Zinc in PDB 7kil: Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc

The structure of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc, PDB code: 7kil was solved by W.Gu, M.V.Airola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.24 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.284, 58.554, 42.897, 90, 100.06, 90
R / Rfree (%)	22.2 / 25.6

The structure of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Zinc atom in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc (pdb code 7kil). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc, PDB code: 7kil:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:37.5 occ:1.00 OD2 A:ASP503 1.8 23.2 1.0 CL A:CL606 2.0 27.4 1.0 CL A:CL608 2.0 32.5 1.0 CL A:CL607 2.3 26.4 1.0 CG A:ASP503 2.7 23.9 1.0 OD1 A:ASP503 3.0 23.4 1.0 HD22 A:ASN505 3.1 31.5 1.0 HD13 A:LEU469 3.7 28.4 1.0 HB2 A:ASN505 3.9 31.6 1.0 HD22 A:LEU469 3.9 26.3 1.0 ND2 A:ASN505 3.9 26.2 1.0 HD2 A:PRO504 4.0 29.6 1.0 CB A:ASP503 4.2 19.6 1.0 HB2 A:ASP503 4.3 23.5 1.0 HD21 A:ASN505 4.3 31.5 1.0 HB3 A:LEU469 4.3 23.2 1.0 O A:HOH763 4.4 34.0 1.0 H A:ASN505 4.5 26.7 1.0 HB3 A:ASP503 4.6 23.5 1.0 CD1 A:LEU469 4.7 23.6 1.0 CD2 A:LEU469 4.7 21.9 1.0 CB A:ASN505 4.7 26.3 1.0 CG A:ASN505 4.8 28.1 1.0 CD A:PRO504 4.9 24.6 1.0 HA A:ASP503 4.9 22.7 1.0 HD21 A:LEU469 4.9 26.3 1.0 HD11 A:LEU469 5.0 28.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:47.9 occ:1.00 O A:HOH755 1.9 31.4 1.0 OD2 A:ASP545 2.0 21.7 1.0 O A:HOH788 2.2 30.4 1.0 O A:HOH785 2.3 12.3 1.0 O A:HOH784 2.4 28.5 1.0 CG A:ASP545 3.0 22.8 1.0 O A:HOH780 3.1 40.9 1.0 HB3 A:ASP545 3.3 23.1 1.0 HB2 A:ASP545 3.3 23.1 1.0 CB A:ASP545 3.5 19.2 1.0 HB2 B:ALA499 3.9 31.9 1.0 O A:HOH726 3.9 42.9 1.0 OD1 A:ASP545 4.1 21.2 1.0 HA A:ILE542 4.3 20.2 1.0 HE2 A:LYS546 4.4 47.3 1.0 HD2 B:PRO498 4.6 28.3 1.0 HG2 A:LYS546 4.7 27.8 1.0 H B:ALA499 4.8 23.7 1.0 CB B:ALA499 4.8 26.5 1.0 HG12 A:ILE542 5.0 17.2 1.0 CA A:ASP545 5.0 19.1 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:80.8 occ:1.00 OE1 A:GLU540 2.4 34.6 1.0 OE2 A:GLU540 2.5 38.0 1.0 O A:HOH744 2.6 32.4 1.0 CD A:GLU540 2.8 37.5 1.0 HE3 A:LYS536 2.8 55.8 1.0 CE A:LYS536 3.7 46.4 1.0 HZ1 A:LYS536 3.9 61.7 1.0 HZ2 A:LYS536 4.0 61.7 1.0 HA A:ALA537 4.0 26.6 1.0 HG2 A:LYS536 4.1 34.8 1.0 NZ A:LYS536 4.1 51.4 1.0 HE2 A:LYS536 4.3 55.8 1.0 CG A:GLU540 4.3 32.4 1.0 HB2 A:ALA537 4.5 29.8 1.0 HD2 A:LYS536 4.6 53.5 1.0 CD A:LYS536 4.7 44.5 1.0 HG3 A:GLU540 4.7 39.0 1.0 HG2 A:GLU540 4.7 39.0 1.0 CA A:ALA537 4.8 22.2 1.0 CG A:LYS536 4.8 28.9 1.0 HB2 A:GLU540 4.8 27.0 1.0 HZ3 A:LYS536 5.0 61.