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Calcium in PDB 7kiq: Crystal Structure of the Mouse Lipin-2 M-Lip Domain

Protein crystallography data

The structure of Crystal Structure of the Mouse Lipin-2 M-Lip Domain, PDB code: 7kiq was solved by J.W.Yang, W.Gu, M.V.Airola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.35 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.706, 84.612, 97.511, 90, 108.9, 90
R / Rfree (%) 21.2 / 25.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain (pdb code 7kiq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain, PDB code: 7kiq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7kiq

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Calcium binding site 1 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:77.7
occ:1.00
 O A:HOH732 2.3 65.2 1.0
OE1 A:GLU494 2.4 46.0 1.0
O A:ILE489 2.5 46.4 1.0
OE2 A:GLU494 3.0 46.5 1.0
CD A:GLU494 3.1 46.7 1.0
C A:ILE489 3.5 41.6 1.0
CA A:ILE490 4.0 37.2 1.0
N A:ILE490 4.2 33.7 1.0
O A:HOH724 4.2 46.2 1.0
N A:THR491 4.4 36.1 1.0
N A:ILE489 4.4 33.9 1.0
C A:HIS488 4.5 39.0 1.0
CG2 A:THR491 4.5 36.4 1.0
CG A:GLU494 4.6 43.4 1.0
O A:HIS488 4.6 32.7 1.0
CA A:ILE489 4.6 42.6 1.0
C A:ILE490 4.7 39.2 1.0
O A:HOH719 4.7 39.8 1.0
O E:HOH729 4.8 45.9 1.0
CA A:HIS488 4.9 38.0 1.0

Calcium binding site 2 out of 10 in 7kiq

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Calcium binding site 2 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:62.2
occ:1.00
 O B:HOH728 2.4 56.0 1.0
O B:ILE489 2.4 46.2 1.0
OE1 B:GLU494 2.5 47.7 1.0
OE2 B:GLU494 3.1 65.4 1.0
CD B:GLU494 3.2 55.8 1.0
C B:ILE489 3.4 45.0 1.0
CA B:ILE490 4.1 38.9 1.0
N B:ILE490 4.1 43.0 1.0
C B:HIS488 4.2 43.3 1.0
N B:ILE489 4.2 39.2 1.0
O B:HIS488 4.3 45.1 1.0
CA B:ILE489 4.5 41.5 1.0
O B:HOH726 4.5 47.1 1.0
N B:THR491 4.6 41.9 1.0
CG B:GLU494 4.7 52.1 1.0
CA B:HIS488 4.8 46.6 1.0
C B:ILE490 4.8 39.0 1.0

Calcium binding site 3 out of 10 in 7kiq

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Calcium binding site 3 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:114.0
occ:1.00
 OE2 C:GLU494 2.4 73.8 1.0
O C:HOH730 2.5 75.2 1.0
CD C:GLU494 3.2 60.0 1.0
OE1 C:GLU494 3.3 51.1 1.0
O C:ILE489 3.5 54.8 1.0
CG C:GLU494 4.6 51.8 1.0
C C:ILE489 4.6 48.3 1.0
C C:HIS488 4.8 48.3 1.0
O C:HIS488 4.9 41.1 1.0
CA C:HIS488 5.0 49.3 1.0

Calcium binding site 4 out of 10 in 7kiq

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Calcium binding site 4 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:91.2
occ:1.00
 OE2 D:GLU494 2.4 51.2 1.0
OE1 D:GLU494 2.5 67.6 1.0
O D:HOH721 2.5 70.5 1.0
O D:HOH709 2.6 63.0 1.0
O D:ILE489 2.7 57.4 1.0
CD D:GLU494 2.8 56.7 1.0
C D:ILE489 3.6 50.5 1.0
CA D:ILE490 4.0 47.9 1.0
N D:ILE490 4.2 40.5 1.0
C D:HIS488 4.3 51.6 1.0
CG D:GLU494 4.3 57.4 1.0
O D:HIS488 4.3 50.9 1.0
N D:ILE489 4.4 47.9 1.0
N D:THR491 4.5 39.5 1.0
CA D:ILE489 4.7 49.9 1.0
CA D:HIS488 4.7 53.5 1.0
C D:ILE490 4.8 44.9 1.0
O D:HOH722 4.8 60.1 1.0
CG1 D:ILE490 4.9 46.3 1.0
CG2 D:THR491 5.0 47.8 1.0

Calcium binding site 5 out of 10 in 7kiq

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Calcium binding site 5 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:57.4
occ:1.00
 O E:HOH725 2.4 49.0 1.0
OE1 E:GLU494 2.4 57.5 1.0
O E:ILE489 2.7 40.3 1.0
CD E:GLU494 3.2 50.9 1.0
OE2 E:GLU494 3.2 47.5 1.0
C E:ILE489 3.8 42.1 1.0
C E:HIS488 4.2 41.9 1.0
N E:ILE489 4.3 39.9 1.0
O E:HIS488 4.3 42.5 1.0
CA E:HIS488 4.5 46.7 1.0
CG E:GLU494 4.6 49.6 1.0
N E:ILE490 4.7 37.7 1.0
CA E:ILE490 4.7 39.3 1.0
CA E:ILE489 4.7 40.1 1.0

Calcium binding site 6 out of 10 in 7kiq

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Calcium binding site 6 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


