Calcium in PDB 4mdv: Crystal Structure of Calcium-Bound Annexin (Sm)1

The structure of Crystal Structure of Calcium-Bound Annexin (Sm)1, PDB code: 4mdv was solved by A.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.10 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.822, 88.486, 68.465, 90.00, 111.18, 90.00
R / Rfree (%)	19 / 25.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Bound Annexin (Sm)1 (pdb code 4mdv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Calcium-Bound Annexin (Sm)1, PDB code: 4mdv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.6 occ:1.00 OD2 A:ASP93 2.4 71.6 1.0 O A:MET49 2.5 0.1 1.0 O A:GLY53 2.5 91.1 1.0 O A:HOH540 2.7 75.3 1.0 O A:GLY51 2.8 0.4 1.0 CG A:ASP93 3.3 92.8 1.0 C A:MET49 3.5 0.0 1.0 OD1 A:ASP93 3.6 0.9 1.0 C A:GLY53 3.6 98.3 1.0 OG1 A:THR54 3.7 90.5 1.0 C A:GLY51 3.9 0.6 1.0 O A:LYS50 3.9 0.1 1.0 C A:PRO52 4.0 0.6 1.0 O A:PRO52 4.0 0.4 1.0 N A:GLY53 4.1 0.8 1.0 CA A:MET49 4.2 83.6 1.0 C A:LYS50 4.2 0.3 1.0 CA A:GLY53 4.3 0.2 1.0 N A:LYS50 4.5 0.5 1.0 N A:GLY51 4.6 0.0 1.0 N A:THR54 4.6 90.0 1.0 CB A:MET49 4.6 66.2 1.0 N A:PRO52 4.6 0.5 1.0 CA A:PRO52 4.6 0.6 1.0 CB A:ASP93 4.7 84.1 1.0 CA A:LYS50 4.7 0.4 1.0 CA A:THR54 4.8 89.4 1.0 CA A:GLY51 4.8 0.6 1.0 CB A:THR54 4.8 96.8 1.0

Calcium binding site 2 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:72.2 occ:1.00 OE2 A:GLU173 2.4 61.7 1.0 O A:GLY123 2.4 77.8 1.0 O A:GLY125 2.4 63.0 1.0 O A:MET121 2.5 53.5 1.0 O A:HOH538 2.6 85.3 1.0 CD A:GLU173 3.3 83.8 1.0 OE1 A:GLU173 3.4 96.7 1.0 C A:GLY125 3.6 65.6 1.0 C A:GLY123 3.6 81.4 1.0 C A:MET121 3.6 57.5 1.0 N A:GLY125 3.9 56.7 1.0 C A:LEU124 4.3 63.3 1.0 OG1 A:THR126 4.3 61.7 1.0 N A:GLY123 4.3 65.8 1.0 CA A:GLY125 4.3 66.0 1.0 CA A:MET121 4.3 50.5 1.0 OD2 B:ASP177 4.3 50.0 1.0 C A:LYS122 4.4 81.4 1.0 CA A:LEU124 4.5 73.3 1.0 N A:LEU124 4.5 81.3 1.0 CA A:GLY123 4.5 69.6 1.0 N A:THR126 4.6 62.3 1.0 N A:LYS122 4.7 56.7 1.0 O A:LYS122 4.7 96.2 1.0 CG A:GLU173 4.7 90.1 1.0 CA A:THR126 4.7 58.9 1.0 CA A:LYS122 4.8 69.8 1.0 O A:LEU124 4.9 59.1 1.0

Calcium binding site 3 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.5 occ:1.00 OE1 A:GLU179 2.4 67.4 1.0 O A:THR174 2.5 91.4 1.0 O A:LYS171 2.6 0.1 1.0 CD A:GLU179 3.5 67.6 1.0 C A:LYS171 3.7 98.5 1.0 C A:THR174 3.7 76.1 1.0 OE2 A:GLU179 3.9 76.1 1.0 CG A:LYS171 4.0 0.8 1.0 CA A:CYS175 4.3 82.4 1.0 CA A:LYS171 4.3 94.1 1.0 N A:CYS175 4.5 74.1 1.0 CB A:CYS175 4.5 64.6 1.0 N A:LYS172 4.7 97.6 1.0 CG A:GLU179 4.7 67.5 1.0 N A:THR174 4.8 60.8 1.0 CB A:LYS171 4.8 0.1 1.0 CA A:THR174 4.9 69.6 1.0 CA A:LYS172 5.0 92.9 1.0

