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Calcium in PDB 4pnw: E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid

Enzymatic activity of E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid

All present enzymatic activity of E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid:
2.7.7.7;

Protein crystallography data

The structure of E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid, PDB code: 4pnw 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) 28.01 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.815, 68.711, 83.055, 90.00, 115.72, 90.00
R / Rfree (%) 18.4 / 23.3

Other elements in 4pnw:

The structure of E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid (pdb code 4pnw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid, PDB code: 4pnw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4pnw

Go back to Calcium Binding Sites List in 4pnw
Calcium binding site 1 out of 4 in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- 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 (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.3
occ:1.00
 O A:HOH599 2.3 20.1 1.0
O A:HOH557 2.3 19.5 1.0
OD1 A:ASN118 2.4 22.7 1.0
O A:HOH555 2.4 13.5 1.0
O A:LEU119 2.4 21.8 1.0
O A:HOH525 2.4 21.9 1.0
C A:LEU119 3.5 23.0 1.0
CG A:ASN118 3.6 22.6 1.0
N A:LEU119 3.7 23.5 1.0
CA A:LEU119 4.1 23.8 1.0
O A:HOH533 4.2 21.4 1.0
C A:ASN118 4.2 23.1 1.0
O A:HOH631 4.3 29.0 1.0
ND2 A:ASN118 4.3 22.0 1.0
OD1 A:ASP121 4.3 19.9 1.0
O A:HOH597 4.3 26.9 1.0
CB A:LEU119 4.5 25.3 1.0
O A:HOH641 4.6 22.2 1.0
OE2 A:GLU52 4.6 20.0 1.0
CA A:ASN118 4.6 23.7 1.0
N A:ASP120 4.6 23.5 1.0
CB A:ASN118 4.7 23.4 1.0
OE1 A:GLU52 4.7 20.3 1.0
C A:ASP120 4.8 21.5 1.0
N A:ASP121 4.9 20.9 1.0
O A:ASP120 4.9 20.9 1.0
O A:ASN118 5.0 24.2 1.0
CA A:ASP120 5.0 22.5 1.0

Calcium binding site 2 out of 4 in 4pnw

Go back to Calcium Binding Sites List in 4pnw
Calcium binding site 2 out of 4 in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- 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 (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:48.9
occ:1.00
 OG A:SER181 3.4 24.4 1.0
O A:SER356 3.5 21.3 1.0
CB A:SER181 3.6 21.7 1.0
O A:HOH584 3.7 39.2 1.0
O A:GLN355 3.8 25.5 1.0
N A:SER181 3.9 20.2 1.0
C A:SER356 4.0 21.7 1.0
CA A:SER181 4.4 21.3 1.0
CA A:SER356 4.5 23.1 1.0
C A:CYS180 4.5 18.6 1.0
O A:VAL179 4.5 16.6 1.0
CG2 A:VAL179 4.5 16.8 1.0
O A:HOH602 4.5 26.6 1.0
CA A:CYS180 4.7 17.6 1.0
N A:ALA357 4.7 20.5 1.0
C A:VAL179 4.8 17.0 1.0
C A:GLN355 4.9 25.3 1.0
CG1 A:VAL179 4.9 16.7 1.0
CA A:ALA357 5.0 18.9 1.0
N A:CYS180 5.0 17.0 1.0

Calcium binding site 3 out of 4 in 4pnw

Go back to Calcium Binding Sites List in 4pnw
Calcium binding site 3 out of 4 in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- 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 (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:22.6
occ:1.00
 O B:HOH627 2.2 23.1 1.0
O B:LEU119 2.3 23.0 1.0
O B:HOH582 2.4 18.3 1.0
O B:HOH535 2.4 16.5 1.0
OD1 B:ASN118 2.4 20.8 1.0
O B:HOH644 2.4 21.0 1.0
O B:HOH553 2.6 15.5 1.0
C B:LEU119 3.5 22.7 1.0
CG B:ASN118 3.6 21.9 1.0
N B:LEU119 3.8 22.5 1.0
CA B:LEU119 4.1 23.4 1.0
O B:HOH765 4.2 23.7 1.0
OD1 B:ASP121 4.3 23.2 1.0
O B:HOH664 4.3 26.9 1.0
C B:ASN118 4.3 21.8 1.0
ND2 B:ASN118 4.4 21.4 1.0
CB B:LEU119 4.4 23.7 1.0
O B:HOH715 4.4 32.0 1.0
N B:ASP120 4.6 22.5 1.0
C B:ASP120 4.7 21.2 1.0
CA B:ASN118 4.7 21.3 1.0
CB B:ASN118 4.7 21.4 1.0
OE2 B:GLU52 4.8 20.4 1.0
O B:HOH587 4.8 26.5 1.0
OE1 B:GLU52 4.8 20.0 1.0
O B:ASP120 4.8 19.3 1.0
N B:ASP121 4.8 21.3 1.0
CA B:ASP120 4.9 21.8 1.0
O B:ASN118 5.0 22.7 1.0

Calcium binding site 4 out of 4 in 4pnw

Go back to Calcium Binding Sites List in 4pnw
Calcium binding site 4 out of 4 in the E. Coli Sliding Clamp in Complex with (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- 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 (R)-6-Bromo-9-(2-((S)-1-Carboxy- 2-Phenylethylamino)-2-Oxoethyl)-2,3,4,9-Tetrahydro-1H-Carbazole-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:49.5
occ:1.00
 OG B:SER181 3.4 30.2 1.0
O B:SER356 3.6 19.8 1.0
O B:HOH706 3.7 37.7 1.0
O B:GLN355 3.7 23.8 1.0
CB B:SER181 3.8 25.4 1.0
N B:SER181 3.9 22.0 1.0
C B:SER356 4.0 20.7 1.0
O B:HOH787 4.4 26.5 1.0
CA B:SER181 4.5 24.2 1.0
C B:CYS180 4.5 20.4 1.0
O B:VAL179 4.5 17.2 1.0
CG2 B:VAL179 4.5 18.4 1.0
CA B:SER356 4.5 21.7 1.0
CA B:CYS180 4.6 18.4 1.0
N B:ALA357 4.7 18.7 1.0
C B:VAL179 4.8 17.9 1.0
C B:GLN355 4.8 23.7 1.0
CA B:ALA357 4.9 18.6 1.0
N B:CYS180 4.9 18.5 1.0
CG1 B:VAL179 5.0 18.5 1.0

Reference:

Z.Yin, A.J.Oakley. Reaching Beyond the Anchor Site: Inhibitor Design Mimicking the Mechanism of Linear Motif Recognition By the E. Coli Sliding Clamp To Be Published.
Page generated: Sun Jul 14 12:10:25 2024

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