Calcium in PDB 2g4n: Anomalous Substructure of Alpha-Lactalbumin

The structure of Anomalous Substructure of Alpha-Lactalbumin, PDB code: 2g4n was solved by C.Mueller-Dieckmann, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.430, 104.800, 119.110, 90.00, 90.00, 90.00
R / Rfree (%)	29.6 / 35.9

The structure of Anomalous Substructure of Alpha-Lactalbumin also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Calcium atom in the Anomalous Substructure of Alpha-Lactalbumin (pdb code 2g4n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Anomalous Substructure of Alpha-Lactalbumin, PDB code: 2g4n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:25.4 occ:0.73 OD1 A:ASP88 2.2 37.0 1.0 O A:ASP84 2.3 41.8 1.0 O A:LYS79 2.4 36.0 1.0 OD1 A:ASP82 2.4 36.0 1.0 OD1 A:ASP87 2.5 33.8 1.0 CG A:ASP88 3.4 40.0 1.0 CG A:ASP87 3.5 38.5 1.0 C A:ASP84 3.5 40.5 1.0 CG A:ASP82 3.6 39.9 1.0 C A:LYS79 3.6 37.6 1.0 OD2 A:ASP87 3.7 30.4 1.0 OD2 A:ASP88 4.0 38.0 1.0 CA A:PHE80 4.1 38.5 1.0 OD2 A:ASP82 4.1 34.9 1.0 CA A:LEU85 4.2 38.3 1.0 N A:LEU85 4.3 40.0 1.0 N A:PHE80 4.3 38.6 1.0 N A:ASP88 4.3 38.6 1.0 CA A:ASP84 4.6 39.3 1.0 O A:ASP82 4.6 35.2 1.0 CB A:ASP88 4.6 40.1 1.0 N A:ASP82 4.6 34.8 1.0 C A:PHE80 4.6 37.5 1.0 N A:ASP87 4.6 36.8 1.0 N A:ASP84 4.6 40.3 1.0 C A:ASP82 4.7 35.0 1.0 CA A:LYS79 4.7 36.9 1.0 C A:LEU85 4.7 37.0 1.0 CD2 A:PHE80 4.8 34.0 1.0 CB A:ASP84 4.8 39.0 1.0 CB A:ASP82 4.8 36.2 1.0 CB A:ASP87 4.8 36.6 1.0 N A:LEU81 4.9 37.7 1.0 CA A:ASP82 4.9 35.0 1.0 CB A:LYS79 5.0 37.9 1.0 CA A:ASP88 5.0 38.6 1.0

Calcium binding site 2 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:24.8 occ:0.71 O B:ASP84 2.3 42.5 1.0 OD1 B:ASP88 2.3 36.0 1.0 O B:LYS79 2.4 34.4 1.0 OD1 B:ASP82 2.5 34.2 1.0 OD1 B:ASP87 2.5 37.5 1.0 CG B:ASP88 3.5 40.9 1.0 CG B:ASP87 3.5 40.4 1.0 C B:ASP84 3.5 41.6 1.0 C B:LYS79 3.6 36.0 1.0 CG B:ASP82 3.6 37.6 1.0 OD2 B:ASP87 3.7 31.0 1.0 OD2 B:ASP88 4.0 38.5 1.0 OD2 B:ASP82 4.1 30.7 1.0 CA B:PHE80 4.2 35.6 1.0 CA B:LEU85 4.3 40.3 1.0 N B:ASP88 4.3 39.8 1.0 N B:LEU85 4.3 42.0 1.0 N B:PHE80 4.3 36.5 1.0 CA B:ASP84 4.5 40.0 1.0 O B:ASP82 4.6 36.5 1.0 N B:ASP84 4.6 41.0 1.0 CB B:ASP88 4.6 40.9 1.0 C B:PHE80 4.6 34.6 1.0 CA B:LYS79 4.7 36.5 1.0 C B:ASP82 4.7 36.5 1.0 N B:ASP87 4.7 37.5 1.0 N B:ASP82 4.7 35.7 1.0 C B:LEU85 4.7 39.2 1.0 CB B:ASP84 4.7 39.3 1.0 CD2 B:PHE80 4.8 34.7 1.0 CB B:ASP82 4.8 36.8 1.0 CB B:ASP87 4.9 36.2 1.0 N B:LEU81 4.9 36.5 1.0 CA B:ASP82 4.9 36.2 1.0 CA B:ASP88 5.0 40.6 1.0 CB B:LYS79 5.0 37.2 1.0

