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Calcium in PDB 1pk0: Crystal Structure of the EF3-Cam Complexed with Pmeapp

Enzymatic activity of Crystal Structure of the EF3-Cam Complexed with Pmeapp

All present enzymatic activity of Crystal Structure of the EF3-Cam Complexed with Pmeapp:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of the EF3-Cam Complexed with Pmeapp, PDB code: 1pk0 was solved by Y.Shen, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 3.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.263, 165.759, 342.409, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.2

Other elements in 1pk0:

The structure of Crystal Structure of the EF3-Cam Complexed with Pmeapp also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the EF3-Cam Complexed with Pmeapp (pdb code 1pk0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the EF3-Cam Complexed with Pmeapp, PDB code: 1pk0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 1 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca800

b:30.3
occ:1.00
 OD1 D:ASP133 2.0 63.4 1.0
OE1 D:GLU140 2.2 54.5 1.0
O D:GLN135 2.2 51.7 1.0
OD1 D:ASP131 2.2 64.3 1.0
OE2 D:GLU140 2.7 49.2 1.0
CD D:GLU140 2.7 51.9 1.0
CG D:ASP133 2.7 62.0 1.0
OD2 D:ASP131 2.9 62.9 1.0
CG D:ASP131 2.9 62.7 1.0
OD2 D:ASP133 3.0 62.4 1.0
C D:GLN135 3.4 52.4 1.0
OD1 D:ASP129 3.6 60.6 1.0
OD2 D:ASP129 3.6 60.5 1.0
CG D:ASP129 3.7 60.0 1.0
CB D:ASP133 3.9 61.0 1.0
CG D:GLU140 4.1 52.6 1.0
CA D:VAL136 4.1 51.0 1.0
N D:ASN137 4.2 51.3 1.0
N D:VAL136 4.2 51.0 1.0
N D:GLN135 4.3 56.7 1.0
N D:ASP133 4.3 60.5 1.0
CB D:ASP131 4.3 60.9 1.0
N D:ASP131 4.3 58.1 1.0
CA D:GLN135 4.4 54.7 1.0
N D:ILE130 4.5 59.1 1.0
ND2 D:ASN137 4.6 51.0 1.0
CB D:ASP129 4.6 59.4 1.0
CA D:ASP129 4.6 60.5 1.0
C D:VAL136 4.6 51.3 1.0
CA D:ASP133 4.7 60.4 1.0
N D:GLY132 4.7 59.5 1.0
CA D:ASP131 4.8 59.0 1.0
N D:GLY134 4.9 58.5 1.0
CB D:GLU140 5.0 52.4 1.0

Calcium binding site 2 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 2 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:37.7
occ:1.00
 OD1 D:ASN97 1.8 54.0 1.0
OD1 D:ASP95 2.0 52.8 1.0
O D:TYR99 2.1 50.0 1.0
OE1 D:GLU104 2.4 56.7 1.0
OD1 D:ASP93 2.7 41.7 1.0
CG D:ASN97 2.8 53.8 1.0
OE2 D:GLU104 2.9 58.8 1.0
CG D:ASP95 2.9 52.7 1.0
CD D:GLU104 3.0 58.3 1.0
OD2 D:ASP95 3.2 55.1 1.0
C D:TYR99 3.3 50.8 1.0
ND2 D:ASN97 3.3 56.2 1.0
CG D:ASP93 3.4 41.7 1.0
CB D:ASN97 4.1 51.5 1.0
OD2 D:ASP93 4.1 42.0 1.0
N D:TYR99 4.1 50.5 1.0
N D:ILE100 4.2 52.4 1.0
CB D:ASP93 4.2 41.0 1.0
CA D:ASP93 4.2 41.6 1.0
CA D:TYR99 4.2 50.5 1.0
N D:ASN97 4.2 50.0 1.0
N D:SER101 4.2 56.4 1.0
CA D:ILE100 4.2 53.7 1.0
CB D:ASP95 4.3 50.9 1.0
CG D:GLU104 4.5 59.9 1.0
N D:ASP95 4.5 48.8 1.0
C D:ILE100 4.6 54.9 1.0
C D:ASP93 4.6 42.3 1.0
CA D:ASN97 4.7 50.7 1.0
CB D:TYR99 4.7 49.8 1.0
N D:GLY96 4.7 49.2 1.0
CB D:SER101 4.8 58.0 1.0
N D:GLY98 4.8 49.8 1.0
CA D:ASP95 4.8 49.1 1.0
N D:LYS94 4.9 44.4 1.0
OG D:SER101 4.9 58.3 1.0
C D:ASP95 5.0 48.8 1.0
C D:ASN97 5.0 50.6 1.0

