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Calcium in PDB 3mkn: Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor

Enzymatic activity of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor

All present enzymatic activity of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor:
3.2.2.8;

Protein crystallography data

The structure of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor, PDB code: 3mkn was solved by G.Garau, A.Fornili, B.Giabbai, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.97 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.851, 86.446, 97.817, 90.00, 98.86, 90.00
R / Rfree (%) 17.4 / 19.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor (pdb code 3mkn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor, PDB code: 3mkn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3mkn

Go back to Calcium Binding Sites List in 3mkn
Calcium binding site 1 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:24.1
occ:1.00
 O A:VAL124 2.3 24.4 1.0
OD1 A:ASP11 2.4 28.1 1.0
OD2 A:ASP240 2.5 28.6 1.0
O A:HOH314 2.6 19.2 1.0
OD1 A:ASP16 2.6 29.3 1.0
O2' A:DNB502 2.6 39.7 1.0
OD2 A:ASP16 2.6 28.9 1.0
O3' A:DNB502 2.7 37.3 1.0
CG A:ASP16 2.9 30.6 1.0
CG A:ASP240 3.4 30.5 1.0
C A:VAL124 3.5 24.2 1.0
CG A:ASP11 3.5 24.9 1.0
C2' A:DNB502 3.6 41.7 1.0
ND2 A:ASN40 3.7 32.6 1.0
C3' A:DNB502 3.7 39.9 1.0
OD1 A:ASP240 3.7 30.2 1.0
OD2 A:ASP11 3.9 24.5 1.0
CA A:GLY125 4.2 21.4 1.0
N A:GLY125 4.2 22.4 1.0
C1' A:DNB502 4.2 44.9 1.0
CB A:ASP16 4.4 33.5 1.0
O A:ASP11 4.5 28.1 1.0
OD1 A:ASN166 4.5 22.5 1.0
N4' A:DNB502 4.5 40.4 1.0
N A:ASP11 4.5 26.1 1.0
ND2 A:ASN166 4.5 20.5 1.0
CB A:VAL124 4.6 27.7 1.0
CG2 A:VAL124 4.6 28.4 1.0
OD1 A:ASP15 4.6 39.9 1.0
CA A:VAL124 4.6 25.4 1.0
OD2 A:ASP15 4.6 41.5 1.0
C4' A:DNB502 4.6 39.5 1.0
CG A:ASN40 4.7 32.5 1.0
N A:ASP16 4.8 36.8 1.0
CB A:ASP240 4.8 32.1 1.0
C A:ASP11 4.8 28.1 1.0
CB A:ASP11 4.8 23.9 1.0
CG A:ASP15 4.9 41.0 1.0
CA A:ASP16 4.9 35.5 1.0
CG A:ASN166 5.0 21.0 1.0
CA A:ASP11 5.0 26.0 1.0

Calcium binding site 2 out of 4 in 3mkn

Go back to Calcium Binding Sites List in 3mkn
Calcium binding site 2 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:13.6
occ:1.00
 OD1 B:ASP11 2.4 15.3 1.0
O B:VAL124 2.4 9.8 1.0
OD2 B:ASP240 2.5 11.1 1.0
OD1 B:ASP16 2.5 13.1 1.0
O3' B:DNB502 2.5 33.1 1.0
OD2 B:ASP16 2.6 12.6 1.0
O2' B:DNB502 2.7 39.3 1.0
O B:HOH315 2.7 14.2 1.0
CG B:ASP16 2.9 12.9 1.0
CG B:ASP240 3.5 11.9 1.0
C B:VAL124 3.5 10.4 1.0
CG B:ASP11 3.5 13.8 1.0
C2' B:DNB502 3.6 42.2 1.0
C3' B:DNB502 3.6 39.2 1.0
ND2 B:ASN40 3.7 19.4 1.0
OD1 B:ASP240 3.8 13.1 1.0
OD2 B:ASP11 4.0 14.0 1.0
CA B:GLY125 4.1 10.5 1.0
OD1 B:ASP15 4.2 24.9 0.4
N B:GLY125 4.2 10.0 1.0
C1' B:DNB502 4.3 45.3 1.0
CB B:ASP16 4.3 13.4 1.0
CG2 B:VAL124 4.4 9.8 1.0
O B:ASP11 4.4 14.2 1.0
N B:ASP11 4.4 12.7 1.0
OD1 B:ASN166 4.5 12.7 1.0
CB B:VAL124 4.5 9.5 1.0
OD1 B:ASP15 4.5 21.0 0.5
N4' B:DNB502 4.5 39.0 1.0
CA B:VAL124 4.6 9.8 1.0
ND2 B:ASN166 4.6 9.4 1.0
C4' B:DNB502 4.7 36.6 1.0
N B:ASP16 4.8 14.6 1.0
CB B:ASP240 4.8 10.6 1.0
C B:ASP11 4.8 14.2 1.0
CG B:ASN40 4.8 20.6 1.0
CB B:ASP11 4.8 13.5 1.0
CA B:ASP16 4.8 13.8 1.0
CA B:ASP11 4.9 13.1 1.0
O B:HOH330 5.0 36.2 1.0
CG B:ASN166 5.0 11.0 1.0