Calcium binding site 4 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:74.3 occ:1.00 OD1 A:ASP346 2.4 90.2 1.0 O A:LEU305 2.5 63.7 1.0 OD2 A:ASP346 2.5 61.7 1.0 O A:MET302 2.6 78.8 1.0 CG A:ASP346 2.7 71.4 1.0 C A:LEU305 2.9 92.7 1.0 CA A:LEU305 3.1 98.9 1.0 O A:GLY304 3.2 92.9 1.0 N A:LEU305 3.4 0.3 1.0 C A:GLY304 3.5 88.4 1.0 O A:HOH506 3.7 59.5 1.0 C A:MET302 3.7 68.8 1.0 N A:GLY306 3.9 0.1 1.0 O A:GLY306 4.2 90.4 1.0 CB A:ASP346 4.2 62.5 1.0 C A:ALA303 4.4 74.4 1.0 O A:ALA303 4.4 67.1 1.0 CA A:MET302 4.4 65.7 1.0 N A:GLY304 4.4 81.3 1.0 CB A:LEU305 4.5 88.2 1.0 CA A:CA405 4.5 100.0 1.0 CA A:GLY304 4.6 73.0 1.0 CA A:GLY306 4.6 0.5 1.0 N A:ALA303 4.8 74.6 1.0 C A:GLY306 4.8 1.0 1.0 CB A:MET302 4.8 47.6 1.0 CA A:ASP346 4.9 57.6 1.0 CA A:ALA303 5.0 62.9 1.0

Calcium binding site 5 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:100.0 occ:1.00 O A:ASP346 2.5 59.8 1.0 O A:HOH506 2.7 59.5 1.0 CA A:GLY306 2.8 0.5 1.0 O A:GLY306 2.8 90.4 1.0 C A:GLY306 3.0 1.0 1.0 N A:GLY306 3.6 0.1 1.0 C A:ASP346 3.6 54.2 1.0 OD2 A:ASP346 3.9 61.7 1.0 C A:LEU305 4.1 92.7 1.0 CG A:ASP346 4.1 71.4 1.0 N A:THR307 4.1 0.7 1.0 O A:LEU305 4.1 63.7 1.0 CA A:ASP346 4.4 57.6 1.0 CB A:ASP346 4.4 62.5 1.0 CA A:CA404 4.5 74.3 1.0 OD1 A:ASP346 4.6 90.2 1.0 N A:THR347 4.7 55.1 1.0 OD1 A:ASP309 4.7 72.1 1.0 CG2 A:THR347 4.8 57.9 1.0 CA A:THR347 4.8 54.6 1.0

Calcium binding site 6 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:0.5 occ:1.00 OE1 A:GLU56 2.5 88.4 1.0 O A:THR54 2.6 92.9 1.0 CD A:GLU56 3.3 96.6 1.0 OE2 A:GLU56 3.3 82.5 1.0 C A:THR54 3.8 83.5 1.0 N A:THR54 4.4 90.0 1.0 CA A:THR54 4.7 89.4 1.0 N A:ASN55 4.7 80.3 1.0 CG A:GLU56 4.8 93.7 1.0 N A:GLU56 4.8 73.6 1.0 CA A:ASN55 4.8 75.8 1.0

Calcium binding site 7 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:91.6 occ:1.00 OD2 B:ASP93 2.4 0.0 1.0 OD1 B:ASP93 2.4 0.3 1.0 O B:MET49 2.6 0.8 1.0 O B:GLY53 2.6 90.2 1.0 O B:HOH552 2.7 74.7 1.0 CG B:ASP93 2.8 100.0 1.0 O B:GLY51 2.9 1.0 1.0 C B:MET49 3.6 0.1 1.0 C B:GLY53 3.7 97.8 1.0 OG1 B:THR54 3.8 93.0 1.0 C B:GLY51 4.0 0.3 1.0 O B:PRO52 4.0 0.3 1.0 C B:PRO52 4.1 1.0 1.0 O B:LYS50 4.1 0.2 1.0 N B:GLY53 4.2 0.8 1.0 CA B:MET49 4.2 86.4 1.0 CB B:ASP93 4.3 82.3 1.0 C B:LYS50 4.4 0.4 1.0 CA B:GLY53 4.4 0.8 1.0 CB B:MET49 4.6 88.8 1.0 CA B:PRO52 4.6 0.9 1.0 N B:LYS50 4.7 0.8 1.0 N B:THR54 4.7 93.3 1.0 N B:GLY51 4.8 0.3 1.0 N B:PRO52 4.8 0.1 1.0 CA B:THR54 4.9 87.6 1.0 CA B:LYS50 4.9 0.9 1.0 CB B:THR54 4.9 84.7 1.0 CA B:GLY51 5.0 0.4 1.0

