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Praseodymium in PDB 9bif: Fab B11-Ospca Complex

Protein crystallography data

The structure of Fab B11-Ospca Complex, PDB code: 9bif was solved by M.J.Rudolph, N.Mantis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 3.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.737, 97.294, 168.343, 97.6, 90.27, 106.21
R / Rfree (%) 24 / 29.5

Other elements in 9bif:

The structure of Fab B11-Ospca Complex also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Fab B11-Ospca Complex (pdb code 9bif). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 8 binding sites of Praseodymium where determined in the Fab B11-Ospca Complex, PDB code: 9bif:
Jump to Praseodymium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Praseodymium binding site 1 out of 8 in 9bif

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Praseodymium binding site 1 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Pr301

b:89.4
occ:1.00
 O L:HOH404 2.3 50.3 1.0
OD1 L:ASN32 2.4 92.2 1.0
O L:HOH407 2.4 42.7 1.0
CG L:ASN32 3.5 74.8 1.0
O L:ASN31 3.7 82.7 1.0
OD1 L:ASP50 3.7 79.0 1.0
ND2 L:ASN32 4.1 90.9 1.0
OD1 B:ASN193 4.2 77.6 1.0
CG L:ASP50 4.2 89.1 1.0
C L:ASN31 4.3 92.7 1.0
NZ B:LYS196 4.5 81.2 1.0
CB L:ASN31 4.5 72.0 1.0
OD2 L:ASP50 4.6 102.7 1.0
CB L:ASN32 4.7 61.9 1.0
ND2 B:ASN193 4.7 48.9 1.0
CA L:ASN32 4.8 60.1 1.0
N L:ASN32 4.8 78.3 1.0
CG L:ASN31 4.9 87.1 1.0
CG B:ASN193 4.9 58.5 1.0
CB L:ASP50 4.9 54.9 1.0

Praseodymium binding site 2 out of 8 in 9bif

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Praseodymium binding site 2 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pr301

b:109.4
occ:1.00
 O D:HOH405 2.5 30.6 1.0
ND2 D:ASN32 2.6 82.4 1.0
OD1 D:ASP50 2.6 55.9 1.0
O A:HOH403 3.2 51.0 1.0
OE2 A:GLU189 3.2 94.9 1.0
CG D:ASN32 3.3 54.9 1.0
OD1 D:ASN32 3.5 63.3 1.0
O D:ASN31 3.5 76.1 1.0
CD A:GLU189 3.7 104.2 1.0
CG D:ASP50 3.7 62.4 1.0
OE1 A:GLU189 3.8 110.8 1.0
OD2 D:ASP50 4.1 72.5 1.0
OD1 A:ASN193 4.3 70.0 1.0
C D:ASN31 4.5 55.2 1.0
CB D:ASN32 4.7 53.1 1.0
CG A:GLU189 4.7 64.6 1.0
CA D:ASN32 4.8 52.0 1.0
CB D:ASP50 5.0 55.7 1.0

Praseodymium binding site 3 out of 8 in 9bif

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Praseodymium binding site 3 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 3 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Pr301

b:67.1
occ:0.75
 OD1 I:ASP50 2.8 52.8 1.0
OD1 I:ASN32 3.1 92.8 1.0
CG I:ASN32 3.3 83.5 1.0
ND2 I:ASN32 3.5 89.2 1.0
OE1 E:GLU189 3.8 95.0 1.0
O I:HOH411 3.8 26.7 1.0
CG I:ASP50 3.9 70.8 1.0
ND2 I:ASN31 4.0 58.7 1.0
CB I:ASN32 4.1 44.7 1.0
CB I:ASN31 4.3 65.7 1.0
CG I:ASN31 4.3 50.3 1.0
OD2 I:ASP50 4.5 69.6 1.0
CA I:ASN32 4.5 44.0 1.0
C I:ASN31 4.8 60.1 1.0
CD E:GLU189 4.8 99.1 1.0
O I:ASN31 4.8 66.1 1.0
N I:ASN32 4.9 51.0 1.0

Praseodymium binding site 4 out of 8 in 9bif

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Praseodymium binding site 4 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 4 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Pr301

b:82.0
occ:1.00
 O K:HOH403 2.4 33.3 1.0
O J:HOH306 2.5 44.0 1.0
OD1 K:ASP50 2.8 71.8 1.0
ND2 K:ASN32 2.9 69.6 1.0
CG K:ASP50 3.6 74.9 1.0
O K:ASN31 3.7 89.7 1.0
CG K:ASN32 3.9 62.9 1.0
OD2 K:ASP50 3.9 95.0 1.0
OD1 K:ASN32 4.4 65.7 1.0
OD1 F:ASN193 4.4 64.7 1.0
CB K:ASP50 4.9 51.4 1.0
C K:ASN31 4.9 79.4 1.0

