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Calcium in PDB 2w3o: Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide

Enzymatic activity of Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide

All present enzymatic activity of Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide:
2.7.1.78; 3.1.3.32;

Protein crystallography data

The structure of Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide, PDB code: 2w3o was solved by A.W.Oliver, A.A.E.Ali, L.H.Pearl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.75 / 1.85
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 56.900, 56.900, 62.770, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide (pdb code 2w3o). 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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide, PDB code: 2w3o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2w3o

Go back to Calcium Binding Sites List in 2w3o
Calcium binding site 1 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1108

b:56.8
occ:1.00
 O A:HOH2052 2.5 30.0 1.0
NH1 A:ARG60 3.1 34.5 1.0
O A:HOH2077 3.3 37.5 1.0
CD A:ARG60 3.5 26.9 1.0
CG2 A:VAL89 3.8 21.7 1.0
CB A:VAL89 4.0 20.5 1.0
CZ A:ARG60 4.1 32.4 1.0
CB A:TRP106 4.1 28.4 1.0
CG1 A:VAL89 4.1 20.7 1.0
NE A:ARG60 4.3 32.1 1.0
CG A:TRP106 4.3 29.6 1.0
CD1 A:TRP106 4.5 32.4 1.0
CG A:ARG60 4.7 24.6 1.0
CB A:ARG60 4.7 20.5 1.0
O A:HOH2090 5.0 19.7 1.0

Calcium binding site 2 out of 6 in 2w3o

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Calcium binding site 2 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1109

b:55.0
occ:1.00
 O A:HOH2089 2.3 35.9 1.0
O A:HOH2088 2.5 29.0 1.0
O A:HOH2091 2.6 39.6 1.0
O A:GLU58 2.8 27.8 1.0
C A:GLU58 3.9 27.3 1.0
NE A:ARG60 4.3 32.1 1.0
CA A:GLU58 4.4 28.0 1.0
O A:PRO57 4.7 27.5 1.0
NH2 A:ARG60 4.8 34.8 1.0
CZ A:ARG60 4.9 32.4 1.0
N A:THR59 4.9 25.8 1.0

Calcium binding site 3 out of 6 in 2w3o

Go back to Calcium Binding Sites List in 2w3o
Calcium binding site 3 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1109

b:52.2
occ:1.00
 O B:HOH2070 2.4 27.3 1.0
O B:HOH2072 2.8 35.7 1.0
OD1 B:ASP56 2.8 30.3 1.0
O B:HOH2038 3.0 46.2 1.0
CG B:ASP56 3.5 29.7 1.0
OD2 B:ASP56 3.9 26.6 1.0
CB B:GLU58 4.4 27.7 1.0
CB B:ASP56 4.5 25.1 1.0
CA B:ASP56 4.8 25.4 1.0
CD B:PRO57 5.0 26.6 1.0

Calcium binding site 4 out of 6 in 2w3o

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Calcium binding site 4 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1110

b:54.1
occ:1.00
 O B:HOH2073 2.3 37.9 1.0
O B:HOH2071 2.5 29.2 1.0
O B:HOH2017 2.6 43.2 1.0
O B:GLU58 2.7 26.9 1.0
C B:GLU58 3.7 27.0 1.0
O B:HOH2037 4.0 34.5 1.0
CA B:GLU58 4.2 27.5 1.0
NE B:ARG60 4.3 35.0 1.0
O B:PRO57 4.6 27.1 1.0
NH1 B:ARG60 4.8 37.5 1.0
N B:THR59 4.9 25.2 1.0

