Chlorine in PDB 2d5z: Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules

The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z was solved by T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.65 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.028, 82.697, 110.343, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.5

The structure of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules (pdb code 2d5z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules, PDB code: 2d5z:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1201 b:16.8 occ:1.00 CL1 A:L351201 0.0 16.8 1.0 C5 A:L351201 1.8 14.2 1.0 C4 A:L351201 2.7 15.5 1.0 C6 A:L351201 2.8 14.0 1.0 O D:HOH1312 3.4 33.3 1.0 C6 D:L351202 3.5 17.9 1.0 C1 D:L351202 3.6 17.1 1.0 N1 D:L351202 3.8 17.2 1.0 C3 A:L351201 4.0 14.3 1.0 CG2 C:VAL96 4.0 16.9 1.0 C1 A:L351201 4.1 13.6 1.0 C2 D:L351202 4.1 16.8 1.0 C7 D:L351202 4.1 18.8 1.0 O1 D:L351202 4.1 18.4 1.0 C5 D:L351202 4.1 18.0 1.0 O C:HOH1349 4.2 42.2 1.0 O B:HOH259 4.3 40.2 1.0 CD C:LYS99 4.4 15.8 1.0 C2 A:L351201 4.5 14.9 1.0 C3 D:L351202 4.5 18.6 1.0 C4 D:L351202 4.6 18.1 1.0 O C:HOH1342 4.8 39.3 1.0 CB C:LYS99 4.9 11.6 1.0 CD2 C:LEU100 4.9 14.8 1.0 O B:HOH253 4.9 38.2 1.0 CL1 D:L351202 5.0 20.6 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1201 b:15.7 occ:1.00 CL2 A:L351201 0.0 15.7 1.0 C3 A:L351201 1.8 14.3 1.0 C4 A:L351201 2.7 15.5 1.0 C2 A:L351201 2.8 14.9 1.0 ND2 D:ASN108 3.2 14.0 1.0 CZ C:PHE36 3.5 12.2 1.0 CD2 C:LEU100 3.6 14.8 1.0 CB C:HIS103 3.7 11.1 1.0 CD2 C:HIS103 3.8 11.4 1.0 CG C:HIS103 3.8 9.9 1.0 CE2 C:PHE36 4.0 11.8 1.0 C5 A:L351201 4.0 14.2 1.0 CA C:LEU100 4.0 11.6 1.0 C1 A:L351201 4.0 13.6 1.0 O C:LYS99 4.1 11.3 1.0 CE1 C:PHE36 4.1 11.7 1.0 C4 D:L351202 4.2 18.1 1.0 CG D:ASN108 4.3 12.4 1.0 CL1 D:L351202 4.4 20.6 1.0 C C:LYS99 4.5 11.2 1.0 N C:LEU100 4.5 11.1 1.0 C6 A:L351201 4.5 14.0 1.0 C5 D:L351202 4.6 18.0 1.0 OD1 D:ASN108 4.7 11.5 1.0 O C:LEU100 4.7 11.9 1.0 CG C:LEU100 4.7 12.7 1.0 NE2 C:HIS103 4.7 10.0 1.0 CB C:LEU100 4.8 11.8 1.0 ND1 C:HIS103 4.8 10.7 1.0 C C:LEU100 4.9 11.6 1.0 O D:HOH1208 4.9 16.6 1.0 CD2 C:PHE36 4.9 11.3 1.0 C3 D:L351202 5.0 18.6 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1200 b:14.6 occ:1.00 CL1 C:L351200 0.0 14.6 1.0 C5 C:L351200 1.8 13.0 1.0 C4 C:L351200 2.7 15.0 1.0 C6 C:L351200 2.7 14.5 1.0 CZ A:PHE36 3.5 11.9 1.0 ND2 B:ASN108 3.6 18.8 1.0 CD2 A:LEU100 3.7 11.9 1.0 CB A:HIS103 3.7 8.6 1.0 CG A:HIS103 3.8 8.2 1.0 CD2 A:HIS103 3.9 8.7 1.0 C3 C:L351200 4.0 15.9 1.0 C1 C:L351200 4.0 15.3 1.0 O A:LYS99 4.1 9.9 1.0 CE2 A:PHE36 4.1 15.1 1.0 CE1 A:PHE36 4.1 12.5 1.0 CA A:LEU100 4.2 10.3 1.0 CG B:ASN108 4.3 14.4 1.0 C2 C:L351200 4.5 14.7 1.0 OD1 B:ASN108 4.5 13.7 1.0 C A:LYS99 4.6 10.3 1.0 N A:LEU100 4.6 9.8 1.0 ND1 A:HIS103 4.7 10.3 1.0 NE2 A:HIS103 4.7 8.6 