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Sodium in PDB 8vtp: Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor

Protein crystallography data

The structure of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor, PDB code: 8vtp was solved by A.U.Singer, H.A.Bruce, L.Blazer, J.J.Adams, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.79 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.75, 72.938, 129.581, 90, 90, 90
R / Rfree (%) 17.5 / 19.5

Other elements in 8vtp:

The structure of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor (pdb code 8vtp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor, PDB code: 8vtp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8vtp

Go back to Sodium Binding Sites List in 8vtp
Sodium binding site 1 out of 5 in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:45.6
occ:1.00
 O G:HOH556 2.8 42.9 1.0
O G:PRO139 2.8 26.7 1.0
N A:ALA139 3.0 28.7 1.0
O A:PRO137 3.2 26.2 1.0
CA A:LEU138 3.6 25.0 1.0
C A:LEU138 3.8 24.5 1.0
CB A:ALA139 3.9 33.3 1.0
C G:PRO139 3.9 28.2 1.0
C A:PRO137 4.0 24.1 1.0
CA A:ALA139 4.0 31.4 1.0
N A:LEU138 4.2 24.3 1.0
CB G:PHE138 4.2 24.1 1.0
CD G:PRO139 4.3 32.4 1.0
N G:PRO139 4.3 25.7 1.0
O A:HOH588 4.4 43.9 1.0
O G:HOH461 4.5 25.8 1.0
O A:HOH407 4.5 48.2 1.0
N G:SER141 4.5 26.5 1.0
O A:HOH603 4.5 45.9 1.0
C G:PRO140 4.5 26.8 1.0
O A:HOH540 4.5 30.5 1.0
C G:PHE138 4.6 25.5 1.0
O A:HOH409 4.6 43.2 1.0
O A:ALA139 4.6 31.8 1.0
CD2 A:LEU138 4.6 24.1 1.0
CA G:PRO139 4.7 26.1 1.0
CD1 G:PHE138 4.7 26.0 1.0
CA G:PHE138 4.7 26.6 1.0
CB A:LEU138 4.8 24.8 1.0
O G:PRO140 4.8 28.9 1.0
CA G:SER141 4.9 29.0 1.0
C A:ALA139 4.9 31.2 1.0
N G:PRO140 4.9 25.2 1.0
CG G:PHE138 4.9 24.9 1.0
CA G:PRO140 5.0 25.2 1.0
O A:LEU138 5.0 25.8 1.0

Sodium binding site 2 out of 5 in 8vtp

Go back to Sodium Binding Sites List in 8vtp
Sodium binding site 2 out of 5 in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:40.8
occ:1.00
 O A:HOH475 2.7 32.1 1.0
OE1 A:GLN44 2.8 30.6 1.0
OH A:TYR103 3.1 33.7 1.0
O A:HOH508 3.1 48.7 1.0
CB A:VAL101 3.4 26.2 1.0
CD A:GLN44 3.6 35.2 1.0
CG2 A:VAL101 3.6 26.4 1.0
O2 G:EDO305 3.6 40.5 1.0
CB A:GLN44 3.7 25.9 1.0
C2 G:EDO305 3.7 43.5 1.0
CG1 A:VAL101 3.8 27.1 1.0
CG A:GLN44 3.8 27.3 1.0
CZ A:TYR103 3.9 35.6 1.0
CE2 A:TYR103 3.9 28.7 1.0
O G:HOH545 4.2 54.3 1.0
O A:GLN44 4.3 25.9 1.0
O A:HOH447 4.4 43.2 1.0
NE2 G:GLN44 4.6 30.2 1.0
NE2 A:GLN44 4.7 30.5 1.0
O A:HOH597 4.8 49.3 1.0
CA A:VAL101 4.8 22.9 1.0
C1 G:EDO305 4.8 50.4 1.0
CA A:GLN44 4.9 23.8 1.0
O1 G:EDO305 4.9 51.3 1.0
C A:GLN44 4.9 26.2 1.0
O A:HOH470 5.0 37.8 1.0

