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Calcium in PDB 4k3k: E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid

Enzymatic activity of E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid

All present enzymatic activity of E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid:
2.7.7.7;

Protein crystallography data

The structure of E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid, PDB code: 4k3k 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) 34.95 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.027, 64.693, 71.789, 74.66, 83.22, 85.18
R / Rfree (%) 19.4 / 23

Other elements in 4k3k:

The structure of E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid (pdb code 4k3k). 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 (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid, PDB code: 4k3k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4k3k

Go back to Calcium Binding Sites List in 4k3k
Calcium binding site 1 out of 4 in the E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic 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 (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:23.9
occ:1.00
 O A:HOH685 2.9 22.1 1.0
OE1 A:GLN61 3.3 25.9 1.0
N A:GLU6 3.6 15.9 1.0
CD2 A:HIS9 3.8 19.9 1.0
CG A:GLU6 3.9 17.2 1.0
CA A:VAL5 4.0 14.7 0.7
O A:HOH544 4.0 16.1 1.0
O A:HOH745 4.1 22.5 1.0
CD A:GLN61 4.2 24.2 1.0
CG2 A:VAL5 4.2 14.5 0.7
CG A:GLN61 4.2 22.9 1.0
CG1 A:VAL60 4.3 18.8 1.0
C A:VAL5 4.3 15.0 0.7
NE2 A:HIS9 4.3 20.3 1.0
CB A:GLU6 4.4 16.7 1.0
O A:THR4 4.4 16.1 1.0
CA A:GLU6 4.6 16.3 1.0
CB A:VAL5 4.7 14.5 0.7
CD A:GLU6 4.7 18.0 1.0
OE2 A:GLU6 4.7 18.4 1.0
N A:VAL5 4.9 14.9 0.7

Calcium binding site 2 out of 4 in 4k3k

Go back to Calcium Binding Sites List in 4k3k
Calcium binding site 2 out of 4 in the E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic 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 (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:40.4
occ:1.00
 O A:HOH798 2.5 18.1 1.0
O A:HOH642 2.6 20.9 1.0
OE2 A:GLU161 2.9 13.3 1.0
OE1 A:GLU161 3.6 13.0 1.0
CD A:GLU161 3.7 12.9 1.0
NE A:ARG245 3.7 19.9 1.0
NH1 A:ARG168 3.7 12.1 1.0
CE1 A:TYR244 3.8 13.0 1.0
CZ A:ARG245 3.9 20.8 1.0
OE1 A:GLU163 3.9 17.2 1.0
CD A:ARG245 3.9 19.1 1.0
O A:HOH517 4.0 13.8 1.0
NH1 A:ARG245 4.2 21.3 1.0
OH A:TYR244 4.3 12.9 1.0
NH2 A:ARG245 4.4 20.8 1.0
CD A:GLU163 4.4 16.4 1.0
O A:HOH657 4.4 37.6 1.0
CZ A:TYR244 4.5 12.9 1.0
OE2 A:GLU163 4.5 16.7 1.0
CG A:ARG245 4.6 18.3 1.0
O A:HOH734 4.6 21.9 1.0
CD1 A:TYR244 4.7 13.0 1.0
OD1 A:ASP243 4.7 15.0 1.0
O A:HOH522 4.8 15.4 1.0
O A:HOH736 4.8 37.0 1.0
CZ A:ARG168 4.8 12.1 1.0

Calcium binding site 3 out of 4 in 4k3k

Go back to Calcium Binding Sites List in 4k3k
Calcium binding site 3 out of 4 in the E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic 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 (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:47.3
occ:1.00
 O A:HOH723 2.4 43.2 1.0
O A:GLY46 3.4 16.9 1.0
C A:GLY46 3.7 17.3 1.0
N A:MET53 4.0 17.6 1.0
N A:THR47 4.0 18.3 1.0
CA A:THR47 4.0 18.9 1.0
O A:MET51 4.2 17.8 1.0
CA A:GLU52 4.2 18.2 1.0
CB A:MET53 4.3 19.0 1.0
C A:GLU52 4.4 17.8 1.0
O A:VAL17 4.5 25.5 1.0
C A:THR47 4.5 19.5 1.0
CG A:MET51 4.6 20.5 1.0
C A:MET51 4.6 18.9 1.0
CA A:GLY46 4.6 16.6 1.0
N A:GLU52 4.6 18.2 1.0
N A:ASP48 4.8 19.6 1.0
CA A:MET53 4.8 17.7 1.0

Calcium binding site 4 out of 4 in 4k3k

Go back to Calcium Binding Sites List in 4k3k
Calcium binding site 4 out of 4 in the E. Coli Sliding Clamp in Complex with (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic 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 (S)-2-(4-Methylpentanamido)-3- Phenylpropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.6
occ:1.00
 O B:GLY85 2.2 10.4 1.0
OE2 B:GLU87 2.3 15.3 1.0
O B:HOH805 2.3 21.1 1.0
O B:HOH804 2.4 21.2 1.0
OE2 B:GLU6 2.5 13.7 1.0
CD B:GLU87 3.4 13.9 1.0
C B:GLY85 3.4 10.9 1.0
CD B:GLU6 3.5 13.3 1.0
CG B:GLU87 3.8 13.1 1.0
CG B:GLU6 4.0 12.8 1.0
CA B:GLY85 4.0 11.1 1.0
O B:HOH549 4.0 12.8 1.0
OE1 B:GLU87 4.4 14.4 1.0
N B:ALA86 4.5 10.8 1.0
N B:GLU87 4.6 11.3 1.0
C B:ALA86 4.6 11.0 1.0
OE1 B:GLU6 4.6 13.5 1.0
CA B:ALA86 4.8 10.8 1.0
O B:ALA86 5.0 11.0 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 08:47:12 2024

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