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Gallium in PDB 6gr0: Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin

Protein crystallography data

The structure of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin, PDB code: 6gr0 was solved by A.Skerra, A.Eichinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.75 / 2.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 95.336, 112.170, 124.849, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.9

Gallium Binding Sites:

The binding sites of Gallium atom in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin (pdb code 6gr0). This binding sites where shown within 5.0 Angstroms radius around Gallium atom.
In total 7 binding sites of Gallium where determined in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin, PDB code: 6gr0:
Jump to Gallium binding site number: 1; 2; 3; 4; 5; 6; 7;

Gallium binding site 1 out of 7 in 6gr0

Go back to Gallium Binding Sites List in 6gr0
Gallium binding site 1 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 1 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ga202

b:34.1
occ:1.00
OBX A:F8W201 1.8 28.9 1.0
OBY A:F8W201 1.8 42.0 1.0
CBW A:F8W201 1.9 39.9 1.0
OBV A:F8W201 2.1 29.2 1.0
OAH A:F8W201 2.1 28.3 1.0
OBU A:F8W201 2.2 28.1 1.0
OAG A:F8W201 2.2 29.9 1.0
CAE A:F8W201 3.0 32.2 1.0
CBR A:F8W201 3.0 31.1 1.0
CBS A:F8W201 3.0 33.5 1.0
CAF A:F8W201 3.0 35.2 1.0
CAW A:F8W201 3.3 40.9 1.0
O A:HOH337 3.7 20.3 1.0
CAV A:F8W201 3.8 35.0 1.0
OAY A:F8W201 3.9 34.4 1.0
NZ A:LYS81 4.0 32.2 1.0
NBB A:F8W201 4.1 38.2 1.0
NAT A:F8W201 4.3 33.2 1.0
CAZ A:F8W201 4.3 41.2 1.0
CAD A:F8W201 4.3 33.3 1.0
O A:HOH315 4.3 33.0 1.0
NH2 A:ARG100 4.3 38.6 1.0
CBQ A:F8W201 4.3 30.3 1.0
CBT A:F8W201 4.3 36.6 1.0
CAA A:F8W201 4.4 32.1 1.0
O A:HOH331 4.4 24.0 1.0
CAU A:F8W201 4.5 34.9 1.0
OH A:TYR106 4.6 29.9 1.0
O A:HOH342 4.6 35.1 1.0
CBA A:F8W201 4.6 41.7 1.0
CE A:LYS81 4.6 32.5 1.0
CD A:LYS81 4.7 31.8 1.0
ND2 A:ASN68 4.7 27.2 1.0

Gallium binding site 2 out of 7 in 6gr0

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Gallium binding site 2 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 2 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ga202

b:26.4
occ:1.00
OBX B:F8W201 1.7 33.0 1.0
CBW B:F8W201 1.9 35.0 1.0
OBY B:F8W201 2.0 26.8 1.0
OAH B:F8W201 2.1 21.5 1.0
OBV B:F8W201 2.1 24.8 1.0
OBU B:F8W201 2.1 21.5 1.0
OAG B:F8W201 2.2 20.1 1.0
CAE B:F8W201 2.9 21.3 1.0
CAF B:F8W201 2.9 23.6 1.0
CBS B:F8W201 2.9 24.8 1.0
CBR B:F8W201 2.9 23.5 1.0
CAW B:F8W201 3.4 33.9 1.0
O B:HOH339 3.7 21.1 1.0
CAV B:F8W201 3.9 31.9 1.0
OAY B:F8W201 3.9 24.5 1.0
NZ B:LYS81 4.0 22.1 1.0
NBB B:F8W201 4.0 31.4 1.0
NAT B:F8W201 4.2 31.5 1.0
O B:HOH328 4.2 29.1 1.0
CAD B:F8W201 4.2 23.6 1.0
CAZ B:F8W201 4.2 31.6 1.0
CAA B:F8W201 4.3 23.0 1.0
O B:HOH334 4.3 30.5 1.0
CBT B:F8W201 4.3 25.5 1.0
CBQ B:F8W201 4.3 22.1 1.0
NH2 B:ARG100 4.4 24.8 1.0
CAU B:F8W201 4.4 32.3 1.0
OH B:TYR106 4.6 22.0 1.0
ND2 B:ASN68 4.6 24.1 1.0
CBA B:F8W201 4.6 31.9 1.0
CE B:LYS81 4.7 24.1 1.0
CD B:LYS81 4.8 24.1 1.0

