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Ruthenium in PDB 5x5p: Human Serum Transferrin Bound to Ruthenium Nta

Protein crystallography data

The structure of Human Serum Transferrin Bound to Ruthenium Nta, PDB code: 5x5p was solved by H.Sun, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 136.748, 158.395, 106.610, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.9

Other elements in 5x5p:

The structure of Human Serum Transferrin Bound to Ruthenium Nta also contains other interesting chemical elements:

Iron (Fe) 1 atom
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Human Serum Transferrin Bound to Ruthenium Nta (pdb code 5x5p). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the Human Serum Transferrin Bound to Ruthenium Nta, PDB code: 5x5p:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 5x5p

Go back to Ruthenium Binding Sites List in 5x5p
Ruthenium binding site 1 out of 4 in the Human Serum Transferrin Bound to Ruthenium Nta


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Human Serum Transferrin Bound to Ruthenium Nta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru703

b:80.3
occ:0.70
O8 A:NTA707 1.8 64.0 0.7
NE2 A:HIS14 2.1 45.5 1.0
N1 A:NTA707 2.2 73.5 0.7
O A:HOH803 2.2 55.5 0.7
C2 A:NTA707 2.2 68.0 0.7
C7 A:NTA707 2.3 71.6 0.7
O4 A:NTA707 2.4 65.6 0.7
C3 A:NTA707 2.5 66.1 0.7
C6 A:NTA707 2.6 78.3 0.7
CE1 A:HIS14 2.9 35.9 1.0
CD2 A:HIS14 3.3 31.6 1.0
O9 A:NTA707 3.4 67.2 0.7
C10 A:NTA707 3.6 75.0 0.7
O5 A:NTA707 3.6 52.6 0.7
ND1 A:HIS14 4.1 28.3 1.0
CG A:HIS14 4.3 24.1 1.0
O12 A:NTA707 4.5 72.3 0.7
C11 A:NTA707 4.5 77.8 0.7

Ruthenium binding site 2 out of 4 in 5x5p

Go back to Ruthenium Binding Sites List in 5x5p
Ruthenium binding site 2 out of 4 in the Human Serum Transferrin Bound to Ruthenium Nta


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Human Serum Transferrin Bound to Ruthenium Nta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru704

b:80.4
occ:0.60
O9 A:NTA708 1.8 55.7 0.6
N1 A:NTA708 1.8 74.4 0.6
NE2 A:HIS578 1.8 0.2 1.0
O5 A:NTA708 2.2 46.3 0.6
C2 A:NTA708 2.3 64.7 0.6
C7 A:NTA708 2.4 67.1 0.6
O13 A:NTA708 2.5 69.9 0.6
C6 A:NTA708 2.5 71.1 0.6
C3 A:NTA708 2.6 56.5 0.6
CE1 A:HIS578 2.6 0.7 1.0
CD2 A:HIS578 2.9 0.2 1.0
C10 A:NTA708 2.9 69.7 0.6
C11 A:NTA708 3.1 70.2 0.6
O8 A:NTA708 3.6 64.2 0.6
ND1 A:HIS578 3.7 0.4 1.0
O4 A:NTA708 3.7 52.0 0.6
CG A:HIS578 3.9 0.9 1.0
O12 A:NTA708 4.3 64.2 0.6
CG A:ARG581 4.5 100.0 1.0
CD A:ARG581 4.9 0.8 1.0

Ruthenium binding site 3 out of 4 in 5x5p

Go back to Ruthenium Binding Sites List in 5x5p
Ruthenium binding site 3 out of 4 in the Human Serum Transferrin Bound to Ruthenium Nta


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Human Serum Transferrin Bound to Ruthenium Nta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru705

b:82.8
occ:0.50
O A:HOH809 2.3 35.2 0.5
NE2 A:HIS273 2.3 97.3 1.0
O A:HOH804 2.4 54.8 1.0
CE1 A:HIS273 3.2 77.1 1.0
CD2 A:HIS273 3.3 83.9 1.0
O A:HOH808 4.3 28.4 0.5
ND1 A:HIS273 4.3 68.2 1.0
CG A:HIS273 4.4 65.3 1.0

Ruthenium binding site 4 out of 4 in 5x5p

Go back to Ruthenium Binding Sites List in 5x5p
Ruthenium binding site 4 out of 4 in the Human Serum Transferrin Bound to Ruthenium Nta


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Human Serum Transferrin Bound to Ruthenium Nta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru706

b:69.5
occ:0.33
NE2 A:HIS289 2.4 0.2 1.0
CD2 A:HIS289 2.8 0.1 1.0
CE1 A:HIS289 3.7 0.0 1.0
CG A:HIS289 4.1 95.7 1.0
ND1 A:HIS289 4.5 0.2 1.0

Reference:

H.Sun, M.Wang, Q.Hao. The Additional Metal-Binding Site on Human Serum Transferrin Surface To Be Published.
Page generated: Wed Dec 16 02:08:44 2020

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