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Calcium in PDB 3kqa: Mura Dead-End Complex with Terreic Acid

Enzymatic activity of Mura Dead-End Complex with Terreic Acid

All present enzymatic activity of Mura Dead-End Complex with Terreic Acid:
2.5.1.7;

Protein crystallography data

The structure of Mura Dead-End Complex with Terreic Acid, PDB code: 3kqa was solved by E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 115.270, 115.270, 277.400, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Mura Dead-End Complex with Terreic Acid (pdb code 3kqa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Mura Dead-End Complex with Terreic Acid, PDB code: 3kqa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3kqa

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Calcium binding site 1 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca420

b:28.8
occ:1.00
 O A:HOH457 2.3 27.2 1.0
O A:LEU138 2.4 23.3 1.0
O4 A:TR9500 2.4 28.0 1.0
O A:HOH451 2.4 20.2 1.0
O1 A:TR9500 2.4 24.0 1.0
C5 A:TR9500 3.2 25.9 1.0
C6 A:TR9500 3.2 27.8 1.0
C A:LEU138 3.6 25.6 1.0
O A:HOH450 3.7 16.5 1.0
N A:LEU138 4.1 22.0 1.0
CA A:LEU138 4.3 24.6 1.0
CB A:LEU138 4.5 27.3 1.0
N A:GLU139 4.6 27.8 1.0
CB A:GLU139 4.6 37.9 1.0
C4 A:TR9500 4.7 26.7 1.0
CA A:GLU139 4.7 33.0 1.0
C1 A:TR9500 4.8 29.3 1.0

Calcium binding site 2 out of 10 in 3kqa

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Calcium binding site 2 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca421

b:27.0
occ:1.00
 O2 A:TR9500 2.3 30.1 1.0
O A:HOH502 2.3 24.2 1.0
O A:ALA116 2.4 31.1 1.0
O A:HOH464 2.4 24.9 1.0
O A:HOH470 2.5 21.8 1.0
O A:HOH446 2.5 16.5 1.0
O3 A:TR9500 2.7 29.7 1.0
C2 A:TR9500 3.3 27.0 1.0
C3 A:TR9500 3.4 26.4 1.0
C A:ALA116 3.6 32.0 1.0
O A:HOH514 3.7 32.1 1.0
OD1 A:ASP123 4.1 37.3 1.0
N A:ALA116 4.2 35.6 1.0
NH1 A:ARG120 4.3 48.1 1.0
CA A:ALA116 4.4 34.2 1.0
OD2 A:ASP123 4.4 36.6 1.0
C1 A:TR9500 4.5 29.3 1.0
O A:HOH535 4.6 28.2 1.0
CG A:ASP123 4.6 33.2 1.0
N A:ILE117 4.6 32.6 1.0
O A:HOH525 4.6 28.8 1.0
O A:ILE117 4.7 29.9 1.0
O A:GLY118 4.7 31.6 1.0
CD A:ARG120 4.8 45.4 1.0
CA A:ILE117 4.8 32.6 1.0
C4 A:TR9500 4.8 26.7 1.0
C A:ILE117 4.9 28.8 1.0

Calcium binding site 3 out of 10 in 3kqa

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Calcium binding site 3 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca420

b:26.4
occ:1.00
 O B:ILE136 2.2 18.0 1.0
O B:HOH483 2.3 31.3 1.0
O B:HOH465 2.3 20.8 1.0
O B:HOH520 2.4 29.0 1.0
C B:ILE136 3.4 21.4 1.0
N B:ILE136 3.8 23.1 1.0
OE1 B:GLU130 3.9 23.7 1.0
CA B:ILE136 4.1 21.3 1.0
N B:LYS137 4.4 23.1 1.0
O B:HOH458 4.5 25.7 1.0
CA B:LYS137 4.7 24.8 1.0
O B:HOH430 4.7 31.9 1.0
C7 B:TR9500 4.8 19.8 1.0
C B:GLU135 4.8 23.5 1.0
CB B:ILE136 4.8 24.2 1.0
CB B:LYS137 4.9 25.7 1.0

