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Calcium in PDB 2au0: Unmodified Preinsertion Binary Complex

Enzymatic activity of Unmodified Preinsertion Binary Complex

All present enzymatic activity of Unmodified Preinsertion Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of Unmodified Preinsertion Binary Complex, PDB code: 2au0 was solved by O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.644, 180.962, 51.571, 90.00, 107.00, 90.00
R / Rfree (%) 26.9 / 31

Calcium Binding Sites:

The binding sites of Calcium atom in the Unmodified Preinsertion Binary Complex (pdb code 2au0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Unmodified Preinsertion Binary Complex, PDB code: 2au0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2au0

Go back to Calcium Binding Sites List in 2au0
Calcium binding site 1 out of 3 in the Unmodified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Unmodified Preinsertion Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1415

b:44.1
occ:1.00
OP1 H:DDG1813 2.3 43.8 1.0
OE2 B:GLU1106 2.5 51.6 1.0
O B:HOH1502 2.5 34.2 1.0
O B:HOH1503 2.8 38.2 1.0
O H:HOH1504 3.2 69.4 1.0
P H:DDG1813 3.3 44.1 1.0
OP2 H:DDG1813 3.5 43.4 1.0
CD B:GLU1106 3.7 52.5 1.0
CG B:GLU1106 4.3 52.2 1.0
O3' H:DA1812 4.3 44.6 1.0
NZ B:LYS1152 4.3 56.7 1.0
CE B:LYS1152 4.4 55.9 1.0
OD2 B:ASP1007 4.4 47.6 1.0
O5' H:DDG1813 4.6 42.8 1.0
OD1 B:ASP1105 4.7 52.3 1.0
OE1 B:GLU1106 4.7 53.3 1.0
C3' H:DA1812 4.9 46.2 1.0
CG B:ASP1007 5.0 47.1 1.0

Calcium binding site 2 out of 3 in 2au0

Go back to Calcium Binding Sites List in 2au0
Calcium binding site 2 out of 3 in the Unmodified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Unmodified Preinsertion Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca1416

b:74.9
occ:1.00
O J:HOH1508 2.1 43.3 1.0
O H:HOH1507 2.4 37.5 1.0
O H:HOH1506 2.6 34.1 1.0
O J:HOH1505 2.8 47.2 1.0
O H:HOH1510 3.2 41.1 1.0
O H:HOH1509 3.3 37.4 1.0
O4' J:DA1917 4.1 62.4 1.0
O2 H:DT1804 4.4 69.0 1.0
C1' J:DA1917 4.6 63.7 1.0
C4' J:DA1917 4.9 62.9 1.0
O3' J:DA1917 5.0 63.1 1.0

Calcium binding site 3 out of 3 in 2au0

Go back to Calcium Binding Sites List in 2au0
Calcium binding site 3 out of 3 in the Unmodified Preinsertion Binary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Unmodified Preinsertion Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:43.1
occ:1.00
O A:HOH502 2.5 42.0 1.0
OE2 A:GLU106 2.6 48.2 1.0
OD1 A:ASP105 2.7 49.6 1.0
O D:HOH501 2.8 35.7 1.0
OP1 D:DDG813 2.9 63.1 1.0
OD2 A:ASP7 3.1 41.8 1.0
OP2 D:DDG813 3.1 61.6 1.0
CD A:GLU106 3.3 50.4 1.0
P D:DDG813 3.4 63.0 1.0
CG A:GLU106 3.5 50.5 1.0
CG A:ASP105 3.5 50.3 1.0
O A:ASP105 3.7 51.1 1.0
OD2 A:ASP105 3.8 47.8 1.0
OG A:SER103 4.0 51.6 1.0
CG A:ASP7 4.3 42.6 1.0
OE1 A:GLU106 4.3 49.9 1.0
CB A:GLU106 4.4 50.9 1.0
O5' D:DDG813 4.4 59.5 1.0
C A:ASP105 4.5 51.1 1.0
O A:HOH503 4.5 32.7 1.0
CB A:ASP105 4.7 51.0 1.0
O3' D:DA812 4.8 63.8 1.0
C5' D:DDG813 5.0 56.5 1.0
NZ A:LYS152 5.0 53.4 1.0

Reference:

O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, D.J.Patel. Stepwise Translocation of DPO4 Polymerase During Error-Free Bypass of An Oxog Lesion Plos Biol. V. 4 1 2006.
ISSN: ISSN 1544-9173
PubMed: 16379496
DOI: 10.1371/JOURNAL.PBIO.0040011
Page generated: Sat Dec 12 03:31:41 2020

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