Gallium binding site 3 out of 7 in 6gr0

Go back to Gallium Binding Sites List in 6gr0
Gallium binding site 3 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 3 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ga205

b:38.0
occ:1.00
OE1 B:GLU143 2.1 40.0 1.0
OAY B:F8W203 2.3 38.9 1.0
O A:HOH301 2.3 47.7 1.0
OBX B:F8W203 2.5 33.4 1.0
GA B:GA206 3.0 34.0 1.0
CD B:GLU143 3.0 36.1 1.0
CBW B:F8W203 3.2 41.8 1.0
CAW B:F8W203 3.2 39.3 1.0
OE2 B:GLU143 3.3 37.2 1.0
NZ A:LYS75 3.7 39.7 1.0
O B:HOH327 3.7 36.2 1.0
NBB B:F8W203 3.9 41.4 1.0
CAV B:F8W203 4.1 38.3 1.0
CE A:LYS75 4.3 39.3 1.0
O A:CYS76 4.4 33.2 1.0
CAZ B:F8W203 4.4 38.7 1.0
CG B:GLU143 4.4 36.3 1.0
OBY B:F8W203 4.4 53.2 1.0
N A:TYR78 4.5 29.8 1.0
CD1 A:TYR78 4.5 33.1 1.0
OAX B:F8W203 4.6 44.0 1.0
OAG B:F8W204 4.6 50.5 1.0
CBA B:F8W203 4.6 41.4 1.0
CBC B:F8W203 4.7 45.1 1.0
CBE B:F8W203 4.8 48.9 1.0
CA A:THR77 4.8 28.4 1.0
CB A:TYR78 4.9 30.2 1.0
CAU B:F8W203 4.9 38.2 1.0
CB B:GLU143 4.9 35.4 1.0

Gallium binding site 4 out of 7 in 6gr0

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Gallium binding site 4 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 4 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ga206

b:34.0
occ:1.00
OE2 B:GLU143 2.0 37.2 1.0
OAX B:F8W203 2.3 44.0 1.0
OAY B:F8W203 2.3 38.9 1.0
OAH B:F8W204 2.4 37.1 1.0
OAG B:F8W204 2.4 50.5 1.0
O A:HOH301 2.6 47.7 1.0
CD B:GLU143 3.0 36.1 1.0
GA B:GA205 3.0 38.0 1.0
CAU B:F8W203 3.2 38.2 1.0
CAE B:F8W204 3.2 49.6 1.0
OE1 B:GLU143 3.2 40.0 1.0
CAF B:F8W204 3.3 50.7 1.0
CAW B:F8W203 3.4 39.3 1.0
CAV B:F8W203 3.4 38.3 1.0
NZ A:LYS75 3.8 39.7 1.0
O B:HOH336 4.1 45.5 1.0
CAZ B:F8W203 4.3 38.7 1.0
CG B:GLU143 4.3 36.3 1.0
O A:CYS76 4.4 33.2 1.0
NAT B:F8W203 4.4 38.4 1.0
CBW B:F8W203 4.5 41.8 1.0
CG B:PRO171 4.5 26.3 1.0
OBX B:F8W203 4.5 33.4 1.0
CE A:LYS75 4.6 39.3 1.0
CAD B:F8W204 4.6 55.6 1.0
CAA B:F8W204 4.6 56.7 1.0
CD B:PRO171 4.8 26.9 1.0
CD A:LYS75 4.9 37.7 1.0

Gallium binding site 5 out of 7 in 6gr0

Go back to Gallium Binding Sites List in 6gr0
Gallium binding site 5 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 5 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ga202

b:38.7
occ:1.00
OBX C:F8W201 1.6 51.8 1.0
OBU C:F8W201 2.0 34.5 1.0
OAH C:F8W201 2.1 39.0 1.0
OBV C:F8W201 2.2 36.7 1.0
CBW C:F8W201 2.2 60.1 1.0
OAG C:F8W201 2.2 35.6 1.0
OBY C:F8W201 2.5 47.2 1.0
CBS C:F8W201 2.9 35.0 1.0
CBR C:F8W201 2.9 36.2 1.0
CAE C:F8W201 3.0 41.4 1.0
CAF C:F8W201 3.0 39.1 1.0
CAW C:F8W201 3.6 54.8 1.0
O C:HOH321 3.8 26.2 1.0
NZ C:LYS81 4.0 33.0 1.0
CAV C:F8W201 4.0 51.0 1.0
NBB C:F8W201 4.0 41.6 1.0
CBT C:F8W201 4.2 37.8 1.0
NAT C:F8W201 4.2 52.2 1.0
NH2 C:ARG100 4.3 42.2 1.0
CBQ C:F8W201 4.3 36.9 1.0
CAD C:F8W201 4.3 41.1 1.0
CAZ C:F8W201 4.3 50.9 1.0
CAA C:F8W201 4.3 42.7 1.0
OAY C:F8W201 4.4 59.6 1.0
CAU C:F8W201 4.5 53.0 1.0
CE C:LYS81 4.6 36.0 1.0
OH C:TYR106 4.6 32.9 1.0
CBA C:F8W201 4.6 51.3 1.0
CD C:LYS81 4.7 37.8 1.0
ND2 C:ASN68 4.8 30.0 1.0
CBC C:F8W201 4.9 41.9 1.0