Calcium binding site 4 out of 10 in 3kqa

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Calcium binding site 4 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca421

b:29.2
occ:1.00
 O B:HOH524 2.2 26.6 1.0
O1 B:TR9500 2.3 24.3 1.0
O4 B:TR9500 2.3 22.2 1.0
O B:HOH542 2.4 33.6 1.0
O B:LEU138 2.4 31.2 1.0
O B:HOH466 2.5 18.5 1.0
C5 B:TR9500 3.1 25.6 1.0
C6 B:TR9500 3.1 27.8 1.0
C B:LEU138 3.6 28.6 1.0
O B:HOH458 3.9 25.7 1.0
N B:LEU138 4.0 25.5 1.0
CA B:LEU138 4.2 27.5 1.0
CB B:LEU138 4.5 26.3 1.0
C4 B:TR9500 4.6 26.2 1.0
N B:GLU139 4.6 29.6 1.0
C1 B:TR9500 4.6 28.8 1.0
CB B:GLU139 4.7 37.8 1.0
CA B:GLU139 4.8 32.3 1.0

Calcium binding site 5 out of 10 in 3kqa

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Calcium binding site 5 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca422

b:31.6
occ:1.00
 O2 B:TR9500 2.3 21.5 1.0
O B:ALA116 2.4 33.7 1.0
O B:HOH490 2.4 24.6 1.0
O B:HOH503 2.4 32.0 1.0
O B:HOH425 2.5 36.9 1.0
O B:HOH531 2.6 25.5 1.0
O B:HOH476 2.6 26.8 1.0
O3 B:TR9500 2.6 28.7 1.0
C2 B:TR9500 3.3 24.5 1.0
C3 B:TR9500 3.4 24.8 1.0
C B:ALA116 3.6 35.5 1.0
OD1 B:ASP123 4.1 33.9 1.0
N B:ALA116 4.2 35.5 1.0
CA B:ALA116 4.4 34.7 1.0
NH1 B:ARG120 4.5 48.4 1.0
C1 B:TR9500 4.5 28.8 1.0
N B:ILE117 4.6 35.1 1.0
OD2 B:ASP123 4.6 34.5 1.0
O B:GLY118 4.6 36.2 1.0
CG B:ASP123 4.7 30.7 1.0
CA B:ILE117 4.7 37.3 1.0
O B:ILE117 4.7 34.5 1.0
O B:HOH552 4.8 30.2 1.0
C B:ILE117 4.8 35.9 1.0
C4 B:TR9500 4.8 26.2 1.0
CB B:ALA116 4.9 35.1 1.0

Calcium binding site 6 out of 10 in 3kqa

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Calcium binding site 6 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca423

b:36.3
occ:1.00
 NE2 B:GLN106 2.2 37.6 1.0
O B:HOH575 2.3 24.8 1.0
O B:PHE104 2.4 18.0 1.0
O B:HOH528 2.7 32.6 1.0
CD B:GLN106 3.5 38.0 1.0
C B:PHE104 3.6 17.2 1.0
O B:HOH551 4.2 34.4 1.0
OE1 B:GLN106 4.3 42.0 1.0
CG B:GLN106 4.3 37.3 1.0
CA B:GLY105 4.5 19.9 1.0
N B:GLY105 4.5 18.9 1.0
CA B:PHE104 4.6 21.1 1.0
CB B:PHE104 4.8 19.6 1.0
C B:GLY105 4.9 21.2 1.0

Calcium binding site 7 out of 10 in 3kqa

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Calcium binding site 7 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca420

b:45.4
occ:1.00
 O2 C:TR9500 2.3 50.8 1.0
O3 C:TR9500 2.3 52.1 1.0
O C:ALA116 2.5 49.0 1.0
O C:HOH489 2.6 35.2 1.0
C3 C:TR9500 3.1 50.8 1.0
C2 C:TR9500 3.1 51.2 1.0
C C:ALA116 3.7 52.5 1.0
N C:ALA116 4.0 54.0 1.0
OD1 C:ASP123 4.1 39.6 1.0
O C:ILE117 4.1 55.3 1.0
O C:GLY118 4.5 47.9 1.0
OD2 C:ASP123 4.5 40.2 1.0
C1 C:TR9500 4.5 52.3 1.0
CA C:ALA116 4.5 53.2 1.0
C4 C:TR9500 4.5 49.0 1.0
O C:GLY114 4.6 57.1 1.0
C C:ILE117 4.7 53.9 1.0
N C:ILE117 4.7 54.1 1.0
CG C:ASP123 4.7 35.1 1.0
CA C:ILE117 4.8 55.7 1.0

