Calcium in PDB 6tp5: Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase

All present enzymatic activity of Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase:
1.14.11.29;

The structure of Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase, PDB code: 6tp5 was solved by M.Myllykoski, A.Sutinen, M.K.Koski, J.P.Kallio, A.Raasakka, J.Myllyharju, R.K.Wierenga, P.Koivunen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.30 / 2.25
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	92.079, 92.079, 129.500, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.1

The structure of Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase (pdb code 6tp5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase, PDB code: 6tp5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase


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 Human Transmembrane Prolyl 4-Hydroxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca721 b:69.0 occ:1.00 O A:HIS204 2.1 78.4 1.0 OD1 A:ASN200 2.3 82.0 1.0 OD1 A:ASP198 2.4 80.3 1.0 OE1 A:GLN206 2.4 73.2 1.0 OD1 A:ASP202 2.4 72.3 1.0 OE2 A:GLU209 2.5 75.5 1.0 OE1 A:GLU209 2.6 74.6 1.0 CD A:GLU209 2.9 70.1 1.0 CG A:ASP202 3.3 77.2 1.0 C A:HIS204 3.3 69.9 1.0 CD A:GLN206 3.4 70.0 1.0 CG A:ASP198 3.4 78.0 1.0 CG A:ASN200 3.4 76.6 1.0 OD2 A:ASP202 3.7 80.0 1.0 NE2 A:GLN206 3.7 60.4 1.0 ND2 A:ASN200 3.9 71.2 1.0 OD2 A:ASP198 4.1 81.9 1.0 N A:HIS204 4.1 68.0 1.0 N A:ASP202 4.2 80.9 1.0 CA A:HIS204 4.2 74.2 1.0 N A:GLN206 4.2 69.2 1.0 N A:LEU205 4.3 75.3 1.0 CA A:ASP198 4.3 75.9 1.0 CB A:ASP198 4.3 70.4 1.0 CG A:GLU209 4.3 62.8 1.0 CA A:LEU205 4.4 66.5 1.0 N A:ARG201 4.5 80.9 1.0 N A:ASN200 4.5 83.0 1.0 CB A:ASP202 4.5 73.7 1.0 CB A:HIS204 4.6 78.7 1.0 CB A:ASN200 4.7 72.6 1.0 C A:ASP198 4.7 80.8 1.0 CG A:GLN206 4.7 64.8 1.0 CA A:ASP202 4.8 86.4 1.0 N A:GLN199 4.8 84.3 1.0 C A:LEU205 4.8 64.7 1.0 C A:ASN200 4.8 90.3 1.0 CA A:ASN200 4.9 84.1 1.0 N A:GLY203 4.9 80.9 1.0 C A:ASP202 5.0 90.6 1.0 CB A:GLN206 5.0 62.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase


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 Human Transmembrane Prolyl 4-Hydroxylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca722 b:77.6 occ:1.00 OD1 A:ASP239 2.3 83.1 1.0 OD1 A:ASP237 2.3 83.3 1.0 O A:HOH841 2.4 70.7 1.0 O A:VAL243 2.4 70.0 1.0 OE1 A:GLU248 2.5 76.3 1.0 OD1 A:ASP241 2.5 93.0 1.0 OE2 A:GLU248 2.5 78.4 1.0 CD A:GLU248 2.8 70.6 1.0 CG A:ASP239 3.2 87.7 1.0 OD2 A:ASP239 3.3 90.3 1.0 CG A:ASP237 3.4 77.3 1.0 CG A:ASP241 3.4 87.7 1.0 C A:VAL243 3.6 60.4 1.0 OD2 A:ASP241 3.7 85.8 1.0 OD2 A:ASP237 4.0 78.2 1.0 CG A:GLU248 4.3 65.6 1.0 N A:VAL243 4.4 57.8 1.0 N A:ASP241 4.5 78.6 1.0 CA A:VAL243 4.5 61.0 1.0 CB A:ASP237 4.5 73.5 1.0 N A:LEU244 4.5 65.8 1.0 CA A:ASP237 4.5 72.7 1.0 CB A:ASP239 4.6 87.5 1.0 CA A:LEU244 4.6 57.3 1.0 N A:ASP239 4.6 76.8 1.0 N A:GLY240 4.7 82.9 1.0 CB A:ASP241 4.7 77.5 1.0 N A:SER245 4.8 65.4 1.0 CB A:VAL243 4.8 67.2 1.0 C A:ASP237 4.8 77.2 1.0 C A:ASP239 5.0 81.7 1.0 CA A:ASP239 5.0 80.8 1.0 N A:PRO238 5.0 71.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase


