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Nickel in PDB 6xvw: Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050

Enzymatic activity of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050

All present enzymatic activity of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050:
2.4.2.30;

Protein crystallography data

The structure of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050, PDB code: 6xvw was solved by J.Pfahler, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.73 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.172, 86.727, 127.635, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 (pdb code 6xvw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050, PDB code: 6xvw:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 6xvw

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Nickel binding site 1 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1101

b:49.3
occ:1.00
 O B:HOH1251 2.0 54.7 1.0
NE2 B:HIS937 2.0 36.4 1.0
NE2 A:HIS934 2.1 43.7 1.0
O B:HOH1306 2.2 37.0 1.0
O B:HOH1269 2.2 44.2 1.0
O B:HOH1254 2.4 45.3 1.0
CE1 B:HIS937 3.0 37.1 1.0
CE1 A:HIS934 3.0 43.2 1.0
CD2 B:HIS937 3.1 36.3 1.0
CD2 A:HIS934 3.1 40.6 1.0
O B:HOH1334 3.6 75.4 1.0
O A:HOH1361 3.7 62.1 1.0
OG A:SER936 4.0 54.5 1.0
ND1 B:HIS937 4.1 37.7 1.0
ND1 A:HIS934 4.1 40.5 1.0
O B:THR887 4.2 45.2 1.0
CG B:HIS937 4.2 38.8 1.0
CG A:HIS934 4.2 39.3 1.0
OD1 B:ASP756 4.4 93.4 1.0
O A:ALA935 4.6 45.9 1.0
CB B:THR887 4.7 46.9 1.0
O A:HOH1380 4.8 54.5 1.0
CG B:ASP756 5.0 90.5 1.0

Nickel binding site 2 out of 6 in 6xvw

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Nickel binding site 2 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1102

b:50.5
occ:1.00
 NE2 A:HIS937 2.0 40.1 1.0
NE2 B:HIS934 2.0 35.5 1.0
O A:HOH1261 2.1 60.6 1.0
O B:HOH1237 2.1 63.3 1.0
O A:HOH1341 2.4 51.0 1.0
O A:HOH1264 2.4 51.4 1.0
CE1 A:HIS937 2.9 38.8 1.0
CE1 B:HIS934 3.0 36.2 1.0
CD2 B:HIS934 3.0 33.9 1.0
CD2 A:HIS937 3.1 40.1 1.0
O B:HOH1328 3.4 54.9 1.0
O A:HOH1255 3.8 49.3 1.0
OG B:SER936 3.9 53.2 1.0
ND1 A:HIS937 4.0 39.5 1.0
ND1 B:HIS934 4.1 35.4 1.0
CG B:HIS934 4.2 34.6 1.0
O A:THR887 4.2 41.4 1.0
CG A:HIS937 4.2 40.9 1.0
OD1 A:ASP756 4.4 73.8 1.0
O B:ALA935 4.5 43.3 1.0
O A:HOH1379 4.5 44.2 1.0
CB A:THR887 4.8 38.9 1.0

Nickel binding site 3 out of 6 in 6xvw

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Nickel binding site 3 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1103

b:78.5
occ:1.00
 O B:HOH1202 1.9 67.5 1.0
NE2 A:HIS909 1.9 47.0 1.0
O A:HOH1339 2.5 55.0 1.0
O A:HOH1322 2.6 47.6 1.0
CE1 A:HIS909 2.7 49.5 1.0
O B:HOH1326 2.8 60.0 1.0
O A:HOH1350 2.8 52.7 1.0
CD2 A:HIS909 3.1 47.4 1.0
OD1 B:ASP981 3.6 0.8 1.0
O A:HOH1310 3.7 51.2 1.0
ND1 A:HIS909 3.9 46.4 1.0
CG A:HIS909 4.1 44.9 1.0
OD2 B:ASP981 4.3 0.8 1.0
CG B:ASP981 4.4 0.8 1.0
OE1 A:GLU763 4.5 96.7 1.0
O A:HOH1204 4.7 65.5 1.0
O B:HOH1342 4.8 54.4 1.0
O A:HOH1234 4.8 43.2 1.0
OE2 A:GLU763 4.8 0.4 1.0
O A:HOH1312 5.0 55.0 1.0

