 4.8 19.6 1.0
C B:ALA302 4.8 15.4 1.0
C B:GLU301 5.0 16.9 1.0
CA B:GLU303 5.0 16.8 1.0
CG B:GLU303 5.0 19.8 1.0

Calcium binding site 7 out of 9 in 4n98

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Calcium binding site 7 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:33.6
occ:1.00
 O B:GLY46 3.5 19.3 1.0
C B:GLY46 3.6 20.6 1.0
OE2 B:GLU202 3.6 21.1 1.0
OE1 B:GLU202 3.7 24.4 1.0
CA B:THR47 3.7 22.3 1.0
N B:THR47 3.7 21.3 1.0
O B:MET51 4.0 21.9 1.0
CD B:GLU202 4.1 21.9 1.0
C B:THR47 4.1 22.0 1.0
N B:ASP48 4.2 21.6 1.0
N B:MET53 4.2 19.0 1.0
CA B:GLU52 4.3 21.4 1.0
O B:VAL17 4.4 24.4 1.0
CA B:GLY46 4.4 19.4 1.0
C B:MET51 4.5 21.0 1.0
C B:GLU52 4.5 20.0 1.0
N B:GLU52 4.6 21.2 1.0
CG B:MET51 4.6 22.4 1.0
O B:HOH502 4.6 25.4 1.0
CB B:MET53 4.7 18.3 1.0
O B:THR47 4.7 25.1 1.0
O B:HOH714 4.9 41.5 1.0

Calcium binding site 8 out of 9 in 4n98

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Calcium binding site 8 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:39.9
occ:1.00
 O B:HOH636 2.8 28.0 1.0
ND1 B:HIS9 3.2 21.3 1.0
N B:GLU6 3.2 22.3 1.0
OE1 B:GLN61 3.4 31.8 1.0
O B:HOH674 3.7 34.6 1.0
CE1 B:HIS9 3.7 21.5 1.0
CA B:VAL5 3.8 23.0 1.0
CB B:GLU6 4.0 25.2 1.0
C B:VAL5 4.0 22.2 1.0
CG B:GLU6 4.0 28.5 1.0
CG1 B:VAL5 4.0 24.5 1.0
CA B:GLU6 4.2 22.4 1.0
O B:HOH639 4.3 21.3 1.0
CG2 B:VAL60 4.3 29.9 1.0
CG B:HIS9 4.4 21.1 1.0
CB B:VAL5 4.4 24.5 1.0
CD B:GLN61 4.5 31.2 1.0
O B:THR4 4.5 23.3 1.0
CD B:GLU6 4.7 31.4 1.0
CG B:GLN61 4.7 29.7 1.0
OE1 B:GLU87 4.8 30.0 1.0
O B:HOH749 4.8 36.1 1.0
CB B:HIS9 4.9 20.9 1.0
CG2 B:VAL5 4.9 24.2 1.0
N B:VAL5 4.9 22.9 1.0
OE2 B:GLU6 4.9 35.9 1.0
NE2 B:HIS9 5.0 21.3 1.0

Calcium binding site 9 out of 9 in 4n98

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Calcium binding site 9 out of 9 in the E. Coli Sliding Clamp in Complex with 4'-Fluorobiphenyl-4-Carboxylic Acid


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 4'-Fluorobiphenyl-4-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:52.9
occ:1.00
 OG B:SER181 2.9 20.3 1.0
O B:SER356 3.7 21.7 1.0
CB B:SER181 3.9 17.9 1.0
O B:GLN355 4.0 21.9 1.0
CG2 B:VAL179 4.0 16.6 1.0
O B:HOH504 4.1 23.6 1.0
N B:SER181 4.1 17.5 1.0
O B:HOH602 4.2 41.2 1.0
C B:SER356 4.4 22.1 1.0
CA B:SER181 4.6 17.2 1.0
C B:CYS180 4.6 16.2 1.0
O B:VAL179 4.7 15.9 1.0
CG1 B:VAL179 4.7 18.1 1.0
CA B:CYS180 4.8 15.8 1.0
C B:VAL179 4.8 15.8 1.0
N B:CYS180 4.9 16.1 1.0
CA B:SER356 4.9 23.1 1.0
CD B:ARG168 5.0 21.5 1.0
CB B:VAL179 5.0 16.9 1.0

Reference:

Z.Yin, L.R.Whittell, Y.Wang, S.Jergic, M.Liu, E.J.Harry, N.E.Dixon, J.L.Beck, M.J.Kelso, A.J.Oakley. Discovery of Lead Compounds Targeting the Bacterial Sliding Clamp Using A Fragment-Based Approach. J.Med.Chem. V. 57 2799 2014.
ISSN: ISSN 0022-2623
PubMed: 24592885
DOI: 10.1021/JM500122R
Page generated: Sun Jul 14 10:57:17 2024

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