Calcium in PDB 5ve9: Structure of HACF7 EF1-EF2-Gar Domains

Protein crystallography data

The structure of Structure of HACF7 EF1-EF2-Gar Domains, PDB code: 5ve9 was solved by T.R.Lane, K.C.Slep, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.35 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.984, 92.984, 90.446, 90.00, 90.00, 120.00
R / Rfree (%) 25.6 / 27.9

Other elements in 5ve9:

The structure of Structure of HACF7 EF1-EF2-Gar Domains also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of HACF7 EF1-EF2-Gar Domains (pdb code 5ve9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of HACF7 EF1-EF2-Gar Domains, PDB code: 5ve9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5ve9

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Calcium binding site 1 out of 4 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7201

b:0.3
occ:1.00
O A:LYS7060 2.3 88.1 1.0
OD2 A:ASP7056 2.4 0.0 1.0
OD1 A:ASP7056 2.4 99.8 1.0
OD1 A:ASP7058 2.4 86.5 1.0
CG A:ASP7056 2.7 0.5 1.0
OD1 A:ASP7054 2.8 83.5 1.0
H A:LYS7060 3.2 0.0 1.0
HB2 A:LYS7060 3.2 0.2 1.0
C A:LYS7060 3.2 86.8 1.0
CG A:ASP7058 3.4 87.7 1.0
OD2 A:ASP7058 3.7 86.3 1.0
H A:ASP7058 3.8 0.1 1.0
N A:LYS7060 3.8 85.0 1.0
HA A:ILE7061 3.9 0.5 1.0
CA A:LYS7060 3.9 85.5 1.0
CG A:ASP7054 3.9 80.4 1.0
CB A:LYS7060 4.0 84.3 1.0
H A:ASP7056 4.1 0.4 1.0
HA A:ASP7054 4.2 96.9 1.0
CB A:ASP7056 4.2 0.9 1.0
HG22 A:ILE7061 4.3 97.0 1.0
N A:ILE7061 4.3 84.1 1.0
HB3 A:LYS7060 4.4 0.2 1.0
HB2 A:ASP7056 4.5 0.5 1.0
HG23 A:ILE7061 4.5 97.0 1.0
CA A:ILE7061 4.5 87.1 1.0
OD2 A:ASP7054 4.6 79.7 1.0
H A:GLY7059 4.6 0.3 1.0
N A:ASP7058 4.6 89.2 1.0
H A:GLN7057 4.6 0.7 1.0
CB A:ASP7058 4.7 89.2 1.0
HB3 A:ASP7056 4.7 0.5 1.0
N A:ASP7056 4.8 0.2 1.0
HA A:LYS7060 4.8 0.7 1.0
CB A:ASP7054 4.8 77.0 1.0
CG2 A:ILE7061 4.8 80.8 1.0
CA A:ASP7054 4.9 80.7 1.0
HD3 A:LYS7060 4.9 94.3 1.0
N A:GLY7059 4.9 84.4 1.0
HB2 A:ASP7054 4.9 92.4 1.0
CA A:ASP7056 4.9 0.5 1.0
HB3 A:ASP7058 4.9 0.1 1.0
OE2 A:GLU7065 4.9 88.1 1.0
N A:GLN7057 4.9 0.7 1.0

Calcium binding site 2 out of 4 in 5ve9

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Calcium binding site 2 out of 4 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7202