Gallium binding site 6 out of 7 in 6gr0

Go back to Gallium Binding Sites List in 6gr0
Gallium binding site 6 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 6 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ga204

b:25.5
occ:1.00
OAY C:F8W203 2.0 26.5 1.0
OBU B:F8W204 2.1 23.1 1.0
OE2 C:GLU143 2.1 27.6 1.0
OAX C:F8W203 2.2 31.0 1.0
OBV B:F8W204 2.2 27.7 1.0
O B:HOH301 2.3 27.0 1.0
GA C:GA205 2.9 25.1 1.0
CBS B:F8W204 3.0 31.0 1.0
CD C:GLU143 3.0 27.7 1.0
CBR B:F8W204 3.0 27.4 1.0
CAU C:F8W203 3.1 31.7 1.0
OE1 C:GLU143 3.2 28.7 1.0
CAW C:F8W203 3.2 28.7 1.0
CAV C:F8W203 3.4 28.8 1.0
O B:HOH305 3.7 31.6 1.0
NZ B:LYS75 3.8 28.4 1.0
O B:HOH303 3.9 39.4 1.0
CAZ C:F8W203 4.1 30.8 1.0
CBW C:F8W203 4.3 29.9 1.0
OBX C:F8W203 4.3 26.3 1.0
CBT B:F8W204 4.3 27.3 1.0
NAT C:F8W203 4.3 31.4 1.0
CBQ B:F8W204 4.3 25.2 1.0
O B:CYS76 4.4 25.7 1.0
CG C:PRO171 4.4 25.5 1.0
CG C:GLU143 4.4 27.1 1.0
CE B:LYS75 4.5 28.6 1.0
CD C:PRO171 4.6 26.6 1.0
NBB C:F8W203 5.0 33.5 1.0
CAS C:F8W203 5.0 31.4 1.0

Gallium binding site 7 out of 7 in 6gr0

Go back to Gallium Binding Sites List in 6gr0
Gallium binding site 7 out of 7 in the Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin


Mono view


Stereo pair view

A full contact list of Gallium with other atoms in the Ga binding site number 7 of Petrobactin-Binding Engineered Lipocalin in Complex with Gallium- Petrobactin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ga205

b:25.1
occ:1.00
OE1 C:GLU143 2.1 28.7 1.0
OBX C:F8W203 2.2 26.3 1.0
OAY C:F8W203 2.2 26.5 1.0
O B:HOH301 2.2 27.0 1.0
GA C:GA204 2.9 25.5 1.0
CBW C:F8W203 3.0 29.9 1.0
CD C:GLU143 3.1 27.7 1.0
CAW C:F8W203 3.1 28.7 1.0
OE2 C:GLU143 3.3 27.6 1.0
NZ B:LYS75 3.8 28.4 1.0
O B:HOH317 3.9 32.9 1.0
CAV C:F8W203 3.9 28.8 1.0
NBB C:F8W203 3.9 33.5 1.0
OBY C:F8W203 4.2 39.2 1.0
CAZ C:F8W203 4.3 30.8 1.0
OBV B:F8W204 4.3 27.7 1.0
CE B:LYS75 4.4 28.6 1.0
O B:CYS76 4.4 25.7 1.0
N B:TYR78 4.4 25.4 1.0
OAX C:F8W203 4.4 31.0 1.0
CG C:GLU143 4.4 27.1 1.0
CBA C:F8W203 4.5 33.5 1.0
CAU C:F8W203 4.7 31.7 1.0
OBU B:F8W204 4.7 23.1 1.0
CB B:TYR78 4.8 27.3 1.0
CA B:THR77 4.8 22.8 1.0
CBC C:F8W203 4.8 34.1 1.0
CB C:GLU143 4.9 27.2 1.0

Reference:

M.Dauner, A.Eichinger, G.Lucking, S.Scherer, A.Skerra. Reprogramming Human Siderocalin to Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus. Angew. Chem. Int. Ed. Engl. V. 57 14619 2018.
ISSN: ESSN 1521-3773
PubMed: 30063283
DOI: 10.1002/ANIE.201807442
Page generated: Wed Oct 28 18:37:01 2020

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