Calcium binding site 3 out of 4 in 3mkn

Go back to Calcium Binding Sites List in 3mkn
Calcium binding site 3 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:27.9
occ:1.00
 OD1 C:ASP11 2.4 32.0 1.0
O C:VAL124 2.5 26.6 1.0
OD2 C:ASP240 2.5 30.8 1.0
OD2 C:ASP16 2.6 32.8 1.0
OD1 C:ASP16 2.6 32.6 1.0
O C:HOH314 2.6 22.2 1.0
O3' C:DNB502 2.7 58.1 1.0
CG C:ASP16 2.9 33.9 1.0
O2' C:DNB502 2.9 60.1 1.0
CG C:ASP240 3.5 31.9 1.0
CG C:ASP11 3.5 30.1 1.0
C C:VAL124 3.6 25.9 1.0
ND2 C:ASN40 3.7 38.8 1.0
OD1 C:ASP240 3.7 32.5 1.0
C3' C:DNB502 3.8 59.1 1.0
C2' C:DNB502 3.8 60.2 1.0
OD2 C:ASP11 3.9 29.5 1.0
CA C:GLY125 4.2 24.3 1.0
N C:GLY125 4.3 24.8 1.0
OD2 C:ASP15 4.3 47.5 1.0
CB C:ASP16 4.4 36.0 1.0
C1' C:DNB502 4.4 61.9 1.0
O C:ASP11 4.4 33.6 1.0
OD1 C:ASN166 4.5 25.7 1.0
N C:ASP11 4.5 29.9 1.0
CG2 C:VAL124 4.5 28.9 1.0
ND2 C:ASN166 4.6 23.4 1.0
CB C:VAL124 4.6 27.9 1.0
N4' C:DNB502 4.6 59.2 1.0
CA C:VAL124 4.7 25.9 1.0
C4' C:DNB502 4.7 57.7 1.0
N C:ASP16 4.8 39.2 1.0
CG C:ASN40 4.8 39.2 1.0
CB C:ASP11 4.8 29.3 1.0
C C:ASP11 4.8 33.2 1.0
CB C:ASP240 4.8 32.7 1.0
CA C:ASP16 4.9 37.5 1.0
CA C:ASP11 4.9 30.8 1.0
CG C:ASN166 5.0 23.9 1.0

Calcium binding site 4 out of 4 in 3mkn

Go back to Calcium Binding Sites List in 3mkn
Calcium binding site 4 out of 4 in the Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the E. Coli Pyrimidine Nucleosidase Yeik Bound to A Competitive Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:16.3
occ:1.00
 O D:VAL124 2.3 13.1 1.0
OD2 D:ASP240 2.4 14.4 1.0
O2' D:DNB502 2.5 30.1 1.0
OD1 D:ASP11 2.5 17.3 1.0
OD1 D:ASP16 2.5 15.9 1.0
O D:HOH314 2.6 12.9 1.0
OD2 D:ASP16 2.6 14.5 1.0
O3' D:DNB502 2.6 24.0 1.0
CG D:ASP16 2.9 16.1 1.0
CG D:ASP240 3.4 15.7 1.0
C D:VAL124 3.5 13.7 1.0
C2' D:DNB502 3.5 33.3 1.0
CG D:ASP11 3.6 14.9 1.0
OD1 D:ASP240 3.6 17.2 1.0
C3' D:DNB502 3.7 30.3 1.0
ND2 D:ASN40 3.7 20.8 1.0
OD2 D:ASP11 4.0 15.5 1.0
C1' D:DNB502 4.1 38.8 1.0
CA D:GLY125 4.2 12.7 1.0
N D:GLY125 4.2 12.9 1.0
OD1 D:ASP15 4.3 30.6 1.0
CB D:ASP16 4.3 17.0 1.0
N4' D:DNB502 4.4 35.9 1.0
O D:ASP11 4.5 15.8 1.0
CB D:VAL124 4.5 14.3 1.0
OD1 D:ASN166 4.5 13.8 1.0
N D:ASP11 4.5 14.4 1.0
CG2 D:VAL124 4.5 14.2 1.0
ND2 D:ASN166 4.5 12.4 1.0
CA D:VAL124 4.5 13.7 1.0
C4' D:DNB502 4.6 31.4 1.0
N D:ASP16 4.7 19.1 1.0
CB D:ASP240 4.7 15.7 1.0
OD2 D:ASP15 4.7 30.7 1.0
CG D:ASN40 4.8 21.6 1.0
CG D:ASP15 4.8 26.1 1.0
CA D:ASP16 4.8 18.0 1.0
C D:ASP11 4.8 15.8 1.0
CB D:ASP11 4.9 14.4 1.0
CG D:ASN166 5.0 12.9 1.0

Reference:

A.Fornili, B.Giabbai, G.Garau, M.Degano. Energy Landscapes Associated with Macromolecular Conformational Changes From Endpoint Structures J.Am.Chem.Soc. V. 132 17570 2010.
ISSN: ISSN 0002-7863
PubMed: 21082835
DOI: 10.1021/JA107640U
Page generated: Sat Dec 12 04:21:01 2020

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