Calcium in PDB 2gtl: Lumbricus Erythrocruorin at 3.5A Resolution

The structure of Lumbricus Erythrocruorin at 3.5A Resolution, PDB code: 2gtl was solved by W.E.Royer Jr., H.Sharma, K.Strand, J.E.Knapp, B.Bhyravbhatla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 3.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	176.080, 257.960, 436.530, 89.69, 97.15, 90.98
R / Rfree (%)	28.8 / 29.7

The structure of Lumbricus Erythrocruorin at 3.5A Resolution also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Lumbricus Erythrocruorin at 3.5A Resolution (pdb code 2gtl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Lumbricus Erythrocruorin at 3.5A Resolution, PDB code: 2gtl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca250 b:20.8 occ:1.00 O M:GLU86 2.4 37.4 1.0 O M:LEU81 2.6 27.4 1.0 OD1 M:ASP84 2.6 42.4 1.0 OD2 M:ASP88 2.6 42.9 1.0 OD1 M:ASP94 2.7 29.4 1.0 OE2 M:GLU95 3.0 55.1 1.0 OE1 M:GLU95 3.0 55.1 1.0 CD M:GLU95 3.3 55.1 1.0 CG M:ASP84 3.3 42.4 1.0 CG M:ASP88 3.4 42.9 1.0 CB M:ASP88 3.4 42.9 1.0 CG M:ASP94 3.4 29.4 1.0 C M:GLU86 3.5 37.4 1.0 OD2 M:ASP84 3.5 42.4 1.0 N M:ASP88 3.6 16.7 1.0 C M:LEU81 3.8 27.4 1.0 OD2 M:ASP94 4.0 29.4 1.0 N M:ASP84 4.1 41.3 1.0 N M:GLU86 4.1 37.4 1.0 CA M:ASP88 4.2 16.7 1.0 CA M:GLU86 4.3 37.4 1.0 N M:CYS83 4.3 32.6 1.0 CB M:ASP94 4.4 29.4 1.0 NH1 B:ARG35 4.4 47.2 1.0 C M:LYS87 4.4 52.3 1.0 N M:LYS87 4.4 52.3 1.0 CA M:PHE82 4.5 30.7 1.0 CA M:LYS87 4.6 52.3 1.0 CB M:ASP84 4.6 42.4 1.0 OD1 M:ASP88 4.6 42.9 1.0 C M:PHE82 4.6 30.7 1.0 CB M:LEU81 4.6 30.4 1.0 N M:PHE82 4.7 30.7 1.0 O M:ASP94 4.7 34.9 1.0 CG M:GLU95 4.7 55.1 1.0 CA M:LEU81 4.7 27.4 1.0 N M:GLY85 4.8 55.9 1.0 CA M:ASP84 4.8 41.3 1.0 CB M:GLU86 4.8 97.0 1.0 C M:ASP94 5.0 34.9 1.0 C M:ASP84 5.0 41.3 1.0

Calcium binding site 2 out of 4 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca251 b:43.0 occ:1.00 OE1 G:GLU9 2.4 41.0 1.0 OD2 G:ASP86 2.7 77.8 1.0 OE2 G:GLU9 2.8 41.0 1.0 CD G:GLU9 2.9 41.0 1.0 OD1 G:ASP86 3.2 77.8 1.0 CG G:ASP86 3.3 77.8 1.0 O M:ASP122 3.7 55.9 1.0 O M:TRP117 3.9 44.4 1.0 O M:LEU123 4.1 53.0 1.0 CG G:GLU9 4.3 41.0 1.0 C M:ASP122 4.8 55.9 1.0 CB G:ASP86 4.8 77.8 1.0 O M:GLU121 4.9 44.8 1.0