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 Human Transmembrane Prolyl 4-Hydroxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca719 b:0.2 occ:1.00 O B:HIS204 2.2 0.4 1.0 OD1 B:ASP202 2.3 0.8 1.0 OD1 B:ASN200 2.3 0.3 1.0 OD1 B:ASP198 2.3 0.3 1.0 OE1 B:GLN206 2.4 0.5 1.0 OE1 B:GLU209 2.5 0.7 1.0 OE2 B:GLU209 2.5 0.9 1.0 CD B:GLU209 2.7 0.5 1.0 C B:HIS204 3.3 1.0 1.0 CG B:ASN200 3.3 98.5 1.0 CG B:ASP202 3.4 0.1 1.0 CG B:ASP198 3.5 1.0 1.0 CD B:GLN206 3.6 97.5 1.0 ND2 B:ASN200 3.6 93.7 1.0 OD2 B:ASP202 3.9 0.3 1.0 N B:GLN206 4.1 87.1 1.0 N B:HIS204 4.1 0.6 1.0 CA B:HIS204 4.1 0.1 1.0 CA B:ASP198 4.1 0.9 1.0 N B:LEU205 4.1 0.4 1.0 CG B:GLU209 4.2 89.3 1.0 NE2 B:GLN206 4.2 97.2 1.0 CA B:LEU205 4.3 98.2 1.0 OD2 B:ASP198 4.3 0.7 1.0 CB B:ASP198 4.3 0.2 1.0 CB B:HIS204 4.4 0.2 1.0 N B:ASP202 4.5 0.2 1.0 C B:ASP198 4.6 0.8 1.0 N B:ASN200 4.6 96.1 1.0 CB B:ASP202 4.6 0.1 1.0 CB B:ASN200 4.7 0.5 1.0 N B:GLN199 4.7 0.1 1.0 C B:LEU205 4.7 88.8 1.0 CG B:GLN206 4.7 84.0 1.0 CB B:GLN206 4.8 83.2 1.0 N B:ARG201 4.8 0.3 1.0 CA B:ASP202 4.9 0.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Transmembrane Prolyl 4-Hydroxylase


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 Human Transmembrane Prolyl 4-Hydroxylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca720 b:0.8 occ:1.00 OE1 B:GLU248 2.3 0.5 1.0 OD1 B:ASP239 2.3 0.1 1.0 O B:VAL243 2.3 98.5 1.0 OD1 B:ASP237 2.4 0.7 1.0 OD1 B:ASP241 2.4 0.5 1.0 OE2 B:GLU248 2.4 0.1 1.0 CD B:GLU248 2.7 0.9 1.0 OD2 B:ASP239 2.9 0.7 1.0 CG B:ASP239 3.0 0.1 1.0 CG B:ASP241 3.2 0.2 1.0 OD2 B:ASP241 3.4 0.1 1.0 CG B:ASP237 3.5 0.9 1.0 C B:VAL243 3.5 95.6 1.0 OD2 B:ASP237 3.9 94.1 1.0 CG B:GLU248 4.2 0.7 1.0 N B:VAL243 4.3 0.1 1.0 CA B:VAL243 4.4 98.8 1.0 CB B:ASP239 4.4 0.1 1.0 N B:ASP241 4.5 95.8 1.0 N B:LEU244 4.5 99.5 1.0 N B:SER245 4.6 0.7 1.0 CB B:ASP241 4.6 0.6 1.0 CA B:LEU244 4.6 1.0 1.0 CB B:VAL243 4.7 0.1 1.0 N B:GLY240 4.7 0.6 1.0 CB B:ASP237 4.7 0.1 1.0 CA B:ASP237 4.8 0.3 1.0 N B:ASP239 4.9 0.7 1.0 CB B:GLU248 4.9 0.3 1.0

M.Myllykoski, A.Sutinen, M.K.Koski, J.Kallio, A.Raasakka, J.Myllyharju, R.Wierenga, P.Koivunen. Structure of Transmembrane Prolyl 4-Hydroxylase Reveals Unique Organization of Ef and Dioxygenase Domains J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X