Nickel binding site 4 out of 6 in 6xvw

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Nickel binding site 4 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1104

b:49.6
occ:1.00
 NE2 A:HIS826 2.1 41.2 1.0
O A:HOH1222 2.1 44.5 1.0
NE2 A:HIS822 2.1 37.5 1.0
OD1 A:ASP830 2.2 46.0 1.0
O A:HOH1356 2.2 45.6 1.0
O A:HOH1317 2.3 41.0 1.0
CE1 A:HIS822 2.9 37.6 1.0
CE1 A:HIS826 2.9 42.0 1.0
CG A:ASP830 3.1 45.3 1.0
CD2 A:HIS826 3.2 40.7 1.0
CD2 A:HIS822 3.3 36.8 1.0
OD2 A:ASP830 3.3 46.8 1.0
O A:HOH1390 3.4 56.1 1.0
O A:HOH1285 3.9 43.8 1.0
ND1 A:HIS822 4.1 38.1 1.0
ND1 A:HIS826 4.1 42.2 1.0
CG A:HIS826 4.2 41.9 1.0
CG A:HIS822 4.3 37.4 1.0
CB A:ASP830 4.4 43.5 1.0
N A:LEU831 4.5 44.1 1.0
O A:LEU831 4.7 46.9 1.0
CA A:ASP830 4.7 42.1 1.0
CE A:LYS819 4.9 68.6 1.0
NZ A:LYS819 4.9 71.0 1.0

Nickel binding site 5 out of 6 in 6xvw

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Nickel binding site 5 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1101

b:79.8
occ:1.00
 NE2 B:HIS909 2.0 41.1 1.0
O A:HOH1207 2.0 87.1 1.0
O B:HOH1320 2.4 65.1 1.0
O B:HOH1289 2.4 47.8 1.0
O B:HOH1299 2.7 78.3 1.0
CE1 B:HIS909 2.8 39.5 1.0
O B:HOH1268 2.9 62.2 1.0
O A:HOH1298 3.1 54.0 1.0
CD2 B:HIS909 3.2 40.3 1.0
O B:HOH1347 3.7 56.5 1.0
O A:HOH1358 3.7 89.9 1.0
O B:HOH1227 3.9 56.5 1.0
ND1 B:HIS909 3.9 37.8 1.0
OD1 A:ASP981 4.0 0.1 1.0
OE2 B:GLU763 4.0 71.9 1.0
CG B:HIS909 4.2 39.1 1.0
ND2 A:ASN980 4.4 95.4 1.0
O B:HOH1345 4.6 73.6 1.0
CD B:GLU763 5.0 69.1 1.0

Nickel binding site 6 out of 6 in 6xvw

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Nickel binding site 6 out of 6 in the Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Catalytic Domain of Human Parp-1 in Complex with the Inhibitor MC2050 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1102

b:75.9
occ:1.00
 NE2 B:HIS822 2.1 50.7 1.0
O B:HOH1222 2.1 50.4 1.0
O B:HOH1305 2.2 68.2 1.0
NE2 B:HIS826 2.3 55.1 1.0
O B:HOH1217 2.3 49.0 1.0
OD1 B:ASP830 2.4 64.9 1.0
CE1 B:HIS822 2.7 51.4 1.0
CE1 B:HIS826 3.1 54.2 1.0
CG B:ASP830 3.3 61.3 1.0
CD2 B:HIS822 3.3 51.3 1.0
CD2 B:HIS826 3.4 53.7 1.0
O B:HOH1343 3.5 66.8 1.0
OD2 B:ASP830 3.5 62.8 1.0
NZ B:LYS819 3.8 68.3 1.0
ND1 B:HIS822 3.9 50.5 1.0
O B:HOH1308 4.0 57.1 1.0
CD B:LYS819 4.2 64.4 1.0
CG B:HIS822 4.3 50.2 1.0
ND1 B:HIS826 4.3 51.9 1.0
CG B:HIS826 4.5 52.2 1.0
O B:HOH1341 4.6 58.7 1.0
CB B:ASP830 4.7 59.7 1.0
CE B:LYS819 4.7 66.3 1.0
N B:LEU831 4.7 51.4 1.0
O B:LEU831 4.8 50.5 1.0
CA B:ASP830 4.9 55.6 1.0

Reference:

S.Tomassi, J.Pfahler, N.Mautone, A.Rovere, C.Esposito, D.Passeri, R.Pellicciari, E.Novellino, M.Pannek, C.Steegborn, A.Paiardini, A.Mai, D.Rotili. From PARP1 to TNKS2 Inhibition: A Structure-Based Approach. Acs Med.Chem.Lett. V. 11 862 2020.
ISSN: ISSN 1948-5875
PubMed: 32435397
DOI: 10.1021/ACSMEDCHEMLETT.9B00654
Page generated: Thu Oct 10 08:59:21 2024

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