Nickel in PDB 4z8g: Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)

The structure of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2), PDB code: 4z8g was solved by M.Boczkowska, G.Rebowski, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.91 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.468, 53.936, 75.604, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.4

The binding sites of Nickel atom in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) (pdb code 4z8g). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2), PDB code: 4z8g:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:17.2 occ:1.00 ND1 A:HIS423 2.0 15.7 1.0 ND1 A:HIS453 2.0 19.0 1.0 NI A:NI507 2.3 36.1 1.0 CE1 A:HIS453 2.8 26.3 1.0 HE1 A:HIS453 2.8 31.6 1.0 CE1 A:HIS423 2.9 21.2 1.0 HE1 A:HIS423 3.0 25.4 1.0 CG A:HIS423 3.0 17.2 1.0 HB3 A:HIS423 3.1 23.4 1.0 CG A:HIS453 3.2 20.2 1.0 HB2 A:HIS453 3.3 19.7 1.0 H A:HIS453 3.4 20.6 1.0 HA A:HIS423 3.4 22.2 1.0 CB A:HIS423 3.5 19.5 1.0 N A:HIS453 3.7 17.2 1.0 HA A:TYR452 3.7 16.7 1.0 CB A:HIS453 3.7 16.4 1.0 CA A:HIS423 4.0 18.5 1.0 NE2 A:HIS453 4.0 27.9 1.0 NE2 A:HIS423 4.0 24.7 1.0 CD2 A:HIS423 4.1 15.3 1.0 C A:TYR452 4.2 20.7 1.0 H A:ASN424 4.2 26.9 1.0 CD2 A:HIS453 4.2 27.7 1.0 CA A:HIS453 4.3 18.0 1.0 HB2 A:HIS423 4.4 23.4 1.0 CA A:TYR452 4.4 13.9 1.0 HB3 A:HIS453 4.6 19.7 1.0 N A:ASN424 4.6 22.4 1.0 HE2 A:HIS453 4.7 33.5 1.0 HE2 A:HIS423 4.8 29.6 1.0 C A:HIS423 4.8 23.4 1.0 HA A:HIS453 4.9 21.6 1.0 N A:TYR452 4.9 13.4 1.0 HD2 A:HIS423 5.0 18.4 1.0

Nickel binding site 2 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:27.4 occ:1.00 NE2 A:HIS427 1.9 31.0 1.0 ND1 A:HIS398 2.0 20.6 1.0 HB3 A:HIS398 2.7 26.0 1.0 CE1 A:HIS427 2.8 35.1 1.0 HE1 A:HIS427 2.9 42.1 1.0 CG A:HIS398 3.0 16.8 1.0 CE1 A:HIS398 3.0 22.4 1.0 CD2 A:HIS427 3.1 31.0 1.0 HE1 A:HIS398 3.2 26.9 1.0 CB A:HIS398 3.3 21.6 1.0 HD2 A:HIS427 3.3 37.2 1.0 ND1 A:HIS427 3.9 30.7 1.0 HB2 A:HIS398 4.0 26.0 1.0 O A:HOH603 4.1 50.7 1.0 HH22 A:ARG370 4.1 85.6 1.0 HB2 A:ARG426 4.1 39.7 1.0 CG A:HIS427 4.1 30.7 1.0 NE2 A:HIS398 4.1 21.3 1.0 CD2 A:HIS398 4.1 21.6 1.0 HA A:HIS398 4.2 26.7 1.0 CA A:HIS398 4.4 22.3 1.0 O A:HIS398 4.7 23.2 1.0 HD1 A:HIS427 4.7 36.8 1.0 NH2 A:ARG370 4.7 71.3 1.0 HH12 A:ARG370 4.8 0.5 1.0 HE2 A:HIS398 4.9 25.5 1.0 HG3 A:ARG426 4.9 80.2 1.0 HD2 A:HIS398 5.0 25.9 1.0 CB A:ARG426 5.0 33.1 1.0

