Calcium in PDB 9nb6: Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex

The structure of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex (pdb code 9nb6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 23 binding sites of Calcium where determined in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex, PDB code: 9nb6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:56.9 occ:1.00 OE1 A:GLU252 2.5 67.6 1.0 OD1 A:ASP186 2.7 75.3 1.0 CD A:GLU252 3.7 60.4 1.0 CG A:ASP186 4.0 70.4 1.0 OE2 A:GLU252 4.3 61.9 1.0 N A:ASP186 4.6 71.4 1.0 OD2 A:ASP185 4.7 65.1 1.0 CB A:ASP185 4.7 51.1 1.0 OD2 A:ASP186 4.7 74.1 1.0 CA A:ASP186 4.7 72.9 1.0 CG A:GLU252 4.8 49.1 1.0 C A:ASP185 4.8 65.7 1.0 CE F:LYS262 4.9 43.8 1.0 CB A:ASP186 4.9 68.8 1.0 NZ F:LYS262 5.0 37.9 1.0

Calcium binding site 2 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1105 b:75.0 occ:1.00 OD2 A:ASP225 2.4 92.0 1.0 OD1 A:ASN247 2.4 82.9 1.0 OD2 A:ASP186 2.4 74.1 1.0 ND2 A:ASN247 2.6 73.1 1.0 OD1 A:ASP224 2.8 72.9 1.0 CG A:ASN247 2.8 77.3 1.0 CG A:ASP225 3.2 91.3 1.0 OD2 A:ASP224 3.2 78.5 1.0 CG A:ASP186 3.3 70.4 1.0 CG A:ASP224 3.4 73.4 1.0 CB A:ASP186 3.6 68.8 1.0 OD1 A:ASP225 3.7 94.2 1.0 CB A:ASP225 4.1 87.3 1.0 SG A:CYS248 4.3 101.5 1.0 CB A:ASN247 4.3 71.4 1.0 OD1 A:ASP186 4.4 75.3 1.0 N A:ASP225 4.5 72.3 1.0 NZ F:LYS262 4.5 37.9 1.0 CA A:ASP225 4.6 81.9 1.0 CB A:ASP224 4.8 68.3 1.0 N A:ASN247 4.9 79.8 1.0

Calcium binding site 3 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1106 b:28.1 occ:1.00 OE2 A:GLU359 2.3 45.8 1.0 OD1 A:ASP293 2.4 38.0 1.0 OD1 A:ASP292 2.5 29.1 1.0 CD A:GLU359 3.5 39.0 1.0 CG A:ASP292 3.6 21.5 1.0 CG A:ASP293 3.6 38.4 1.0 OD2 A:ASP292 4.0 23.8 1.0 OE1 A:GLU359 4.3 36.0 1.0 OD2 A:ASP293 4.4 41.2 1.0 CG A:GLU359 4.4 27.6 1.0 N A:ASP293 4.4 23.7 1.0 CA A:ASP293 4.5 21.2 1.0 CB A:ASP293 4.5 22.6 1.0 C A:ASP292 4.8 23.3 1.0 CB A:ASP292 4.8 13.2 1.0

Calcium binding site 4 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1107 b:21.5 occ:1.00 OD2 A:ASP299 2.4 20.7 1.0 OD2 A:ASP296 2.4 24.9 1.0 O A:GLY294 2.4 23.5 1.0 O A:VAL333 2.6 19.7 1.0 CG A:ASP299 3.1 20.1 1.0 OD1 A:ASP299 3.1 26.1 1.0 CA A:SER334 3.2 24.3 1.0 CG A:ASP296 3.3 26.1 1.0 C A:VAL333 3.5 23.0 1.0 C A:GLY294 3.6 17.0 1.0 N A:SER334 3.8 24.8 1.0 CB A:SER334 3.9 22.0 1.0 OD1 A:ASP296 3.9 37.6 1.0 N A:CYS335 3.9 27.5 1.0 C A:SER334 4.1 28.4 1.0 N A:ASP296 4.2 11.6 1.0 CB A:ASP296 4.3 18.2 1.0 CA A:GLY294 4.4 15.8 1.0 CB A:ASP299 4.6 9.5 1.0 N A:TRP295 4.6 14.5 1.0 CA A:TRP295 4.8 15.3 1.0 O A:CYS335 4.9 38.9 1.0 CA A:VAL333 4.9 19.5 1.0 CA A:ASP296 4.9 10.9 1.0 C A:TRP295 4.9 15.9 1.0