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 Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca601

b:139.0
occ:1.00
 O F:HOH714 2.4 74.4 1.0
OE1 F:GLU494 2.4 78.7 1.0
OE2 F:GLU494 2.4 85.7 1.0
O F:HOH711 2.4 62.1 1.0
CD F:GLU494 2.7 78.6 1.0
O F:ILE489 2.8 66.4 1.0
C F:ILE489 3.8 57.7 1.0
CG F:GLU494 4.2 66.9 1.0
CA F:ILE490 4.3 54.5 1.0
C F:HIS488 4.4 63.3 1.0
N F:ILE489 4.4 60.9 1.0
N F:ILE490 4.5 57.9 1.0
N F:THR491 4.5 56.4 1.0
O F:HIS488 4.6 55.7 1.0
CA F:HIS488 4.6 61.3 1.0
CA F:ILE489 4.8 57.3 1.0
OG1 F:THR491 4.8 67.5 1.0
O J:HOH709 4.8 55.7 1.0
O F:GLU487 4.9 76.0 1.0
C F:ILE490 5.0 52.0 1.0

Calcium binding site 7 out of 10 in 7kiq

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Calcium binding site 7 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca601

b:81.7
occ:1.00
 OE2 G:GLU494 2.4 56.8 1.0
O G:HOH717 2.5 76.3 1.0
O G:ILE489 2.7 47.6 1.0
OE1 G:GLU494 3.0 69.9 1.0
CD G:GLU494 3.0 57.9 1.0
C G:ILE489 3.7 46.4 1.0
C G:HIS488 4.2 52.4 1.0
O G:HOH716 4.2 54.3 1.0
N G:ILE489 4.2 46.9 1.0
O G:HIS488 4.4 49.4 1.0
CA G:ILE490 4.5 51.6 1.0
CG G:GLU494 4.5 57.4 1.0
O C:HOH732 4.5 68.0 1.0
N G:ILE490 4.5 37.5 1.0
CA G:HIS488 4.6 57.1 1.0
CA G:ILE489 4.6 50.1 1.0
O G:GLU487 4.8 57.3 1.0
N G:THR491 4.8 43.2 1.0
CG2 G:THR491 4.9 39.6 1.0

Calcium binding site 8 out of 10 in 7kiq

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Calcium binding site 8 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca601

b:76.7
occ:1.00
 O H:HOH720 2.4 69.7 1.0
OE2 H:GLU494 2.4 69.2 1.0
OE1 H:GLU494 2.5 74.5 1.0
O H:ILE489 2.7 59.2 1.0
CD H:GLU494 2.8 67.7 1.0
O H:HOH724 3.2 68.8 1.0
C H:ILE489 3.7 50.8 1.0
CG H:GLU494 4.3 61.6 1.0
CA H:ILE490 4.3 52.4 1.0
O H:HOH725 4.3 66.1 1.0
C H:HIS488 4.4 56.9 1.0
N H:ILE490 4.4 56.0 1.0
N H:ILE489 4.5 51.9 1.0
O H:HIS488 4.5 55.1 1.0
N H:THR491 4.7 48.0 1.0
CA H:ILE489 4.7 52.2 1.0
CA H:HIS488 4.8 55.2 1.0
O H:GLU487 4.9 45.2 1.0
CG2 H:THR491 4.9 50.9 1.0

Calcium binding site 9 out of 10 in 7kiq

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Calcium binding site 9 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca601

b:93.5
occ:1.00
 O I:HOH715 2.4 56.0 1.0
O I:HOH721 2.4 74.6 1.0
OE2 I:GLU494 2.5 77.1 1.0
OE1 I:GLU494 2.5 61.1 1.0
O I:ILE489 2.7 55.7 1.0
CD I:GLU494 2.8 63.1 1.0
C I:ILE489 3.9 54.3 1.0
CG2 I:THR491 4.1 52.8 1.0
CG I:GLU494 4.3 65.0 1.0
O I:HOH717 4.3 44.7 1.0
O H:HOH725 4.5 66.1 1.0
CA I:ILE490 4.5 48.4 1.0
N I:THR491 4.5 53.3 1.0
O I:HOH714 4.5 57.2 1.0
N I:ILE489 4.6 48.9 1.0
N I:ILE490 4.6 52.1 1.0
C I:HIS488 4.7 56.7 1.0
CA I:ILE489 4.9 51.9 1.0
C I:ILE490 5.0 50.2 1.0

Calcium binding site 10 out of 10 in 7kiq

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Calcium binding site 10 out of 10 in the Crystal Structure of the Mouse Lipin-2 M-Lip Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Mouse Lipin-2 M-Lip Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca601

b:98.8
occ:1.00
 O J:ILE489 2.6 65.9 1.0
OE1 J:GLU494 2.9 66.1 1.0
C J:ILE489 3.4 57.7 1.0
OE2 J:GLU494 3.6 77.4 1.0
O J:HIS488 3.6 56.2 1.0
C J:HIS488 3.6 62.0 1.0
CD J:GLU494 3.6 65.5 1.0
N J:ILE489 3.9 54.9 1.0
N J:ILE490 4.0 51.6 1.0
CA J:ILE490 4.1 50.1 1.0
CA J:HIS488 4.1 61.0 1.0
CA J:ILE489 4.3 54.4 1.0
CG1 J:ILE490 4.4 46.7 1.0
CB J:ILE490 4.9 48.9 1.0
CB J:HIS488 4.9 57.6 1.0
O J:GLU487 4.9 73.7 1.0

Reference:

W.Gu, J.W.Yang, M.V.Airola. The Middle Lipin (M-Lip) Domain Is A New Protein Fold That Dimerizes and Binds Membranes To Be Published.
Page generated: Wed Jul 9 22:56:28 2025

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