Calcium binding site 8 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:70.6 occ:0.96 O B:MET121 2.4 48.5 1.0 OE2 B:GLU173 2.5 95.4 1.0 O B:GLY123 2.6 75.8 1.0 OE1 B:GLU173 2.6 58.3 1.0 O B:GLY125 2.6 65.7 1.0 O A:HOH556 2.6 53.9 1.0 CD B:GLU173 2.9 84.8 1.0 O A:HOH544 3.3 70.5 1.0 C B:MET121 3.6 54.5 1.0 C B:GLY123 3.8 79.5 1.0 C B:GLY125 3.8 65.3 1.0 N B:GLY125 4.1 59.9 1.0 N B:GLY123 4.3 65.9 1.0 CA B:MET121 4.4 52.9 1.0 OG1 B:THR126 4.4 50.1 1.0 CG B:GLU173 4.4 88.6 1.0 C B:LYS122 4.5 85.0 1.0 C B:LEU124 4.5 63.2 1.0 CA B:GLY125 4.5 63.0 1.0 OD2 A:ASP177 4.5 56.8 1.0 CA B:GLY123 4.6 70.0 1.0 N B:LYS122 4.7 57.3 1.0 N B:LEU124 4.7 80.9 1.0 CA B:LEU124 4.7 68.3 1.0 N B:THR126 4.8 60.9 1.0 O B:LYS122 4.8 99.9 1.0 CA B:LYS122 4.8 74.9 1.0 CA B:THR126 4.9 56.9 1.0

Calcium binding site 9 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:86.1 occ:1.00 OE1 B:GLU179 2.4 92.1 1.0 O B:LYS171 2.5 0.1 1.0 OE2 B:GLU179 2.5 82.1 1.0 O B:THR174 2.6 90.4 1.0 O B:HOH535 2.7 70.6 1.0 CD B:GLU179 2.8 85.5 1.0 O B:HOH550 3.1 71.0 1.0 C B:LYS171 3.4 98.9 1.0 C B:THR174 3.7 73.8 1.0 CA B:LYS171 3.8 92.6 1.0 CB B:LYS171 4.2 80.5 1.0 CG B:GLU179 4.3 67.6 1.0 CA B:CYS175 4.4 80.8 1.0 N B:CYS175 4.5 73.4 1.0 N B:LYS172 4.6 95.8 1.0 O B:HOH519 4.7 57.1 1.0 CA B:THR174 4.8 65.9 1.0 N B:THR174 4.8 59.9 1.0 CB B:CYS175 4.9 56.8 1.0 CG B:LYS171 5.0 75.7 1.0 CB B:GLU179 5.0 68.3 1.0

Calcium binding site 10 out of 13 in the Crystal Structure of Calcium-Bound Annexin (Sm)1


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 Calcium-Bound Annexin (Sm)1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:61.6 occ:0.46 OD2 B:ASP275 2.4 91.7 1.0 OD2 A:ASP128 2.4 62.9 1.0 O A:HOH552 2.6 71.9 1.0 O A:HOH502 2.6 37.4 0.5 CA B:CA405 2.7 64.6 0.5 O A:HOH519 2.8 52.5 1.0 OD2 A:ASP275 2.8 68.3 1.0 CG B:ASP275 3.0 67.8 1.0 CB B:ASP275 3.5 56.4 1.0 CG A:ASP128 3.6 68.6 1.0 CG A:ASP275 3.8 63.0 1.0 OD1 B:ASP275 3.9 55.7 1.0 N B:ASP275 3.9 52.3 1.0 OD1 A:ASP275 4.2 55.9 1.0 OD1 A:ASP128 4.2 66.8 1.0 CA B:ASP275 4.3 59.9 1.0 OD2 B:ASP128 4.4 73.3 1.0 O A:HOH502 4.5 23.2 0.5 CB A:ASP128 4.6 62.4 1.0 O B:HOH533 4.6 69.4 1.0 O B:HOH501 4.9 24.7 0.5 CB A:ASP275 4.9 51.2 1.0

C.Y.Leow, C.Willis, A.Osman, L.Mason, A.Simon, B.J.Smith, R.B.Gasser, M.K.Jones, A.Hofmann. Crystal Structure and Immunological Properties of the First Annexin From Schistosoma Mansoni: Insights Into the Structural Integrity of the Schistosomal Tegument. Febs J. 2013.
ISSN: ISSN 1742-464X
PubMed: 24428567
DOI: 10.1111/FEBS.12700