Calcium binding site 3 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 3 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca802

b:83.6
occ:1.00
 OE1 E:GLU140 2.1 56.3 1.0
O E:GLN135 2.1 56.6 1.0
OD1 E:ASP133 2.2 66.6 1.0
OD1 E:ASP131 2.5 64.5 1.0
CD E:GLU140 2.6 57.5 1.0
OE2 E:GLU140 2.7 57.5 1.0
CG E:ASP133 2.8 67.6 1.0
OD2 E:ASP131 2.9 66.2 1.0
OD2 E:ASP133 3.0 69.2 1.0
CG E:ASP131 3.1 65.2 1.0
C E:GLN135 3.3 58.0 1.0
OD2 E:ASP129 3.8 62.0 1.0
OD1 E:ASP129 3.8 61.4 1.0
CG E:ASP129 3.9 63.1 1.0
CA E:VAL136 3.9 56.1 1.0
N E:ASN137 3.9 54.6 1.0
CG E:GLU140 4.0 56.8 1.0
N E:VAL136 4.0 57.2 1.0
CB E:ASP133 4.1 66.0 1.0
N E:GLN135 4.3 60.7 1.0
CA E:GLN135 4.3 59.8 1.0
C E:VAL136 4.4 55.6 1.0
ND2 E:ASN137 4.4 54.9 1.0
CB E:ASP131 4.5 64.4 1.0
N E:ASP133 4.6 64.5 1.0
N E:ASP131 4.6 61.8 1.0
N E:ILE130 4.6 60.8 1.0
CA E:ASP129 4.7 64.5 1.0
CB E:ASP129 4.8 63.3 1.0
CB E:ASN137 4.8 54.0 1.0
CB E:GLU140 4.8 56.1 1.0
CA E:ASP133 4.8 64.6 1.0
CG E:ASN137 4.9 53.4 1.0
CB E:GLN135 4.9 61.5 1.0
CG E:GLN135 4.9 64.2 1.0
CA E:ASN137 5.0 54.4 1.0

Calcium binding site 4 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 4 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca803

b:47.0
occ:1.00
 OD1 E:ASN97 2.0 53.2 1.0
O E:TYR99 2.1 53.6 1.0
OD1 E:ASP95 2.1 55.0 1.0
OE1 E:GLU104 2.2 58.6 1.0
OE2 E:GLU104 2.8 58.6 1.0
CD E:GLU104 2.9 60.0 1.0
OD1 E:ASP93 2.9 41.2 1.0
CG E:ASN97 2.9 55.2 1.0
CG E:ASP95 3.1 54.4 1.0
C E:TYR99 3.2 54.6 1.0
OD2 E:ASP95 3.4 54.3 1.0
ND2 E:ASN97 3.4 58.4 1.0
CG E:ASP93 3.5 41.7 1.0
N E:SER101 4.1 60.0 1.0
N E:ILE100 4.1 55.9 1.0
CA E:ILE100 4.1 57.8 1.0
OD2 E:ASP93 4.2 41.9 1.0
CB E:ASN97 4.2 54.3 1.0
N E:TYR99 4.2 53.5 1.0
CA E:ASP93 4.2 42.7 1.0
CA E:TYR99 4.2 54.5 1.0
CB E:ASP93 4.2 41.8 1.0
CG E:GLU104 4.3 61.6 1.0
N E:ASN97 4.4 53.4 1.0
CB E:ASP95 4.4 52.7 1.0
C E:ILE100 4.5 58.9 1.0
N E:ASP95 4.6 51.0 1.0
CB E:SER101 4.6 60.2 1.0
C E:ASP93 4.6 42.6 1.0
CB E:TYR99 4.7 55.0 1.0
OG E:SER101 4.8 59.5 1.0
CA E:ASN97 4.8 54.5 1.0
N E:GLY96 4.9 49.5 1.0
N E:LYS94 4.9 44.6 1.0
CA E:ASP95 5.0 51.1 1.0
N E:GLY98 5.0 54.1 1.0
CB E:GLU104 5.0 64.4 1.0