Calcium binding site 5 out of 6 in 2w3o

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Calcium binding site 5 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1008

b:53.8
occ:1.00
 O1P C:SEP518 2.3 25.0 0.4
O C:HOH2009 2.4 41.6 1.0
O2P D:TPO519 2.4 30.5 1.0
OG D:SEP518 3.0 27.9 0.4
O1P C:SEP518 3.2 34.5 0.6
P C:SEP518 3.5 27.2 0.4
O C:HOH2012 3.6 56.4 1.0
O2P C:SEP518 3.6 26.7 0.4
P D:TPO519 3.6 25.6 1.0
CB D:SEP518 3.7 29.3 0.4
O1P D:TPO519 3.9 23.7 1.0
N D:TPO519 4.0 28.2 1.0
O C:HOH2008 4.0 33.7 1.0
O3P D:SEP518 4.1 28.5 0.4
CB D:SEP518 4.1 29.4 0.6
NH1 B:ARG48 4.2 29.4 1.0
P D:SEP518 4.2 30.6 0.4
O C:HOH2011 4.3 46.0 1.0
OG C:SEP518 4.3 24.9 0.4
O3P C:SEP518 4.3 33.0 0.6
CA D:SEP518 4.4 29.2 0.6
CA D:SEP518 4.4 28.8 0.4
P C:SEP518 4.4 36.7 0.6
OG1 D:TPO519 4.5 27.4 1.0
CB D:TPO519 4.5 27.8 1.0
C D:SEP518 4.7 28.6 1.0
O C:HOH2017 4.7 19.5 0.3
O D:TPO519 4.7 30.0 1.0
O3P C:SEP518 4.7 25.6 0.4
O3P D:TPO519 4.7 23.9 1.0
CA D:TPO519 4.8 28.5 1.0
CB C:SEP518 4.8 28.7 0.6
O1P D:SEP518 4.9 29.0 0.4

Calcium binding site 6 out of 6 in 2w3o

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Calcium binding site 6 out of 6 in the Crystal Structure of the Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide


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 Human Pnkp Fha Domain in Complex with An XRCC1-Derived Phosphopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1008

b:56.4
occ:1.00
 O3P D:SEP518 2.1 28.5 0.4
O2P C:TPO519 2.3 30.4 1.0
O D:HOH2008 2.8 45.6 1.0
O3P C:SEP518 3.1 25.6 0.4
O1P D:SEP518 3.2 34.1 0.6
P D:SEP518 3.4 30.6 0.4
P C:TPO519 3.6 26.2 1.0
O1P C:SEP518 3.8 25.0 0.4
O D:HOH2009 3.8 46.8 1.0
O1P D:SEP518 3.8 29.0 0.4
N C:TPO519 4.0 27.1 1.0
O1P C:TPO519 4.0 23.5 1.0
O D:HOH2007 4.0 33.5 1.0
NH1 A:ARG48 4.1 27.7 1.0
O3P D:SEP518 4.1 34.1 0.6
P C:SEP518 4.1 27.2 0.4
CB C:SEP518 4.2 28.7 0.6
O2P D:SEP518 4.2 29.3 0.4
O C:HOH2011 4.2 46.0 1.0
P D:SEP518 4.3 37.2 0.6
O C:HOH2017 4.3 19.5 0.3
CA C:SEP518 4.4 28.1 0.6
CA C:SEP518 4.4 27.3 0.4
CB C:SEP518 4.5 27.3 0.4
OG D:SEP518 4.5 27.9 0.4
OG1 C:TPO519 4.5 27.3 1.0
CB C:TPO519 4.5 26.9 1.0
C C:SEP518 4.7 27.1 1.0
O C:TPO519 4.7 27.9 1.0
O3P C:TPO519 4.7 23.7 1.0
CA C:TPO519 4.8 26.9 1.0
CB D:SEP518 4.8 29.4 0.6
CB D:SEP518 4.9 29.3 0.4

Reference:

A.A.E.Ali, R.M.Jukes, L.H.Pearl, A.W.Oliver. Specific Recognition of A Multiply Phosphorylated Motif in the Dna Repair Scaffold XRCC1 By the Fha Domain of Human Pnk. Nucleic Acids Res. V. 37 1701 2009.
ISSN: ISSN 0305-1048
PubMed: 19155274
DOI: 10.1093/NAR/GKN1086
Page generated: Fri Jul 12 18:29:19 2024

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