Nickel binding site 3 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:58.9 occ:1.00 ND1 A:HIS374 1.8 34.4 1.0 O A:HOH697 2.5 69.0 1.0 OD2 A:ASP372 2.6 51.0 1.0 CE1 A:HIS374 2.6 50.1 1.0 HE1 A:HIS374 2.6 60.1 1.0 CG A:HIS374 3.0 33.6 1.0 HB2 A:HIS374 3.1 27.4 1.0 CG A:ASP372 3.2 40.9 1.0 OD1 A:ASP372 3.4 23.0 1.0 HG21 A:ILE210 3.5 43.4 1.0 CB A:HIS374 3.6 22.8 1.0 NE2 A:HIS374 3.7 62.0 1.0 H A:HIS374 3.8 30.1 1.0 CD2 A:HIS374 4.0 34.2 1.0 HB3 A:HIS374 4.2 27.4 1.0 HG13 A:ILE210 4.2 48.8 1.0 HE2 A:HIS374 4.5 74.4 1.0 CG2 A:ILE210 4.5 36.2 1.0 CB A:ASP372 4.5 32.7 1.0 N A:HIS374 4.5 25.1 1.0 HB2 A:ASP372 4.5 39.2 1.0 NI A:NI504 4.6 65.8 1.0 CA A:HIS374 4.7 23.0 1.0 HD12 A:ILE210 4.7 44.6 1.0 HG23 A:ILE210 4.8 43.4 1.0 HD2 A:HIS374 4.9 41.1 1.0 HB3 A:ASP372 4.9 39.2 1.0

Nickel binding site 4 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:65.8 occ:1.00 HE2 A:HIS374 2.1 74.4 1.0 HE1 A:HIS374 2.1 60.1 1.0 NE2 A:HIS374 2.5 62.0 1.0 CE1 A:HIS374 2.5 50.1 1.0 ND1 A:HIS374 3.7 34.4 1.0 CD2 A:HIS374 3.8 34.2 1.0 HD2 A:HIS374 4.3 41.1 1.0 CG A:HIS374 4.4 33.6 1.0 NI A:NI503 4.6 58.9 1.0

Nickel binding site 5 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni505 b:72.1 occ:1.00 HE2 A:HIS398 2.7 25.5 1.0 HE A:ARG426 2.8 99.8 1.0 HH11 A:ARG426 3.2 73.2 1.0 O A:HOH683 3.4 48.1 1.0 HH12 A:ARG206 3.5 87.8 1.0 NE2 A:HIS398 3.5 21.3 1.0 NE A:ARG426 3.6 83.2 1.0 HE A:ARG370 3.7 61.0 1.0 NH1 A:ARG426 3.9 61.0 1.0 HH11 A:ARG206 3.9 87.8 1.0 HG2 A:ARG370 3.9 68.6 1.0 NH1 A:ARG206 4.0 73.2 1.0 HH11 A:ARG370 4.0 0.5 1.0 HG3 A:ARG426 4.1 80.2 1.0 O A:HOH642 4.1 21.6 1.0 CZ A:ARG426 4.1 88.0 1.0 NE A:ARG370 4.2 50.8 1.0 HG3 A:ARG370 4.3 68.6 1.0 NI A:NI508 4.3 0.3 1.0 NH1 A:ARG370 4.4 99.5 1.0 CE1 A:HIS398 4.4 22.4 1.0 HE1 A:HIS398 4.4 26.9 1.0 CD2 A:HIS398 4.5 21.6 1.0 CG A:ARG370 4.5 57.1 1.0 CD A:ARG426 4.5 73.9 1.0 HD2 A:HIS398 4.5 25.9 1.0 HH12 A:ARG426 4.6 73.2 1.0 HD2 A:ARG426 4.6 88.7 1.0 CZ A:ARG370 4.6 61.2 1.0 O A:HOH609 4.7 42.3 1.0 CG A:ARG426 4.8 66.8 1.0 CD A:ARG370 5.0 42.2 1.0 HH12 A:ARG370 5.0 0.5 1.0

Nickel binding site 6 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni506 b:64.3 occ:1.00 O A:HOH692 2.1 46.7 1.0 HD2 A:HIS453 2.9 33.3 1.0 HH21 A:ARG460 3.0 70.1 1.0 HE A:ARG460 3.4 35.9 1.0 CD2 A:HIS453 3.8 27.7 1.0 NH2 A:ARG460 3.8 58.4 1.0 O A:HOH667 4.0 22.1 1.0 NE A:ARG460 4.2 29.9 1.0 HE2 A:HIS453 4.3 33.5 1.0 HH22 A:ARG460 4.4 70.1 1.0 O A:HOH699 4.5 48.3 1.0 NE2 A:HIS453 4.5 27.9 1.0 CZ A:ARG460 4.5 62.3 1.0 CG A:HIS453 5.0 20.2 1.0