1.0 O A:LEU100 4.9 10.9 1.0 CG A:LEU100 4.9 11.8 1.0 CB A:LEU100 4.9 10.5 1.0 O4 D:L351202 4.9 35.8 1.0 O C:HOH1219 5.0 21.3 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1200 b:17.7 occ:1.00 CL2 C:L351200 0.0 17.7 1.0 C3 C:L351200 1.8 15.9 1.0 C4 C:L351200 2.7 15.0 1.0 C2 C:L351200 2.7 14.7 1.0 NE B:ARG104 3.5 24.0 1.0 O B:HOH259 3.7 40.2 1.0 C13 D:L351202 3.8 24.0 1.0 CZ B:ARG104 3.9 27.8 1.0 C5 C:L351200 4.0 13.0 1.0 NH1 B:ARG104 4.0 28.5 1.0 C12 D:L351202 4.0 24.0 1.0 O4 D:L351202 4.0 35.8 1.0 C1 C:L351200 4.0 15.3 1.0 O C:HOH1342 4.1 39.3 1.0 CD B:ARG104 4.2 18.0 1.0 CD A:LYS99 4.3 18.4 1.0 CG2 A:VAL96 4.5 15.3 1.0 C6 C:L351200 4.5 14.5 1.0 C17 D:L351202 4.6 33.7 1.0 NH2 B:ARG104 4.7 29.4 1.0 CB A:LYS99 4.8 11.3 1.0 C15 D:L351202 4.9 30.5 1.0 CD2 A:LEU100 4.9 11.9 1.0 O1 C:L351200 4.9 14.9 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1202 b:20.6 occ:1.00 CL1 D:L351202 0.0 20.6 1.0 C5 D:L351202 1.8 18.0 1.0 C4 D:L351202 2.7 18.1 1.0 C6 D:L351202 2.8 17.9 1.0 O D:HOH1243 3.5 23.7 1.0 O D:HOH1232 3.5 21.0 1.0 O D:HOH1204 3.9 15.2 1.0 C4 A:L351201 4.0 15.5 1.0 C3 D:L351202 4.0 18.6 1.0 O D:HOH1240 4.1 23.6 1.0 C1 D:L351202 4.1 17.1 1.0 O B:HOH268 4.2 43.1 1.0 CE1 C:PHE36 4.2 11.7 1.0 CL2 A:L351201 4.4 15.7 1.0 C3 A:L351201 4.5 14.3 1.0 C2 D:L351202 4.5 16.8 1.0 C5 A:L351201 4.7 14.2 1.0 CZ C:PHE36 4.8 12.2 1.0 O D:HOH1206 4.8 15.9 1.0 O D:HOH1312 4.9 33.3 1.0 OD1 D:ASN108 4.9 11.5 1.0 CL1 A:L351201 5.0 16.8 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of T-State Human Hemoglobin Complexed with Three L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1202 b:18.7 occ:1.00 CL2 D:L351202 0.0 18.7 1.0 C3 D:L351202 1.8 18.6 1.0 C4 D:L351202 2.7 18.1 1.0 C2 D:L351202 2.7 16.8 1.0 O D:HOH1208 3.3 16.6 1.0 O D:HOH1221 3.4 19.5 1.0 O D:ARG104 3.5 9.3 1.0 ND2 D:ASN108 3.6 14.0 1.0 C1 A:L351201 3.6 13.6 1.0 C D:ARG104 3.7 10.4 1.0 CD2 D:LEU105 3.7 13.2 1.0 CA D:LEU105 3.7 10.2 1.0 N1 A:L351201 3.8 15.1 1.0 C2 A:L351201 3.8 14.9 1.0 N D:LEU105 3.8 9.8 1.0 CG D:ASN108 3.9 12.4 1.0 CB D:ASN108 3.9 10.8 1.0 C5 D:L351202 4.0 18.0 1.0 C1 D:L351202 4.0 17.1 1.0 C6 A:L351201 4.1 14.0 1.0 C3 A:L351201 4.3 14.3 1.0 C7 A:L351201 4.4 15.8 1.0 CG D:LEU105 4.5 10.7 1.0 CB D:ARG104 4.5 11.4 1.0 C6 D:L351202 4.5 17.9 1.0 C5 A:L351201 4.6 14.2 1.0 CB D:LEU105 4.6 10.1 1.0 OD1 D:ASN108 4.6 11.5 1.0 CA D:ARG104 4.7 10.6 1.0 C D:LEU105 4.7 10.6 1.0 C4 A:L351201 4.7 15.5 1.0 O D:HOH1206 4.7 15.9 1.0 O1 A:L351201 4.8 15.0 1.0 O D:LEU105 4.8 11.2 1.0

T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame. R-State Haemoglobin with Low Oxygen Affinity: Crystal Structures of Deoxy Human and Carbonmonoxy Horse Haemoglobin Bound to the Effector Molecule L35 J.Mol.Biol. V. 356 790 2006.
ISSN: ISSN 0022-2836
PubMed: 16403522
DOI: 10.1016/J.JMB.2005.12.018