Calcium binding site 3 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:27.2 occ:0.85 O C:ASP84 2.2 40.1 1.0 OD1 C:ASP88 2.2 43.9 1.0 OD1 C:ASP87 2.4 28.4 1.0 O C:LYS79 2.4 35.8 1.0 OD1 C:ASP82 2.6 36.6 1.0 O C:HOH210 2.7 27.1 1.0 CG C:ASP88 3.3 40.6 1.0 C C:ASP84 3.4 39.1 1.0 CG C:ASP87 3.5 34.1 1.0 CG C:ASP82 3.6 33.2 1.0 C C:LYS79 3.6 35.5 1.0 OD2 C:ASP87 3.8 37.0 1.0 OD2 C:ASP82 3.8 39.9 1.0 OD2 C:ASP88 3.9 38.1 1.0 CA C:PHE80 4.2 33.4 1.0 CA C:ASP84 4.3 39.1 1.0 N C:ASP84 4.3 39.4 1.0 N C:LEU85 4.3 39.2 1.0 CA C:LEU85 4.3 38.5 1.0 N C:ASP88 4.3 40.0 1.0 N C:PHE80 4.4 33.5 1.0 O C:ASP82 4.4 33.7 1.0 CB C:ASP84 4.5 40.1 1.0 CB C:ASP88 4.5 38.7 1.0 C C:ASP82 4.6 34.9 1.0 CA C:LYS79 4.7 35.7 1.0 C C:PHE80 4.7 33.0 1.0 C C:LEU85 4.8 36.9 1.0 N C:ASP82 4.8 34.3 1.0 CD2 C:PHE80 4.8 43.8 1.0 CB C:ASP82 4.8 35.4 1.0 N C:ASP87 4.8 38.8 1.0 CB C:ASP87 4.8 36.8 1.0 CA C:ASP82 5.0 34.7 1.0 CB C:LYS79 5.0 37.4 1.0 N C:LEU81 5.0 34.2 1.0 N C:THR86 5.0 36.8 1.0

Calcium binding site 4 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:26.9 occ:0.82 O D:ASP84 2.2 39.2 1.0 OD1 D:ASP88 2.2 44.7 1.0 OD1 D:ASP87 2.4 29.0 1.0 O D:LYS79 2.4 36.3 1.0 O D:HOH212 2.5 24.2 1.0 OD1 D:ASP82 2.7 35.3 1.0 CG D:ASP88 3.4 37.8 1.0 C D:ASP84 3.4 38.3 1.0 CG D:ASP87 3.5 34.1 1.0 CG D:ASP82 3.6 33.6 1.0 C D:LYS79 3.6 36.7 1.0 OD2 D:ASP87 3.8 34.5 1.0 OD2 D:ASP82 3.8 38.5 1.0 OD2 D:ASP88 3.9 43.6 1.0 CA D:PHE80 4.2 34.8 1.0 N D:ASP84 4.2 38.5 1.0 CA D:ASP84 4.3 38.4 1.0 N D:ASP88 4.3 38.8 1.0 N D:LEU85 4.3 37.7 1.0 CA D:LEU85 4.3 37.5 1.0 N D:PHE80 4.4 34.3 1.0 O D:ASP82 4.5 33.9 1.0 CB D:ASP84 4.5 39.2 1.0 CB D:ASP88 4.6 37.6 1.0 C D:ASP82 4.6 35.0 1.0 C D:PHE80 4.7 34.2 1.0 N D:ASP82 4.7 33.8 1.0 CA D:LYS79 4.7 36.1 1.0 CD2 D:PHE80 4.7 39.6 1.0 C D:LEU85 4.8 35.9 1.0 CB D:ASP82 4.8 33.8 1.0 N D:ASP87 4.8 37.5 1.0 CB D:ASP87 4.8 35.5 1.0 N D:LEU81 4.9 35.2 1.0 CA D:ASP82 4.9 34.4 1.0

