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Nickel in PDB 6xte: Human Karyopherin RANBP5 (Isoform-1)

Protein crystallography data

The structure of Human Karyopherin RANBP5 (Isoform-1), PDB code: 6xte was solved by C.Swale, A.A.Mccarthy, R.W.H.Ruigrok, T.Crepin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.49 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.091, 96.313, 156.979, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 26

Other elements in 6xte:

The structure of Human Karyopherin RANBP5 (Isoform-1) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Human Karyopherin RANBP5 (Isoform-1) (pdb code 6xte). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Human Karyopherin RANBP5 (Isoform-1), PDB code: 6xte:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6xte

Go back to Nickel Binding Sites List in 6xte
Nickel binding site 1 out of 2 in the Human Karyopherin RANBP5 (Isoform-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Human Karyopherin RANBP5 (Isoform-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1201

b:0.4
occ:1.00
ND1 A:HIS807 3.2 68.8 1.0
O A:CYS802 3.7 66.8 1.0
CE1 A:HIS807 3.7 69.2 1.0
ND2 A:ASN804 3.7 70.2 1.0
SG A:CYS768 3.9 73.6 1.0
CD2 A:HIS765 4.0 85.2 1.0
N A:ASN804 4.0 65.0 1.0
CB A:CYS768 4.2 71.2 1.0
CG A:ASN804 4.2 69.2 1.0
NE2 A:HIS765 4.3 86.5 1.0
CG A:HIS807 4.4 66.9 1.0
CA A:LEU803 4.5 64.7 1.0
CB A:ASN804 4.5 66.1 1.0
C A:CYS802 4.6 65.5 1.0
C A:LEU803 4.7 65.1 1.0
CA A:ASN804 4.9 65.3 1.0
NE1 A:TRP764 4.9 81.4 1.0
CG A:HIS765 5.0 83.6 1.0
CB A:HIS807 5.0 64.4 1.0
N A:LEU803 5.0 64.8 1.0
OD1 A:ASN804 5.0 70.3 1.0

Nickel binding site 2 out of 2 in 6xte

Go back to Nickel Binding Sites List in 6xte
Nickel binding site 2 out of 2 in the Human Karyopherin RANBP5 (Isoform-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Human Karyopherin RANBP5 (Isoform-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1202

b:79.5
occ:1.00
NE2 A:GLN974 3.5 57.6 1.0
NE1 A:TRP1017 3.7 50.1 1.0
ND1 A:HIS1013 3.8 52.8 1.0
OG A:SER1016 4.1 53.5 1.0
CG A:GLN974 4.4 54.4 1.0
CD A:GLN974 4.5 57.2 1.0
CE2 A:TRP1017 4.5 49.6 1.0
CD1 A:TRP1017 4.6 49.4 1.0
CE1 A:HIS1013 4.7 53.2 1.0
CZ2 A:TRP1017 4.7 50.1 1.0
CG A:HIS1013 4.7 50.7 1.0
CB A:HIS1013 4.8 48.6 1.0

Reference:

C.Swale, B.Da Costa, L.Sedano, F.Garzoni, A.A.Mccarthy, I.Berger, C.Bieniossek, R.W.H.Ruigrok, B.Delmas, T.Crepin. X-Ray Structure of the Human Karyopherin RANBP5, An Essential Factor For Influenza Polymerase Nuclear Trafficking. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 32222384
DOI: 10.1016/J.JMB.2020.03.021
Page generated: Wed Dec 16 01:57:08 2020

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