b:72.3
occ:1.00
O A:TYR7096 2.2 65.7 1.0
OD1 A:ASP7092 2.3 74.1 1.0
OD1 A:ASP7090 2.4 64.7 1.0
OE1 A:GLU7101 2.4 63.2 1.0
O A:HOH7301 2.5 78.2 1.0
OD2 A:ASP7094 2.5 68.2 1.0
OE2 A:GLU7101 2.5 68.2 1.0
OD2 A:ASP7092 2.7 78.2 1.0
CD A:GLU7101 2.8 65.3 1.0
CG A:ASP7092 2.8 76.7 1.0
CG A:ASP7094 3.4 74.2 1.0
C A:TYR7096 3.4 67.0 1.0
H A:ASP7092 3.5 90.8 1.0
HA A:ILE7097 3.6 74.8 1.0
CG A:ASP7090 3.6 60.4 1.0
H A:ASP7094 3.6 88.4 1.0
HA A:ASP7090 3.6 72.8 1.0
OD1 A:ASP7094 3.7 77.5 1.0
H A:ASP7098 3.8 79.1 1.0
H A:TYR7096 3.9 86.5 1.0
H A:GLY7093 3.9 88.1 1.0
OD2 A:ASP7098 4.1 73.2 1.0
CB A:ASP7092 4.2 80.2 1.0
HB2 A:TYR7096 4.2 88.8 1.0
CG A:GLU7101 4.2 65.2 1.0
N A:ILE7097 4.3 65.7 1.0
N A:TYR7096 4.3 72.1 1.0
CA A:TYR7096 4.3 69.7 1.0
N A:ASP7092 4.3 75.7 1.0
CA A:ILE7097 4.4 62.4 1.0
CA A:ASP7090 4.4 60.7 1.0
HB3 A:ASP7092 4.4 96.3 1.0
OD2 A:ASP7090 4.4 59.0 1.0
N A:ASP7094 4.4 73.6 1.0
H A:ARG7091 4.4 75.6 1.0
N A:ASP7098 4.4 65.9 1.0
HG3 A:GLU7101 4.5 78.3 1.0
N A:GLY7093 4.5 73.4 1.0
CB A:ASP7094 4.6 77.4 1.0
CB A:ASP7090 4.6 59.0 1.0
C A:ASP7090 4.6 62.4 1.0
HB3 A:ASP7094 4.7 92.9 1.0
N A:ARG7091 4.7 63.0 1.0
CB A:TYR7096 4.7 74.0 1.0
CA A:ASP7092 4.7 80.1 1.0
HB3 A:ASP7098 4.7 86.1 1.0
HG2 A:GLU7101 4.7 78.3 1.0
H A:GLY7095 4.8 77.6 1.0
HB2 A:GLU7101 4.8 77.1 1.0
HB2 A:ASP7092 4.8 96.3 1.0
HB3 A:TYR7096 4.8 88.8 1.0
CG A:ASP7098 4.9 71.8 1.0
HB2 A:ASP7090 4.9 70.9 1.0
C A:ILE7097 4.9 64.8 1.0
CA A:ASP7094 5.0 75.5 1.0

Calcium binding site 3 out of 4 in 5ve9

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Calcium binding site 3 out of 4 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7201

b:77.5
occ:1.00
O B:LYS7060 2.3 90.0 1.0
OD1 B:ASP7056 2.4 0.4 1.0
OD1 B:ASP7054 2.4 97.6 1.0
OD1 B:ASP7058 2.5 97.8 1.0
OD2 B:ASP7056 2.6 0.6 1.0
CG B:ASP7056 2.8 0.0 1.0
CG B:ASP7058 3.4 97.7 1.0
HA B:ILE7061 3.5 98.0 1.0
C B:LYS7060 3.6 79.2 1.0
OD2 B:ASP7058 3.6 0.9 1.0
CG B:ASP7054 3.6 92.4 1.0
HG22 B:ILE7061 3.7 0.7 1.0
HA B:ASP7054 3.8 0.8 1.0
H B:LYS7060 3.8 86.5 1.0
H B:ASP7058 3.8 0.7 1.0
H B:ASP7056 3.9 0.5 1.0
HG3 B:LYS7060 4.0 86.0 1.0
CB B:ASP7056 4.2 0.6 1.0
CA B:ILE7061 4.3 81.7 1.0
HG2 B:LYS7060 4.4 86.0 1.0
H B:GLN7057 4.4 0.4 1.0
OD2 B:ASP7054 4.4 86.8 1.0
N B:ILE7061 4.4 78.3 1.0
HG23 B:ILE7061 4.5 0.7 1.0
CG2 B:ILE7061 4.5 89.7 1.0
N B:LYS7060 4.5 72.1 1.0
CA B:ASP7054 4.5 0.5 1.0
N B:ASP7056 4.6 0.9 1.0
CB B:ASP7054 4.6 93.6 1.0
CA B:LYS7060 4.6 70.0 1.0
CG B:LYS7060 4.6 71.7 1.0
HB2 B:ASP7056 4.6 0.9 1.0
H B:LYS7055 4.6 0.0 1.0
HZ2 B:LYS7060 4.6 0.8 1.0
N B:ASP7058 4.7 89.8 1.0
OE1 B:GLU7065 4.7 91.2 1.0
CB B:ASP7058 4.8 92.7 1.0
HB3 B:ASP7056 4.8 0.9 1.0
HB2 B:ASP7054 4.8 0.3 1.0
N B:GLN7057 4.8 0.7 1.0
CA B:ASP7056 4.9 1.0 1.0
H B:GLY7059 4.9 94.4 1.0
N B:LYS7055 4.9 0.7 1.0
C B:ASP7054 4.9 0.4 1.0