Sodium binding site 3 out of 5 in 8vtp

Go back to Sodium Binding Sites List in 8vtp
Sodium binding site 3 out of 5 in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:62.5
occ:1.00
 O A:HOH405 2.1 37.3 1.0
O A:HOH531 2.3 38.6 1.0
O A:HOH425 2.3 39.6 1.0
O A:HOH430 2.6 43.2 1.0
O A:HOH574 3.8 55.0 1.0
O A:HOH551 3.9 50.1 1.0
O A:VAL164 3.9 33.9 1.0
OE1 A:GLU162 4.0 34.5 1.0
OE2 A:GLU162 4.1 36.4 1.0
CD2 A:LEU192 4.3 29.4 1.0
CD A:GLU162 4.5 43.9 1.0
N A:ALA182 4.8 26.3 1.0
CB A:PRO163 4.9 30.1 1.0
O A:PHE180 5.0 24.9 1.0
N A:VAL164 5.0 28.8 1.0

Sodium binding site 4 out of 5 in 8vtp

Go back to Sodium Binding Sites List in 8vtp
Sodium binding site 4 out of 5 in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na313

b:56.5
occ:1.00
 C1 A:EDO303 2.7 41.0 1.0
O1 A:EDO303 2.9 53.3 1.0
OG1 A:THR207 3.0 43.2 1.0
NZ A:LYS224 3.4 49.6 1.0
CE A:LYS224 3.9 47.6 1.0
CA A:THR207 3.9 32.6 1.0
N A:THR207 3.9 37.5 1.0
C A:GLN206 4.0 41.2 1.0
O A:GLY204 4.0 54.3 1.0
CB A:THR207 4.1 37.7 1.0
O A:GLN206 4.1 39.5 1.0
C2 A:EDO303 4.2 53.0 1.0
C A:THR205 4.4 48.1 1.0
C A:GLY204 4.4 52.9 1.0
N A:GLN206 4.5 38.6 1.0
CA A:THR205 4.6 47.2 1.0
O A:HOH442 4.6 31.1 1.0
N A:THR205 4.7 43.7 1.0
O A:THR205 4.7 60.6 1.0
O2 A:EDO303 4.8 37.8 1.0
CA A:GLN206 4.8 39.9 1.0
CG2 A:THR207 4.9 41.1 1.0

Sodium binding site 5 out of 5 in 8vtp

Go back to Sodium Binding Sites List in 8vtp
Sodium binding site 5 out of 5 in the Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of FABS1CE-Epr-1, A High Affinity Antibody For the Erythropoeitin Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na317

b:63.0
occ:1.00
 O G:SER9 3.2 40.2 1.0
O G:HOH511 3.8 36.4 0.5
O G:GLY121 3.8 39.0 1.0
O G:HOH511 4.0 38.5 0.5
C G:GLY121 4.1 38.9 1.0
C G:SER9 4.2 48.5 1.0
N G:LYS123 4.2 38.9 1.0
O G:HOH483 4.2 46.4 1.0
O G:GLN120 4.3 36.7 1.0
N G:THR122 4.5 37.1 1.0
CB G:LYS123 4.6 37.9 1.0
CA G:SER9 4.6 44.3 1.0
CA G:THR122 4.6 36.3 1.0
CB G:SER9 4.6 44.9 1.0
CA G:GLY121 4.7 32.9 1.0
C G:THR122 4.7 40.5 1.0

Reference:

H.A.Bruce, A.U.Singer, L.L.Blazer, K.Luu, L.Ploder, A.Pavlenco, I.Kurinov, J.J.Adams, S.S.Sidhu. Antigen-Binding Fragments with Improved Crystal Lattice Packing and Enhanced Conformational Flexibility at the Elbow Region As Crystallization Chaperones. Protein Sci. V. 33 E5081 2024.
ISSN: ESSN 1469-896X
PubMed: 38924648
DOI: 10.1002/PRO.5081
Page generated: Wed Oct 9 14:11:35 2024

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