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

Protein crystallography data

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

Other elements in 3u0d:

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

Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore 2,3-Dhba, PDB code: 3u0d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3u0d

Go back to Iron Binding Sites List in 3u0d
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe179

b:33.8
occ:1.00
O3 A:DBH181 1.7 34.0 1.0
O9 A:DBH181 2.1 28.9 1.0
O6 A:DBH180 2.1 38.6 1.0
O6 A:DBH182 2.1 29.1 1.0
O3 A:DBH180 2.2 37.2 1.0
O3 A:DBH182 2.3 30.4 1.0
C3 A:DBH181 2.8 32.9 1.0
C6 A:DBH180 2.9 39.4 1.0
C3 A:DBH180 2.9 38.7 1.0
C6 A:DBH182 2.9 30.4 1.0
C3 A:DBH182 3.0 30.0 1.0
C21 A:DBH181 3.0 33.0 1.0
C18 A:DBH181 3.3 32.0 1.0
OH A:TYR106 3.9 28.0 1.0
NZ A:LYS134 4.1 27.3 1.0
C6 A:DBH181 4.1 33.5 1.0
O17 A:DBH181 4.2 34.0 1.0
C9 A:DBH180 4.2 40.5 1.0
NZ A:LYS125 4.3 33.2 1.0
C9 A:DBH182 4.3 32.7 1.0
C18 A:DBH180 4.3 41.2 1.0
NE1 A:TRP79 4.4 34.5 1.0
C18 A:DBH182 4.4 29.3 1.0
O6 A:DBH181 4.5 35.5 1.0
CE A:LYS134 4.5 26.9 1.0
CE2 A:TYR106 4.7 29.2 1.0
O9 A:DBH180 4.7 40.5 1.0
O9 A:DBH182 4.7 34.3 1.0
C15 A:DBH181 4.7 32.3 1.0
CZ A:TYR106 4.8 29.1 1.0

Iron binding site 2 out of 4 in 3u0d

Go back to Iron Binding Sites List in 3u0d
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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:Fe179

b:31.9
occ:1.00
O3 B:DBH180 2.0 30.6 1.0
O3 B:DBH182 2.0 28.9 1.0
O9 B:DBH180 2.0 33.8 1.0
O6 B:DBH181 2.1 34.6 1.0
O3 B:DBH181 2.2 31.2 1.0
O6 B:DBH182 2.2 24.6 1.0
C3 B:DBH182 2.9 24.7 1.0
C3 B:DBH181 2.9 32.3 1.0
C6 B:DBH181 2.9 35.0 1.0
C3 B:DBH180 3.0 31.8 1.0
C21 B:DBH180 3.0 37.7 1.0
C6 B:DBH182 3.0 24.9 1.0
C18 B:DBH180 3.3 36.4 1.0
O B:HOH214 3.8 24.1 1.0
OH B:TYR106 3.9 23.8 1.0
NZ B:LYS134 4.0 22.9 1.0
O17 B:DBH180 4.1 38.7 1.0
C18 B:DBH182 4.3 24.5 1.0
C6 B:DBH180 4.3 32.5 1.0
C9 B:DBH181 4.3 32.7 1.0
C9 B:DBH182 4.4 24.9 1.0
C18 B:DBH181 4.4 34.2 1.0
O B:HOH217 4.4 49.5 1.0
NE1 B:TRP79 4.4 32.8 1.0
O9 B:DBH182 4.5 23.0 1.0
O9 B:DBH181 4.5 35.8 1.0
O6 B:DBH180 4.6 33.5 1.0
CE B:LYS134 4.7 23.6 1.0
C15 B:DBH180 4.7 35.8 1.0
NZ B:LYS125 4.8 31.1 1.0
CE2 B:TYR106 4.8 24.7 1.0
CZ B:TYR106 4.9 23.9 1.0
C21 B:DBH182 4.9 26.2 1.0