Calcium binding site 4 out of 4 in 5ve9

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Calcium binding site 4 out of 4 in the Structure of HACF7 EF1-EF2-Gar Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of HACF7 EF1-EF2-Gar Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7202

b:54.5
occ:1.00
OD1 B:ASP7090 2.3 72.9 1.0
OD1 B:ASP7094 2.3 81.6 1.0
OD1 B:ASP7092 2.3 78.1 1.0
O B:TYR7096 2.3 67.1 1.0
O B:HOH7303 2.4 0.8 1.0
OE1 B:GLU7101 2.5 66.3 1.0
OE2 B:GLU7101 2.5 68.6 1.0
CD B:GLU7101 2.9 66.6 1.0
CG B:ASP7094 3.0 79.9 1.0
OD2 B:ASP7094 3.1 78.5 1.0
CG B:ASP7092 3.4 76.7 1.0
CG B:ASP7090 3.4 70.9 1.0
C B:TYR7096 3.4 67.2 1.0
HA B:ASP7090 3.5 80.6 1.0
HA B:ILE7097 3.6 77.8 1.0
H B:TYR7096 3.7 88.1 1.0
OD2 B:ASP7092 3.8 75.7 1.0
H B:ASP7092 3.8 92.7 1.0
H B:ASP7098 3.9 82.7 1.0
H B:ASP7094 4.0 96.8 1.0
HB2 B:TYR7096 4.0 85.8 1.0
OD2 B:ASP7090 4.2 72.3 1.0
CA B:ASP7090 4.2 67.2 1.0
N B:TYR7096 4.3 73.5 1.0
H B:ARG7091 4.3 83.0 1.0
N B:ILE7097 4.3 64.9 1.0
CA B:TYR7096 4.3 70.5 1.0
CB B:ASP7090 4.3 67.8 1.0
CA B:ILE7097 4.4 64.8 1.0
O B:ASP7092 4.4 79.9 1.0
CG B:GLU7101 4.4 66.1 1.0
CB B:ASP7094 4.4 81.0 1.0
N B:ASP7092 4.5 77.3 1.0
HB3 B:ASP7094 4.5 97.2 1.0
HB2 B:ASP7090 4.6 81.3 1.0
C B:ASP7090 4.6 68.7 1.0
N B:ARG7091 4.6 69.2 1.0
N B:ASP7098 4.6 68.9 1.0
H B:GLY7095 4.7 92.3 1.0
CB B:TYR7096 4.7 71.5 1.0
CB B:ASP7092 4.7 77.7 1.0
HG3 B:GLU7101 4.7 79.3 1.0
OD2 B:ASP7098 4.7 81.4 1.0
N B:ASP7094 4.7 80.7 1.0
C B:ASP7092 4.8 80.8 1.0
HG2 B:GLU7101 4.8 79.3 1.0
CA B:ASP7092 4.9 78.9 1.0
HB2 B:GLU7101 5.0 77.6 1.0
HG12 B:ILE7097 5.0 77.6 1.0

Reference:

T.R.Lane, E.Fuchs, K.C.Slep. Structure of the ACF7 Ef-Hand-Gar Module and Delineation of Microtubule Binding Determinants. Structure V. 25 1130 2017.
ISSN: ISSN 1878-4186
PubMed: 28602822
DOI: 10.1016/J.STR.2017.05.006
Page generated: Sat Dec 12 05:47:25 2020

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