Calcium binding site 5 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca206 b:18.8 occ:0.54 O E:HOH212 1.9 35.6 1.0 O E:ASP84 2.1 38.0 1.0 OD1 E:ASP87 2.3 38.4 1.0 O E:LYS79 2.3 35.6 1.0 OD1 E:ASP88 2.4 47.3 1.0 OD1 E:ASP82 2.7 32.8 1.0 C E:ASP84 3.3 38.5 1.0 CG E:ASP87 3.4 40.6 1.0 C E:LYS79 3.5 35.5 1.0 CG E:ASP88 3.6 39.6 1.0 CG E:ASP82 3.6 35.8 1.0 OD2 E:ASP87 3.8 40.8 1.0 OD2 E:ASP82 4.0 37.9 1.0 CA E:PHE80 4.1 36.2 1.0 CA E:ASP84 4.1 38.6 1.0 OD2 E:ASP88 4.1 43.2 1.0 O E:HOH215 4.2 54.4 1.0 N E:ASP84 4.2 38.4 1.0 N E:PHE80 4.2 35.3 1.0 N E:LEU85 4.3 37.6 1.0 N E:ASP88 4.3 39.6 1.0 CB E:ASP84 4.3 39.0 1.0 CA E:LEU85 4.5 37.7 1.0 O E:ASP82 4.5 32.6 1.0 CD2 E:PHE80 4.6 35.9 1.0 CA E:LYS79 4.6 35.3 1.0 N E:ASP82 4.7 35.2 1.0 C E:PHE80 4.7 36.4 1.0 C E:ASP82 4.7 34.8 1.0 CB E:ASP88 4.8 40.4 1.0 N E:ASP87 4.8 39.1 1.0 CB E:ASP87 4.8 38.9 1.0 CB E:ASP82 4.9 35.9 1.0 C E:LEU85 4.9 38.3 1.0 CA E:ASP82 4.9 35.6 1.0 CB E:LYS79 5.0 35.3 1.0 N E:LEU81 5.0 35.6 1.0

Calcium binding site 6 out of 6 in the Anomalous Substructure of Alpha-Lactalbumin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Anomalous Substructure of Alpha-Lactalbumin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca205 b:16.9 occ:0.54 O F:ASP84 2.1 39.6 1.0 O F:HOH211 2.1 31.8 1.0 OD1 F:ASP87 2.2 35.2 1.0 O F:LYS79 2.3 36.0 1.0 O F:HOH212 2.4 43.7 1.0 OD1 F:ASP88 2.5 56.0 1.0 OD1 F:ASP82 2.6 32.4 1.0 CG F:ASP87 3.3 37.9 1.0 C F:ASP84 3.4 39.0 1.0 C F:LYS79 3.5 35.6 1.0 CG F:ASP82 3.5 34.3 1.0 OD2 F:ASP87 3.6 38.2 1.0 CG F:ASP88 3.6 41.8 1.0 OD2 F:ASP82 3.8 36.4 1.0 CA F:PHE80 4.1 37.4 1.0 OD2 F:ASP88 4.1 48.3 1.0 N F:PHE80 4.2 35.8 1.0 CA F:ASP84 4.2 38.7 1.0 N F:LEU85 4.3 38.0 1.0 N F:ASP84 4.4 38.6 1.0 N F:ASP88 4.4 39.7 1.0 CB F:ASP84 4.4 39.1 1.0 CA F:LEU85 4.5 38.2 1.0 CA F:LYS79 4.6 35.9 1.0 CD2 F:PHE80 4.6 34.2 1.0 O F:ASP82 4.7 34.1 1.0 CB F:ASP87 4.7 38.0 1.0 C F:PHE80 4.7 37.5 1.0 N F:ASP82 4.7 35.9 1.0 N F:ASP87 4.8 38.8 1.0 CB F:ASP82 4.8 35.2 1.0 CB F:LYS79 4.8 36.1 1.0 C F:ASP82 4.8 35.3 1.0 CB F:ASP88 4.9 41.4 1.0 C F:LEU85 4.9 38.6 1.0 CA F:ASP82 5.0 35.6 1.0

C.Mueller-Dieckmann, S.Panjikar, A.Schmidt, S.Mueller, J.Kuper, A.Geerlof, M.Wilmanns, R.K.Singh, P.A.Tucker, M.S.Weiss. On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part IV. Efficient Determination of Anomalous Substructures in Biomacromolecules Using Longer X-Ray Wavelengths. Acta Crystallogr.,Sect.D V. 63 366 2007.
ISSN: ISSN 0907-4449
PubMed: 17327674
DOI: 10.1107/S0907444906055624