Nickel binding site 7 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni507 b:36.1 occ:1.00 NI A:NI501 2.3 17.2 1.0 H A:HIS453 2.4 20.6 1.0 HA A:HIS423 2.6 22.2 1.0 H A:ASN424 2.9 26.9 1.0 HB2 A:HIS453 3.1 19.7 1.0 N A:HIS453 3.1 17.2 1.0 HA A:TYR452 3.2 16.7 1.0 HD1 A:TYR452 3.3 26.1 1.0 ND1 A:HIS423 3.4 15.7 1.0 CA A:HIS423 3.5 18.5 1.0 ND1 A:HIS453 3.6 19.0 1.0 N A:ASN424 3.6 22.4 1.0 HB3 A:HIS423 3.7 23.4 1.0 CD1 A:TYR452 3.7 21.7 1.0 CB A:HIS453 3.8 16.4 1.0 C A:TYR452 3.9 20.7 1.0 CA A:TYR452 3.9 13.9 1.0 CB A:HIS423 3.9 19.5 1.0 O A:HOH645 4.0 26.2 1.0 CA A:HIS453 4.0 18.0 1.0 CG A:HIS423 4.1 17.2 1.0 HE1 A:TYR452 4.1 21.6 1.0 C A:HIS423 4.1 23.4 1.0 CG A:HIS453 4.2 20.2 1.0 CE1 A:TYR452 4.2 18.0 1.0 O A:HIS453 4.2 21.2 1.0 CE1 A:HIS423 4.4 21.2 1.0 CG A:TYR452 4.5 18.5 1.0 N A:HIS423 4.5 17.2 1.0 HA A:ASN424 4.6 29.7 1.0 C A:HIS453 4.6 20.5 1.0 HE1 A:HIS423 4.6 25.4 1.0 HB3 A:HIS453 4.7 19.7 1.0 CA A:ASN424 4.7 24.8 1.0 CB A:TYR452 4.7 14.4 1.0 CE1 A:HIS453 4.7 26.3 1.0 HA A:HIS453 4.8 21.6 1.0 O A:PHE422 4.9 18.4 1.0 HB2 A:HIS423 4.9 23.4 1.0 H A:HIS423 4.9 20.6 1.0 HB2 A:ASN424 5.0 46.0 1.0

Nickel binding site 8 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni508 b:0.3 occ:1.00 HH11 A:ARG370 2.6 0.5 1.0 HH12 A:ARG370 2.8 0.5 1.0 NH1 A:ARG370 3.0 99.5 1.0 HE1 A:HIS398 3.2 26.9 1.0 CE1 A:HIS398 4.0 22.4 1.0 HE2 A:HIS398 4.2 25.5 1.0 CZ A:ARG370 4.3 61.2 1.0 NI A:NI505 4.3 72.1 1.0 NE2 A:HIS398 4.5 21.3 1.0 HE A:ARG370 4.7 61.0 1.0 NE A:ARG370 4.9 50.8 1.0 HG3 A:ARG426 5.0 80.2 1.0

Nickel binding site 9 out of 9 in the Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Chimera of Tropomodulin-1 and Leiomodin-1 Actin-Binding Site 2 (TL1 ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni509 b:83.5 occ:1.00 HD22 A:ASN203 2.7 24.1 1.0 HD21 A:ASN201 2.8 49.2 1.0 ND2 A:ASN203 3.5 20.1 1.0 HB2 A:ASN203 3.5 17.1 1.0 ND2 A:ASN201 3.7 41.0 1.0 HD21 A:ASN203 4.0 24.1 1.0 HD22 A:ASN201 4.1 49.2 1.0 HB3 A:ASN203 4.1 17.1 1.0 CB A:ASN203 4.2 14.3 1.0 O A:HOH698 4.2 45.4 1.0 CG A:ASN203 4.4 24.4 1.0 HD22 A:ASN204 4.5 31.9 1.0 CG A:ASN201 4.6 27.1 1.0 OD1 A:ASN201 4.6 29.4 1.0 HD21 A:ASN204 4.7 31.9 1.0 O A:HOH656 4.8 46.5 1.0 ND2 A:ASN204 4.9 26.6 1.0

M.Boczkowska, G.Rebowski, E.Kremneva, P.Lappalainen, R.Dominguez. How Leiomodin and Tropomodulin Use A Common Fold For Different Actin Assembly Functions. Nat Commun V. 6 8314 2015.
ISSN: ESSN 2041-1723
PubMed: 26370058
DOI: 10.1038/NCOMMS9314