Calcium binding site 8 out of 10 in 3kqa

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Calcium binding site 8 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca421

b:50.4
occ:1.00
 O C:LEU138 2.3 42.3 1.0
O4 C:TR9500 2.4 44.6 1.0
O1 C:TR9500 2.8 52.6 1.0
C6 C:TR9500 3.4 49.8 1.0
C C:LEU138 3.5 41.4 1.0
C5 C:TR9500 3.5 50.4 1.0
CA C:GLU139 4.3 43.6 1.0
CB C:LEU138 4.4 41.9 1.0
N C:GLU139 4.4 41.5 1.0
CA C:LEU138 4.4 41.7 1.0
CB C:GLU139 4.4 46.2 1.0
N C:LEU138 4.6 40.8 1.0
O C:HOH508 4.8 41.3 1.0
C1 C:TR9500 4.8 52.3 1.0
C4 C:TR9500 5.0 49.0 1.0

Calcium binding site 9 out of 10 in 3kqa

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Calcium binding site 9 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca420

b:34.9
occ:1.00
 O D:LEU138 2.2 49.1 1.0
O D:HOH434 2.3 20.9 1.0
O1 D:TR9500 2.4 40.4 1.0
O4 D:TR9500 2.4 34.8 1.0
C5 D:TR9500 3.2 37.1 1.0
C6 D:TR9500 3.2 36.4 1.0
C D:LEU138 3.4 47.6 1.0
OE1 D:GLU139 3.9 52.2 1.0
O D:HOH471 3.9 32.9 1.0
CA D:LEU138 4.2 46.7 1.0
N D:LEU138 4.2 47.9 1.0
CB D:LEU138 4.3 45.5 1.0
CD D:GLU139 4.3 51.5 1.0
N D:GLU139 4.4 46.6 1.0
CA D:GLU139 4.6 47.2 1.0
C4 D:TR9500 4.7 38.8 1.0
OE2 D:GLU139 4.7 51.8 1.0
C1 D:TR9500 4.7 38.6 1.0

Calcium binding site 10 out of 10 in 3kqa

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Calcium binding site 10 out of 10 in the Mura Dead-End Complex with Terreic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Mura Dead-End Complex with Terreic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca421

b:34.5
occ:1.00
 O3 D:TR9500 2.2 41.8 1.0
O D:HOH460 2.4 30.4 1.0
O2 D:TR9500 2.5 37.7 1.0
O D:ALA116 2.5 31.4 1.0
C3 D:TR9500 3.1 40.6 1.0
C2 D:TR9500 3.2 39.8 1.0
C D:ALA116 3.7 36.0 1.0
N D:ALA116 4.0 40.8 1.0
OD2 D:ASP123 4.3 42.1 1.0
OD1 D:ASP123 4.4 45.7 1.0
CA D:ALA116 4.5 37.5 1.0
C4 D:TR9500 4.5 38.8 1.0
C1 D:TR9500 4.6 38.6 1.0
N D:ILE117 4.6 36.4 1.0
O D:GLY118 4.7 46.4 1.0
O D:ILE117 4.7 38.2 1.0
O D:GLY114 4.7 47.5 1.0
CG D:ASP123 4.7 44.4 1.0
CA D:ILE117 4.7 38.3 1.0
C D:ILE117 4.8 38.5 1.0

Reference:

H.Han, Y.Yang, S.H.Olesen, A.Becker, S.Betzi, E.Schonbrunn. The Fungal Product Terreic Acid Is A Covalent Inhibitor of the Bacterial Cell Wall Biosynthetic Enzyme Udp-N-Acetylglucosamine 1-Carboxyvinyltransferase (Mura) . Biochemistry V. 49 4276 2010.
ISSN: ISSN 0006-2960
PubMed: 20392080
DOI: 10.1021/BI100365B
Page generated: Sat Jul 13 12:36:36 2024

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