Calcium binding site 5 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1108 b:102.5 occ:1.00 OD1 A:ASP746 2.4 102.8 1.0 OE1 A:GLU812 2.4 104.5 1.0 CG A:ASP746 3.3 110.7 1.0 OD1 A:ASP745 3.3 106.0 1.0 OE2 C:GLU981 3.4 110.9 1.0 OD2 A:ASP746 3.4 114.5 1.0 CD A:GLU812 3.6 110.1 1.0 OD2 A:ASP745 4.0 111.4 1.0 CG A:ASP745 4.0 108.1 1.0 OE2 A:GLU812 4.3 112.6 1.0 CD C:GLU981 4.3 105.6 1.0 CB A:GLU812 4.5 105.1 1.0 CG A:GLU812 4.6 110.7 1.0 CB A:ASP746 4.7 113.7 1.0 CG C:GLU981 4.9 95.4 1.0 NZ C:LYS1021 4.9 79.2 1.0 N A:ASP746 4.9 111.2 1.0

Calcium binding site 6 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1109 b:104.9 occ:1.00 OD2 A:ASP752 2.4 108.6 1.0 O A:MET786 2.4 115.8 1.0 O A:SER747 2.8 116.2 1.0 CA A:LYS787 2.8 121.1 1.0 C A:MET786 3.1 120.3 1.0 N A:LYS787 3.3 120.9 1.0 CG A:ASP752 3.4 108.4 1.0 CB A:LYS787 3.7 123.3 1.0 N A:CYS788 3.8 118.1 1.0 C A:LYS787 3.8 123.5 1.0 C A:SER747 3.8 112.4 1.0 OG A:SER747 3.9 124.2 1.0 CB A:ASP752 4.0 96.3 1.0 CG A:LYS787 4.0 122.8 1.0 OD1 A:ASP749 4.1 93.2 1.0 OD2 A:ASP749 4.1 91.0 1.0 CB A:SER747 4.3 117.1 1.0 CA A:MET786 4.4 126.3 1.0 CG A:ASP749 4.4 94.4 1.0 OD1 A:ASP752 4.5 112.0 1.0 CB A:MET786 4.5 120.6 1.0 CA A:SER747 4.6 107.8 1.0 N A:TRP748 4.8 106.1 1.0 CA A:TRP748 5.0 94.0 1.0 O A:LYS787 5.0 128.0 1.0

Calcium binding site 7 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1110 b:133.0 occ:1.00 OD1 A:ASN807 2.4 134.6 1.0 OD2 A:ASP784 2.4 139.5 1.0 OE2 A:GLU785 2.5 120.7 1.0 OD1 A:ASP784 2.6 132.2 1.0 CD A:GLU785 2.7 126.0 1.0 OE1 A:GLU785 2.8 131.7 1.0 CG A:ASP784 2.8 134.9 1.0 SG A:CYS808 3.2 135.2 1.0 CG A:ASN807 3.3 134.7 1.0 ND2 A:ASN807 3.5 133.2 1.0 CG A:GLU785 3.7 123.2 1.0 SG A:CYS744 4.1 134.8 1.0 CB A:ASP784 4.2 125.9 1.0 OD2 A:ASP746 4.3 114.5 1.0 N A:GLU785 4.5 125.4 1.0 CB A:ASN807 4.6 132.9 1.0 CB A:GLU785 4.6 128.9 1.0 CB A:ASP746 4.6 113.7 1.0 N A:CYS808 4.7 131.5 1.0 CB A:CYS808 4.7 123.2 1.0 CB A:CYS744 4.9 115.4 1.0 CG A:ASP746 5.0 110.7 1.0 CA A:GLU785 5.0 127.6 1.0 C A:ASP784 5.0 122.4 1.0 C A:ASN807 5.0 134.2 1.0

