Chlorine in PDB 3u0d: The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba

The structure of The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba, PDB code: 3u0d was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.01 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.476, 116.452, 120.194, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 28.8

The structure of The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Chlorine atom in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba (pdb code 3u0d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba, PDB code: 3u0d:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl183 b:55.8 occ:1.00 OH A:TYR138 3.2 36.3 1.0 OG1 A:THR54 3.4 31.0 1.0 C9 A:DBH180 4.1 40.5 1.0 CE2 A:TYR52 4.1 32.5 1.0 CG2 A:THR136 4.1 29.6 1.0 CZ A:TYR138 4.1 35.6 1.0 NH2 A:ARG81 4.2 31.0 1.0 OH A:TYR52 4.2 33.1 1.0 NZ A:LYS134 4.2 27.3 1.0 CB A:THR54 4.3 30.9 1.0 CG2 A:THR54 4.3 29.7 1.0 CE1 A:TYR138 4.3 35.6 1.0 CZ A:PHE123 4.4 25.6 1.0 OG A:SER68 4.5 28.7 1.0 CG2 A:VAL33 4.6 27.8 1.0 CZ A:TYR52 4.6 33.1 1.0 CE2 A:PHE123 4.7 25.9 1.0 C12 A:DBH180 4.9 41.8 1.0 CE A:LYS134 4.9 26.9 1.0 CB A:THR136 4.9 30.3 1.0 OG1 A:THR136 5.0 30.6 1.0

Chlorine binding site 2 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl183 b:47.2 occ:1.00 OH B:TYR138 2.8 28.6 1.0 OG1 B:THR54 2.9 31.1 1.0 CG2 B:THR54 3.5 28.5 1.0 CB B:THR54 3.6 30.1 1.0 CZ B:TYR138 3.7 28.2 1.0 CE1 B:TYR138 3.7 28.0 1.0 OG B:SER68 3.9 29.5 1.0 NH2 B:ARG81 4.0 34.8 1.0 CE2 B:TYR52 4.1 30.7 1.0 CG2 B:VAL33 4.3 28.0 1.0 OH B:TYR52 4.3 30.4 1.0 C9 B:DBH182 4.4 24.9 1.0 CZ B:PHE123 4.7 27.9 1.0 CZ B:TYR52 4.7 31.0 1.0 CG2 B:THR136 4.8 29.8 1.0 OH B:TYR56 4.9 32.1 1.0 NZ B:LYS134 5.0 22.9 1.0 CE2 B:TYR138 5.0 29.4 1.0

Chlorine binding site 3 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl183 b:48.1 occ:1.00 OH D:TYR138 3.0 35.6 1.0 OG1 D:THR54 3.2 38.1 1.0 NH2 D:ARG81 3.8 39.1 1.0 CZ D:TYR138 3.9 36.4 1.0 OG D:SER68 4.0 33.3 1.0 CE1 D:TYR138 4.0 36.0 1.0 CB D:THR54 4.0 38.2 1.0 CG2 D:THR54 4.1 37.4 1.0 CE2 D:TYR52 4.1 35.2 1.0 C9 D:DBH180 4.1 38.0 1.0 OH D:TYR52 4.5 36.6 1.0 CZ D:PHE123 4.5 39.1 1.0 CG2 D:THR136 4.6 39.8 1.0 CG2 D:VAL33 4.7 36.3 1.0 NZ D:LYS134 4.8 35.2 1.0 CZ D:TYR52 4.8 36.0 1.0 O6 D:DBH180 4.9 40.8 1.0 C12 D:DBH180 4.9 37.3 1.0

C.Correnti, V.Richardson, A.K.Sia, A.D.Bandaranayake, M.Ruiz, Y.Suryo Rahmanto, Z.Kovacevic, M.C.Clifton, M.A.Holmes, B.K.Kaiser, J.Barasch, K.N.Raymond, D.R.Richardson, R.K.Strong. Siderocalin/LCN2/Ngal/24P3 Does Not Drive Apoptosis Through Gentisic Acid Mediated Iron Withdrawal in Hematopoietic Cell Lines. Plos One V. 7 43696 2012.
ISSN: ESSN 1932-6203
PubMed: 22928018
DOI: 10.1371/JOURNAL.PONE.0043696