Calcium binding site 5 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 5 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca804

b:45.0
occ:1.00
 OD1 F:ASP133 2.1 66.3 1.0
OE1 F:GLU140 2.1 50.3 1.0
O F:GLN135 2.2 53.0 1.0
OD1 F:ASP131 2.3 61.4 1.0
OE2 F:GLU140 2.5 50.5 1.0
CD F:GLU140 2.6 50.8 1.0
CG F:ASP133 2.9 66.2 1.0
CG F:ASP131 2.9 62.6 1.0
OD2 F:ASP131 3.0 63.1 1.0
OD1 F:ASP129 3.3 60.4 1.0
OD2 F:ASP133 3.3 66.1 1.0
CG F:ASP129 3.4 60.9 1.0
C F:GLN135 3.4 54.5 1.0
OD2 F:ASP129 3.4 60.6 1.0
CG F:GLU140 4.0 51.1 1.0
CB F:ASP133 4.1 64.9 1.0
CA F:VAL136 4.1 53.1 1.0
N F:ASP131 4.1 59.6 1.0
N F:ILE130 4.2 58.8 1.0
N F:VAL136 4.2 53.2 1.0
N F:GLN135 4.2 57.1 1.0
CA F:ASP129 4.2 61.8 1.0
CB F:ASP129 4.3 60.5 1.0
N F:ASP133 4.3 63.1 1.0
N F:ASN137 4.3 52.2 1.0
CB F:ASP131 4.3 62.2 1.0
CA F:GLN135 4.4 56.5 1.0
N F:GLY132 4.5 60.3 1.0
CA F:ASP131 4.7 60.6 1.0
C F:ASP129 4.7 60.3 1.0
C F:VAL136 4.7 52.6 1.0
CA F:ASP133 4.7 63.5 1.0
ND2 F:ASN137 4.8 52.0 1.0
N F:GLY134 4.9 60.2 1.0
CB F:GLU140 4.9 51.2 1.0

Calcium binding site 6 out of 6 in 1pk0

Go back to Calcium Binding Sites List in 1pk0
Calcium binding site 6 out of 6 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the EF3-Cam Complexed with Pmeapp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca805

b:48.9
occ:1.00
 OD1 F:ASN97 1.8 53.9 1.0
O F:TYR99 2.0 50.6 1.0
OD1 F:ASP95 2.2 58.2 1.0
OE1 F:GLU104 2.4 59.0 1.0
CG F:ASN97 2.8 54.6 1.0
OD1 F:ASP93 2.8 41.9 1.0
OE2 F:GLU104 3.0 58.0 1.0
CD F:GLU104 3.1 59.6 1.0
C F:TYR99 3.1 51.2 1.0
CG F:ASP95 3.1 56.8 1.0
ND2 F:ASN97 3.2 57.4 1.0
OD2 F:ASP95 3.4 57.8 1.0
CG F:ASP93 3.5 43.9 1.0
N F:ILE100 4.0 53.4 1.0
N F:TYR99 4.0 50.7 1.0
CA F:ILE100 4.1 55.1 1.0
CA F:TYR99 4.1 50.4 1.0
OD2 F:ASP93 4.1 43.7 1.0
CB F:ASN97 4.1 52.8 1.0
N F:SER101 4.1 57.5 1.0
CB F:ASP93 4.2 43.8 1.0
CA F:ASP93 4.3 45.2 1.0
N F:ASN97 4.3 51.1 1.0
C F:ILE100 4.5 56.3 1.0
CB F:TYR99 4.5 50.6 1.0
CB F:ASP95 4.5 54.1 1.0
CG F:GLU104 4.5 61.4 1.0
CA F:ASN97 4.7 51.6 1.0
CB F:SER101 4.7 58.8 1.0
C F:ASP93 4.7 46.7 1.0
N F:ASP95 4.7 52.0 1.0
N F:GLY98 4.8 49.7 1.0
N F:GLY96 4.9 51.1 1.0
OG F:SER101 5.0 57.9 1.0
C F:ASN97 5.0 50.6 1.0
N F:LYS94 5.0 48.7 1.0

Reference:

Y.Shen, N.L.Zhukovskaya, M.I.Zimmer, S.Soelaiman, P.Bergson, C.R.Wang, C.S.Gibbs, W.J.Tang. Selective Inhibition of Anthrax Edema Factor By Adefovir, A Drug For Chronic Hepatitis B Virus Infection. Proc.Natl.Acad.Sci.Usa V. 101 3242 2004.
ISSN: ISSN 0027-8424
PubMed: 14978283
DOI: 10.1073/PNAS.0306552101
Page generated: Sat Dec 12 03:14:11 2020

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