Calcium binding site 8 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1111 b:72.5 occ:1.00 OE1 A:GLU1022 2.4 74.1 1.0 OD1 A:ASP956 3.2 72.4 1.0 CD A:GLU1022 3.5 75.4 1.0 OD2 A:ASP955 3.6 87.3 1.0 OD1 A:ASP955 3.8 83.1 1.0 OE2 A:GLU1022 3.9 69.5 1.0 CG A:ASP955 4.0 82.4 1.0 CG A:ASP956 4.4 74.1 1.0 CG A:GLU1022 4.8 77.7 1.0 CA A:ASP956 4.9 74.8 1.0 CD A:LYS980 4.9 83.5 1.0 OG B:SER771 4.9 76.5 1.0

Calcium binding site 9 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1112 b:93.8 occ:1.00 O A:VAL996 2.3 106.8 1.0 OD2 A:ASP959 2.3 102.5 1.0 OD2 A:ASP962 2.4 96.7 1.0 O A:SER957 2.4 90.6 1.0 CA A:LYS997 2.9 110.0 1.0 OD1 A:ASP962 2.9 107.8 1.0 CG A:ASP962 3.0 102.3 1.0 C A:VAL996 3.3 104.2 1.0 CG A:ASP959 3.3 102.2 1.0 CG A:LYS997 3.4 105.7 1.0 N A:LYS997 3.5 104.5 1.0 CB A:LYS997 3.6 109.9 1.0 C A:SER957 3.6 87.6 1.0 N A:CYS998 4.0 110.9 1.0 C A:LYS997 4.0 110.8 1.0 CB A:SER957 4.0 84.7 1.0 OD1 A:ASP959 4.0 105.1 1.0 N A:ASP959 4.1 95.6 1.0 CB A:ASP959 4.3 98.2 1.0 CA A:SER957 4.4 84.2 1.0 CB A:ASP962 4.4 98.3 1.0 N A:TRP958 4.6 84.4 1.0 CA A:VAL996 4.7 102.2 1.0 CA A:TRP958 4.7 88.3 1.0 CA A:ASP959 4.8 95.2 1.0 CD A:LYS997 4.9 104.2 1.0 C A:TRP958 4.9 91.8 1.0

Calcium binding site 10 out of 23 in the Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of the CD163/Hp(1-1)Hb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1104 b:100.6 occ:1.00 OE1 B:GLU359 2.4 101.5 1.0 OD1 B:ASP293 2.5 95.8 1.0 OD2 B:ASP292 3.3 91.5 1.0 CD B:GLU359 3.4 99.3 1.0 CG B:ASP293 3.6 96.2 1.0 NZ E:LYS83 3.7 80.6 1.0 OE2 B:GLU359 3.8 102.8 1.0 OD2 B:ASP293 4.2 97.9 1.0 CG B:ASP292 4.4 88.4 1.0 N B:ASP293 4.7 93.3 1.0 CB B:ASP292 4.8 84.1 1.0 CG B:GLU359 4.8 90.8 1.0 CA E:GLY84 4.8 101.1 1.0 CB B:ASP293 4.8 89.6 1.0 N E:GLY84 4.8 100.9 1.0 CA B:ASP293 4.9 89.4 1.0

C.-S.Huang, H.Wang, J.B.R.White, O.Degtjarik, C.Huynh, K.Brannstrom, M.T.Horn, S.P.Muench, W.S.Somers, J.Chaparro-Riggers, L.Lin, L.Mosyak. Structural Elucidation of the Haptoglobin-Hemoglobin Clearance Mechanism By Macrophage Scavenger Receptor CD163 To Be Published.