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:69.3 occ:1.00 OD2 A:ASP475 2.0 50.2 1.0 OD1 A:ASP475 2.3 35.1 1.0 CG A:ASP475 2.5 42.6 1.0 O A:HOH782 2.6 39.0 1.0 HH12 A:ARG477 3.9 51.9 1.0 CB A:ASP475 4.0 32.2 1.0 O A:HOH749 4.1 41.9 1.0 HB2 A:ASP475 4.4 38.6 1.0 HB3 A:ASP475 4.4 38.6 1.0 NH1 A:ARG477 4.5 43.2 1.0 HA A:ASP475 4.8 33.0 1.0 HH11 A:ARG477 4.8 51.9 1.0 CA A:ASP475 4.9 27.4 1.0 HH22 A:ARG477 5.0 59.0 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:64.3 occ:1.00 CL A:CL611 1.8 57.4 1.0 OXT A:PRO548 2.0 37.5 1.0 NE2 A:HIS476 2.1 48.6 1.0 CL A:CL610 2.1 41.1 1.0 HE1 A:HIS476 2.6 53.5 1.0 CE1 A:HIS476 2.6 44.6 1.0 C A:PRO548 2.9 33.0 1.0 O A:PRO548 3.1 28.5 1.0 CD2 A:HIS476 3.3 36.6 1.0 HD2 A:HIS476 3.7 44.0 1.0 ND1 A:HIS476 3.9 42.8 1.0 O A:HOH800 4.0 38.1 1.0 CG A:HIS476 4.3 35.3 1.0 CA A:PRO548 4.3 33.1 1.0 HB2 A:PRO548 4.3 40.7 1.0 HA A:PRO548 4.5 39.8 1.0 HD1 A:HIS476 4.6 51.4 1.0 O A:SER474 4.8 28.1 1.0 CB A:PRO548 4.9 33.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:40.5 occ:1.00 OD2 B:ASP503 1.8 24.5 1.0 CL B:CL604 2.2 24.2 1.0 CG B:ASP503 2.7 20.1 1.0 HD22 B:ASN505 2.7 24.2 1.0 OD1 B:ASP503 2.8 17.7 1.0 ND2 B:ASN505 3.5 20.1 1.0 HD2 B:PRO504 3.7 27.4 1.0 HD21 B:ASN505 3.7 24.2 1.0 HB2 B:ASN505 3.9 22.3 1.0 CB B:ASP503 4.1 20.9 1.0 HD22 B:LEU469 4.1 23.9 1.0 O B:HOH765 4.3 29.7 1.0 HB2 B:ASP503 4.3 25.2 1.0 H B:ASN505 4.3 20.6 1.0 CG B:ASN505 4.5 26.5 1.0 CD B:PRO504 4.6 22.8 1.0 HA B:ASP503 4.6 21.2 1.0 HB3 B:ASP503 4.6 25.2 1.0 CB B:ASN505 4.7 18.6 1.0 HD13 B:LEU469 4.7 32.4 1.0 O B:HOH805 4.9 35.6 1.0 HD3 B:PRO504 4.9 27.4 1.0 CA B:ASP503 4.9 17.6 1.0 HB3 B:LEU469 5.0 22.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:43.7 occ:1.00 CL B:CL606 2.2 27.9 1.0 OD2 B:ASP545 2.2 27.3 1.0 CL B:CL605 2.2 28.0 1.0 O B:HOH741 2.6 31.2 1.0 CG B:ASP545 3.2 24.8 1.0 HB2 B:ASP545 3.3 33.0 1.0 HB3 B:ASP545 3.4 33.0 1.0 CB B:ASP545 3.5 27.4 1.0 O B:HOH726 3.8 16.6 1.0 HB2 A:ALA499 3.8 28.5 1.0 HE2 B:LYS546 3.9 44.7 1.0 HA B:ILE542 4.2 25.9 1.0 HD2 A:PRO498 4.3 20.2 1.0 OD1 B:ASP545 4.3 26.5 1.0 H A:ALA499 4.6 21.5 1.0 HG2 A:PRO498 4.6 23.3 1.0 HG2 B:LYS546 4.6 38.2 1.0 HG12 B:ILE542 4.7 22.4 1.0 CB A:ALA499 4.7 23.7 1.0 O B:SER541 4.8 19.6 1.0 HB2 A:PRO498 4.8 21.3 1.0 CE B:LYS546 4.9 37.2 1.0 OG B:SER541 4.9 22.3 1.0 HD3 B:LYS546 4.9 35.7 1.0 N A:ALA499 4.9 17.9 1.0 HG B:SER541 5.0 26.8 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Mouse Lipin-1 M-Lip Domain with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:70.5 occ:1.00 OE1 B:GLU540 2.0 51.1 1.0 O B:HOH783 2.2 46.2 1.0 CL B:CL608 2.2 56.3 1.0 CL B:CL607 2.5 32.8 1.0 CD B:GLU540 2.8 40.1 1.0 OE2 B:GLU540 2.9 37.2 1.0 HE3 B:LYS536 3.0 67.6 1.0 HG2 B:LYS536 3.6 60.1 1.0 HZ2 B:LYS536 3.7 70.9 1.0 O B:HOH705 3.7 41.5 1.0 CE B:LYS536 3.8 56.3 1.0 HD2 B:LYS536 3.8 71.1 1.0 NZ B:LYS536 4.1 59.1 1.0 CD B:LYS536 4.1 59.2 1.0 CG B:GLU540 4.2 31.7 1.0 HZ1 B:LYS536 4.3 70.9 1.0 CG B:LYS536 4.3 50.1 1.0 HG3 B:GLU540 4.5 38.0 1.0 HG2 B:GLU540 4.5 38.0 1.0 HE2 B:LYS536 4.6 67.6 1.0 HA B:ALA537 4.7 32.7 1.0 HG3 B:LYS536 4.8 60.1 1.0 HZ3 B:LYS536 5.0 70.9 1.0

W.Gu, M.V.Airola. The Middle Lipin (M-Lip) Domain Is A New Protein Fold That Dimerizes and Binds Membranes To Be Published.