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Potassium in PDB 5dmj: Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab

Protein crystallography data

The structure of Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab, PDB code: 5dmj was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.26 / 2.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 199.300, 48.700, 138.800, 90.00, 118.20, 90.00
R / Rfree (%) 22.9 / 25.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab (pdb code 5dmj). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab, PDB code: 5dmj:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5dmj

Go back to Potassium Binding Sites List in 5dmj
Potassium binding site 1 out of 3 in the Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:45.5
occ:1.00
 O A:PHE129 2.5 29.8 1.0
OG A:SER152 2.6 38.3 1.0
O A:VAL154 2.7 22.5 1.0
O A:HOH401 2.7 18.3 1.0
O A:CYS125 2.9 40.3 1.0
O A:SER126 3.2 37.1 1.0
O A:ASP153 3.5 37.0 1.0
CB A:SER152 3.5 32.2 1.0
C A:SER126 3.7 34.5 1.0
C A:PHE129 3.7 30.6 1.0
C A:CYS125 3.8 37.9 1.0
C A:VAL154 3.9 26.4 1.0
CA A:PRO127 4.1 27.4 1.0
N A:PRO127 4.1 27.9 1.0
N A:SER156 4.3 24.8 1.0
N A:PHE129 4.4 27.6 1.0
N A:SER126 4.5 32.3 1.0
CA A:SER155 4.5 25.2 1.0
CA A:SER126 4.5 30.9 1.0
CB A:CYS125 4.5 34.9 1.0
C A:SER152 4.5 32.2 1.0
O A:SER152 4.5 30.4 1.0
CG2 A:VAL154 4.6 30.5 1.0
CA A:PHE129 4.6 27.2 1.0
CA A:SER152 4.6 29.2 1.0
N A:SER155 4.6 25.4 1.0
C A:ASP153 4.6 35.3 1.0
N A:GLY128 4.7 28.9 1.0
N A:GLY130 4.7 26.6 1.0
C A:SER155 4.7 28.1 1.0
CA A:CYS125 4.8 33.6 1.0
C A:PRO127 4.8 32.7 1.0
CA A:GLY130 4.8 27.5 1.0
CB A:SER156 4.8 24.6 1.0
O A:GLU159 4.9 28.8 1.0
O A:SER156 4.9 27.8 1.0
CA A:VAL154 5.0 27.8 1.0

Potassium binding site 2 out of 3 in 5dmj

Go back to Potassium Binding Sites List in 5dmj
Potassium binding site 2 out of 3 in the Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:43.2
occ:1.00
 O D:PHE129 2.4 48.5 1.0
O D:HOH403 2.5 14.2 1.0
O D:CYS125 2.6 47.1 1.0
O D:VAL154 2.7 41.0 1.0
O D:SER126 3.1 50.9 1.0
C D:CYS125 3.4 47.9 1.0
OG D:SER152 3.5 60.7 1.0
C D:PHE129 3.5 47.9 1.0
C D:SER126 3.5 52.3 1.0
CB D:SER152 3.6 50.8 1.0
C D:VAL154 3.8 41.2 1.0
CB D:CYS125 4.0 45.0 1.0
N D:PRO127 4.1 50.0 1.0
N D:SER126 4.1 46.1 1.0
N D:SER156 4.2 29.7 1.0
CA D:SER126 4.2 47.0 1.0
CA D:PRO127 4.2 50.4 1.0
CA D:CYS125 4.3 43.8 1.0
CA D:SER155 4.3 32.0 1.0
CB D:PHE129 4.4 52.9 1.0
N D:GLY130 4.4 38.3 1.0
N D:SER155 4.5 34.0 1.0
CA D:PHE129 4.5 50.5 1.0
N D:GLY128 4.5 53.9 1.0
CA D:GLY130 4.6 37.5 1.0
CG2 D:VAL154 4.6 41.6 1.0
C D:SER155 4.7 34.8 1.0
O D:SER156 4.8 27.1 1.0
CA D:VAL154 4.8 40.0 1.0
C D:PRO127 4.9 56.7 1.0
N D:VAL154 4.9 42.6 1.0
CA D:SER152 4.9 46.8 1.0
O D:GLU159 4.9 48.6 1.0
C D:SER152 5.0 51.7 1.0

Potassium binding site 3 out of 3 in 5dmj

Go back to Potassium Binding Sites List in 5dmj
Potassium binding site 3 out of 3 in the Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Extracellular Domain of the CD40 in Complex with 3H56-5 Dab within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K301

b:63.4
occ:1.00
 O F:PHE129 2.4 65.8 1.0
O F:VAL154 2.7 59.9 1.0
OG F:SER152 2.7 73.8 1.0
O F:CYS125 2.8 63.6 1.0
O F:SER126 3.0 65.2 1.0
CB F:SER152 3.4 63.9 1.0
C F:SER126 3.5 66.3 1.0
C F:CYS125 3.5 64.6 1.0
C F:PHE129 3.6 65.9 1.0
C F:VAL154 3.9 58.7 1.0
N F:PRO127 3.9 63.8 1.0
CB F:CYS125 4.0 64.5 1.0
CA F:PRO127 4.0 63.5 1.0
N F:SER126 4.1 61.8 1.0
CA F:SER126 4.2 61.8 1.0
N F:GLY128 4.3 63.6 1.0
N F:SER156 4.4 52.7 1.0
CA F:CYS125 4.4 62.0 1.0
CB F:PHE129 4.5 64.5 1.0
CA F:SER155 4.5 51.7 1.0
N F:GLY130 4.5 61.1 1.0
CA F:PHE129 4.6 62.5 1.0
CA F:SER152 4.6 60.8 1.0
N F:SER155 4.7 53.1 1.0
C F:PRO127 4.7 67.2 1.0
CA F:GLY130 4.7 60.0 1.0
C F:SER152 4.8 62.4 1.0
N F:VAL154 4.8 55.5 1.0
C F:SER155 4.8 56.4 1.0
O F:SER152 4.9 60.9 1.0
CA F:VAL154 5.0 54.0 1.0
O F:SER156 5.0 58.7 1.0
CB F:SER156 5.0 56.4 1.0
SG F:CYS125 5.0 69.6 1.0

Reference:

A.P.Yamniuk, A.Suri, S.R.Krystek, J.Tamura, V.Ramamurthy, R.Kuhn, K.Carroll, C.Fleener, R.Ryseck, L.Cheng, Y.An, P.Drew, S.Grant, S.J.Suchard, S.G.Nadler, J.W.Bryson, S.Sheriff. Functional Antagonism of Human CD40 Achieved By Targeting A Unique Species-Specific Epitope. J.Mol.Biol. V. 428 2860 2016.
ISSN: ESSN 1089-8638
PubMed: 27216500
DOI: 10.1016/J.JMB.2016.05.014
Page generated: Mon Aug 12 13:17:14 2024

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