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Iron in PDB 4k19: The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin

Protein crystallography data

The structure of The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin, PDB code: 4k19 was solved by C.Correnti, M.C.Clifton, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.95 / 2.74
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.200, 114.200, 119.300, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 29.4

Other elements in 4k19:

The structure of The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin (pdb code 4k19). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin, PDB code: 4k19:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 4k19

Go back to Iron Binding Sites List in 4k19
Iron binding site 1 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin


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 Fluvibactin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:35.5
occ:1.00
O42 A:1OD206 1.7 41.0 1.0
O44 A:1OD206 2.1 31.8 1.0
O28 A:1OD206 2.2 39.0 1.0
O45 A:1OD206 2.3 34.0 1.0
O27 A:1OD206 2.4 32.0 1.0
O41 A:1OD206 2.8 35.6 1.0
C36 A:1OD206 2.8 38.5 1.0
C6 A:1OD206 3.0 31.9 1.0
C25 A:1OD206 3.0 35.8 1.0
C5 A:1OD206 3.1 32.4 1.0
C26 A:1OD206 3.1 34.1 1.0
C37 A:1OD206 3.3 35.2 1.0
OH A:TYR106 3.8 20.9 1.0
C35 A:1OD206 4.1 43.3 1.0
N32 A:1OD206 4.1 55.9 1.0
NZ A:LYS134 4.2 19.2 1.0
NZ A:LYS125 4.2 31.3 1.0
NE1 A:TRP79 4.3 24.5 1.0
C1 A:1OD206 4.3 35.0 1.0
C24 A:1OD206 4.3 35.5 1.0
C4 A:1OD206 4.4 35.1 1.0
CE2 A:TYR106 4.4 24.1 1.0
C21 A:1OD206 4.5 37.1 1.0
C33 A:1OD206 4.5 51.7 1.0
CE A:LYS134 4.6 18.9 1.0
CZ A:TYR106 4.6 23.9 1.0
C38 A:1OD206 4.6 32.6 1.0
N11 A:1OD206 4.7 42.6 1.0
C29 A:1OD206 4.8 54.9 1.0
CE A:LYS125 4.8 30.7 1.0
CD A:LYS125 4.9 30.4 1.0
O2 A:SO4203 4.9 73.9 1.0

Iron binding site 2 out of 3 in 4k19

Go back to Iron Binding Sites List in 4k19
Iron binding site 2 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin


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 Fluvibactin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:73.2
occ:1.00
O28 B:1OD202 2.0 73.3 1.0
O27 B:1OD202 2.1 71.5 1.0
O42 B:1OD202 2.1 61.7 1.0
O41 B:1OD202 2.4 57.0 1.0
O44 B:1OD202 2.4 88.6 1.0
O45 B:1OD202 2.4 86.9 1.0
C25 B:1OD202 2.7 73.4 1.0
C26 B:1OD202 2.8 73.2 1.0
C36 B:1OD202 3.0 62.5 1.0
C37 B:1OD202 3.1 61.0 1.0
C6 B:1OD202 3.2 87.9 1.0
C5 B:1OD202 3.3 87.5 1.0
NZ B:LYS134 3.9 61.6 1.0
C24 B:1OD202 4.1 74.2 1.0
OH B:TYR106 4.1 57.2 1.0
C21 B:1OD202 4.2 75.1 1.0
C35 B:1OD202 4.3 66.4 1.0
C15 B:1OD202 4.4 84.3 1.0
NE1 B:TRP79 4.4 79.2 1.0
C38 B:1OD202 4.5 61.0 1.0
C1 B:1OD202 4.6 87.8 1.0
C4 B:1OD202 4.6 87.0 1.0
NZ B:LYS125 4.6 55.7 1.0
CE B:LYS134 4.6 61.9 1.0
N32 B:1OD202 4.6 76.7 1.0
N18 B:1OD202 4.7 80.9 1.0
N11 B:1OD202 4.9 89.3 1.0
C19 B:1OD202 4.9 78.1 1.0
CE2 B:TYR106 5.0 55.6 1.0
CD1 B:TRP79 5.0 78.6 1.0
N14 B:1OD202 5.0 85.3 1.0

Iron binding site 3 out of 3 in 4k19

Go back to Iron Binding Sites List in 4k19
Iron binding site 3 out of 3 in the The Structure of Human Siderocalin Bound to the Bacterial Siderophore Fluvibactin


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 Fluvibactin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:33.8
occ:1.00
O42 C:1OD207 1.7 22.9 1.0
O44 C:1OD207 1.9 27.4 1.0
O28 C:1OD207 1.9 40.0 1.0
O27 C:1OD207 2.1 37.1 1.0
O45 C:1OD207 2.2 22.4 1.0
O41 C:1OD207 2.5 29.0 1.0
C25 C:1OD207 2.7 39.0 1.0
C36 C:1OD207 2.8 25.7 1.0
C26 C:1OD207 2.8 39.5 1.0
C6 C:1OD207 2.8 28.2 1.0
C5 C:1OD207 2.9 23.2 1.0
C37 C:1OD207 3.1 26.5 1.0
OH C:TYR106 4.0 13.0 1.0
NE1 C:TRP79 4.0 28.8 1.0
C29 C:1OD207 4.0 50.7 1.0
C35 C:1OD207 4.0 31.1 1.0
NZ C:LYS125 4.1 24.2 1.0
C24 C:1OD207 4.1 38.7 1.0
N32 C:1OD207 4.1 50.4 1.0
C1 C:1OD207 4.2 31.8 1.0
C21 C:1OD207 4.2 40.9 1.0
NZ C:LYS134 4.2 18.0 1.0
C4 C:1OD207 4.3 24.1 1.0
N11 C:1OD207 4.4 40.2 1.0
C38 C:1OD207 4.5 23.5 1.0
C33 C:1OD207 4.5 41.5 1.0
CE C:LYS134 4.6 15.5 1.0
C30 C:1OD207 4.6 51.5 1.0
CD1 C:TRP79 4.7 28.7 1.0
CE2 C:TYR106 4.7 13.3 1.0
C7 C:1OD207 4.8 36.2 1.0
CZ C:TYR106 4.9 11.4 1.0
CE2 C:TRP79 4.9 30.2 1.0
N18 C:1OD207 4.9 45.8 1.0
C31 C:1OD207 5.0 51.0 1.0
C19 C:1OD207 5.0 44.3 1.0

Reference:

B.E.Allred, C.Correnti, M.C.Clifton, R.K.Strong, K.N.Raymond. Siderocalin Outwits the Coordination Chemistry of Vibriobactin, A Siderophore of Vibrio Cholerae. Acs Chem.Biol. V. 8 1882 2013.
ISSN: ISSN 1554-8929
PubMed: 23755875
DOI: 10.1021/CB4002552
Page generated: Sun Dec 13 15:38:59 2020

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