Calcium binding site 3 out of 4 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca250 b:15.4 occ:1.00 OD2 N:ASP88 2.5 25.0 1.0 O N:HIS86 2.6 30.2 1.0 OD2 N:ASP84 2.7 35.5 1.0 OE1 N:GLU95 2.7 45.1 1.0 O N:LEU81 2.8 7.5 1.0 OD1 N:ASP94 2.8 34.5 1.0 CG N:ASP84 3.2 35.5 1.0 CG N:ASP88 3.3 25.0 1.0 CB N:ASP88 3.4 25.0 1.0 OD1 N:ASP84 3.4 35.5 1.0 CD N:GLU95 3.7 45.1 1.0 C N:LEU81 3.7 7.5 1.0 CB N:LEU81 3.7 10.6 1.0 C N:HIS86 3.8 30.2 1.0 O N:ASP94 3.8 16.5 1.0 CG N:ASP94 3.8 34.5 1.0 N N:ASP88 3.9 26.3 1.0 OE2 N:GLU95 3.9 45.1 1.0 N N:ASP84 4.0 20.1 1.0 CA N:LEU81 4.1 7.5 1.0 N N:HIS86 4.2 30.2 1.0 CA N:ASP88 4.3 26.3 1.0 CB N:ASP94 4.4 34.5 1.0 CB N:ASP84 4.4 35.5 1.0 CA N:HIS86 4.5 30.2 1.0 OD1 N:ASP88 4.5 25.0 1.0 NH1 F:ARG35 4.6 50.7 1.0 N N:GLY85 4.7 61.2 1.0 O N:VAL82 4.7 60.6 1.0 CA N:ASP84 4.7 20.1 1.0 C N:LYS87 4.7 40.7 1.0 C N:VAL82 4.7 60.6 1.0 N N:LYS87 4.8 40.7 1.0 C N:ASP94 4.8 16.5 1.0 OD2 N:ASP94 4.8 34.5 1.0 CB N:HIS86 4.8 0.4 1.0 N N:VAL82 4.8 60.6 1.0 N N:CYS83 4.9 22.0 1.0 CA N:LYS87 4.9 40.7 1.0 CA N:CYS83 4.9 22.0 1.0 C N:CYS83 5.0 22.0 1.0

Calcium binding site 4 out of 4 in the Lumbricus Erythrocruorin at 3.5A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lumbricus Erythrocruorin at 3.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca250 b:23.7 occ:1.00 O O:HIS86 2.5 52.5 1.0 O O:PHE81 2.6 34.0 1.0 OD2 O:ASP88 2.8 59.5 1.0 OE2 O:GLU95 2.8 40.2 1.0 OD2 O:ASP84 2.8 40.8 1.0 OD1 O:ASP94 2.9 48.5 1.0 CB O:ASP88 3.4 59.5 1.0 CG O:ASP94 3.4 48.5 1.0 CG O:ASP88 3.5 59.5 1.0 N O:ASP88 3.5 41.2 1.0 CG O:ASP84 3.5 40.8 1.0 C O:PHE81 3.5 34.0 1.0 CD O:GLU95 3.6 40.2 1.0 CG O:GLU95 3.6 40.2 1.0 OD1 O:ASP84 3.6 40.8 1.0 CB O:ASP94 3.7 48.5 1.0 C O:HIS86 3.7 52.5 1.0 O O:ASP94 3.7 54.5 1.0 CB O:PHE81 3.9 75.4 1.0 CA O:ASP88 4.1 41.2 1.0 CA O:PHE81 4.2 34.0 1.0 OD2 O:ASP94 4.3 48.5 1.0 C O:ASP94 4.4 54.5 1.0 N O:VAL82 4.4 30.7 1.0 C O:ASN87 4.5 64.7 1.0 N O:HIS86 4.5 52.5 1.0 CA O:HIS86 4.6 52.5 1.0 N O:ASP84 4.6 62.8 1.0 N O:ASN87 4.6 64.7 1.0 N O:CYS83 4.6 40.5 1.0 CA O:ASN87 4.6 64.7 1.0 CA O:VAL82 4.6 30.7 1.0 OD1 O:ASP88 4.7 59.5 1.0 CA O:ASP94 4.7 54.5 1.0 OE1 O:GLU95 4.7 40.2 1.0 CB O:HIS86 4.7 0.5 1.0 CB O:ASP84 4.8 40.8 1.0 C O:VAL82 4.9 30.7 1.0 CG O:PHE81 5.0 75.4 1.0

W.E.Royer Jr., H.Sharma, K.Strand, J.E.Knapp, B.Bhyravbhatla. Lumbricus Erythrocruorin at 3.5 A Resolution: Architecture of A Megadalton Respiratory Complex. Structure V. 14 1167 2006.
ISSN: ISSN 0969-2126
PubMed: 16843898
DOI: 10.1016/J.STR.2006.05.011