Praseodymium binding site 5 out of 8 in 9bif

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Praseodymium binding site 5 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 5 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Pr301

b:164.8
occ:0.83
 OD1 P:ASN32 2.5 105.5 1.0
ND2 P:ASN32 2.6 124.1 1.0
CG P:ASN32 2.8 117.4 1.0
OE2 M:GLU189 3.0 79.0 1.0
OD1 P:ASP50 3.5 94.9 1.0
ND2 M:ASN193 3.6 85.7 1.0
CD M:GLU189 3.8 106.8 1.0
OD1 M:ASN193 4.0 82.0 1.0
CG M:GLU189 4.2 73.4 1.0
CB P:ASN32 4.2 85.1 1.0
CG M:ASN193 4.2 86.9 1.0
CG P:ASP50 4.7 107.9 1.0
OE1 M:GLU189 4.8 124.2 1.0

Praseodymium binding site 6 out of 8 in 9bif

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Praseodymium binding site 6 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 6 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Pr301

b:75.2
occ:1.00
 ND2 R:ASN32 2.7 89.1 1.0
OD1 R:ASP50 3.4 57.0 1.0
OD1 R:ASN31 3.7 73.7 1.0
CG R:ASN32 3.9 55.2 1.0
CG R:ASP50 4.1 63.2 1.0
CG R:ASN31 4.1 53.7 1.0
CB R:ASN31 4.2 47.3 1.0
OD1 R:ASN32 4.4 56.7 1.0
OD1 N:ASN193 4.5 71.9 1.0
OD2 R:ASP50 4.6 86.7 1.0
NZ N:LYS196 4.7 88.3 1.0
O R:ASN31 4.8 33.4 1.0
C R:ASN31 4.8 46.9 1.0
CB R:ASP50 4.9 56.9 1.0
CB R:ASN32 4.9 43.3 1.0
CA R:ASN32 4.9 39.8 1.0

Praseodymium binding site 7 out of 8 in 9bif

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Praseodymium binding site 7 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 7 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Pr301

b:237.8
occ:1.00
 O S:HOH407 2.9 47.3 1.0
OE2 S:GLU189 3.2 79.2 1.0
OD1 V:ASP50 3.3 108.3 1.0
O V:ASN31 3.9 110.3 1.0
CG V:ASN32 4.2 99.6 1.0
CB V:ASN32 4.2 85.1 1.0
OD1 V:ASN32 4.2 103.6 1.0
CG V:ASP50 4.2 119.6 1.0
C V:ASN31 4.3 89.2 1.0
CD S:GLU189 4.4 92.1 1.0
ND2 S:ASN193 4.5 53.0 1.0
CA V:ASN32 4.5 86.4 1.0
CB V:ASN31 4.6 100.8 1.0
ND2 V:ASN32 4.7 99.4 1.0
N V:ASN32 4.7 96.3 1.0
OD2 V:ASP50 4.9 115.6 1.0

Praseodymium binding site 8 out of 8 in 9bif

Go back to Praseodymium Binding Sites List in 9bif
Praseodymium binding site 8 out of 8 in the Fab B11-Ospca Complex


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 8 of Fab B11-Ospca Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Pr301

b:111.8
occ:1.00
 O T:HOH406 2.5 45.0 1.0
ND2 X:ASN32 2.6 66.7 1.0
OD1 X:ASP50 3.0 70.5 1.0
CG X:ASN32 3.2 50.8 1.0
OD1 X:ASN32 3.2 62.0 1.0
O X:ASN31 3.8 30.1 1.0
CG X:ASP50 4.1 34.8 1.0
OE2 T:GLU189 4.1 87.3 1.0
C X:ASN31 4.2 27.3 1.0
OD1 T:ASN193 4.3 75.4 1.0
CB X:ASN32 4.4 38.4 1.0
CB X:ASN31 4.4 66.2 1.0
CA X:ASN32 4.5 45.7 1.0
N X:ASN32 4.6 44.1 1.0
CD T:GLU189 4.6 97.6 1.0
OD2 X:ASP50 4.6 60.0 1.0
CA X:ASN31 4.9 33.4 1.0
OE1 T:GLU189 4.9 101.3 1.0
ND2 T:ASN193 5.0 67.4 1.0

Reference:

M.J.Rudolph, Y.Chen, C.Vorauer, D.J.Vance, C.L.Piazza, G.G.Willsey, K.Mccarthy, B.Muriuki, L.A.Cavacini, M.Guttman, N.J.Mantis. Structure of A Human Monoclonal Antibody in Complex with Outer Surface Protein C of the Lyme Disease Spirochete, Borreliella Burgdorferi. J Immunol. V. 213 1234 2024.
ISSN: ESSN 1550-6606
PubMed: 39240158
DOI: 10.4049/JIMMUNOL.2400247
Page generated: Wed Nov 27 20:44:26 2024

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