Iron binding site 3 out of 4 in 3u0d

Go back to Iron Binding Sites List in 3u0d
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe 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
C:Fe179

b:38.2
occ:1.00
O3 C:DBH181 1.8 38.1 1.0
O3 C:DBH180 1.9 39.5 1.0
O6 C:DBH182 2.1 35.7 1.0
O9 C:DBH181 2.2 39.4 1.0
O3 C:DBH182 2.2 38.2 1.0
O6 C:DBH180 2.5 35.7 1.0
C3 C:DBH181 2.8 38.8 1.0
C6 C:DBH182 2.9 34.5 1.0
C3 C:DBH182 2.9 35.9 1.0
C3 C:DBH180 2.9 37.2 1.0
C21 C:DBH181 3.0 39.3 1.0
C6 C:DBH180 3.1 36.1 1.0
C18 C:DBH181 3.3 38.4 1.0
O C:HOH202 3.5 32.9 1.0
OH C:TYR106 3.9 37.7 1.0
NZ C:LYS134 4.0 33.2 1.0
C6 C:DBH181 4.1 39.4 1.0
O17 C:DBH181 4.2 41.8 1.0
C9 C:DBH182 4.2 36.0 1.0
C18 C:DBH180 4.3 39.5 1.0
C18 C:DBH182 4.3 34.2 1.0
O9 C:DBH180 4.5 51.0 1.0
O6 C:DBH181 4.5 40.1 1.0
NE1 C:TRP79 4.5 44.6 1.0
C9 C:DBH180 4.5 37.4 1.0
NZ C:LYS125 4.5 45.2 1.0
CE C:LYS134 4.6 34.6 1.0
O9 C:DBH182 4.6 34.7 1.0
O C:HOH191 4.6 45.9 1.0
CE2 C:TYR106 4.6 39.9 1.0
C15 C:DBH181 4.7 39.4 1.0
CZ C:TYR106 4.7 38.9 1.0
C21 C:DBH180 4.9 43.9 1.0

Iron binding site 4 out of 4 in 3u0d

Go back to Iron Binding Sites List in 3u0d
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe binding site number 4 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:Fe179

b:35.0
occ:1.00
O9 D:DBH181 1.9 42.1 1.0
O3 D:DBH182 2.0 28.1 1.0
O3 D:DBH181 2.1 44.5 1.0
O3 D:DBH180 2.2 40.5 1.0
O6 D:DBH182 2.3 29.2 1.0
O6 D:DBH180 2.3 40.8 1.0
C3 D:DBH182 2.9 29.4 1.0
C21 D:DBH181 2.9 43.5 1.0
C6 D:DBH182 3.0 28.3 1.0
C3 D:DBH181 3.0 44.3 1.0
C3 D:DBH180 3.0 40.5 1.0
C6 D:DBH180 3.1 37.8 1.0
C18 D:DBH181 3.3 43.1 1.0
NZ D:LYS134 3.9 35.2 1.0
O D:HOH197 4.0 55.7 1.0
O17 D:DBH181 4.1 38.9 1.0
OH D:TYR106 4.2 41.5 1.0
C18 D:DBH182 4.3 30.8 1.0
C6 D:DBH181 4.3 48.9 1.0
O9 D:DBH182 4.3 35.2 1.0
C9 D:DBH182 4.4 28.3 1.0
C18 D:DBH180 4.5 38.6 1.0
C9 D:DBH180 4.5 38.0 1.0
NE1 D:TRP79 4.6 45.3 1.0
CE D:LYS134 4.6 36.6 1.0
O9 D:DBH180 4.6 42.7 1.0
C15 D:DBH181 4.7 47.3 1.0
O6 D:DBH181 4.8 55.2 1.0
C21 D:DBH182 4.9 34.1 1.0
CE2 D:TYR106 4.9 43.3 1.0

Reference:

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
Page generated: Sun Dec 13 15:22:47 2020

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