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Nickel in PDB 6x5e: Crystal Structure of A Lewis-Binding Fab (CH88.2)

Protein crystallography data

The structure of Crystal Structure of A Lewis-Binding Fab (CH88.2), PDB code: 6x5e was solved by C.Soliman, P.A.Ramsland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.49 / 2.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.423, 68.480, 91.750, 110.50, 99.29, 90.01
R / Rfree (%) 23 / 28.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Lewis-Binding Fab (CH88.2) (pdb code 6x5e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of A Lewis-Binding Fab (CH88.2), PDB code: 6x5e:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 6x5e

Go back to Nickel Binding Sites List in 6x5e
Nickel binding site 1 out of 3 in the Crystal Structure of A Lewis-Binding Fab (CH88.2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Lewis-Binding Fab (CH88.2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni301

b:73.0
occ:1.00
HZ1 L:LYS188 1.9 0.5 1.0
HE3 L:LYS188 2.1 99.1 1.0
HE2 L:LYS188 2.4 99.1 1.0
CE L:LYS188 2.4 82.6 1.0
NZ L:LYS188 2.4 86.3 1.0
NE2 L:HIS189 2.5 64.8 1.0
OD2 L:ASP185 2.7 73.0 1.0
HZ2 L:LYS188 2.7 0.5 1.0
HZ3 L:LYS188 3.2 0.5 1.0
CD2 L:HIS189 3.4 68.9 1.0
CE1 L:HIS189 3.5 70.0 1.0
HD2 L:HIS189 3.5 82.7 1.0
HE1 L:HIS189 3.6 84.0 1.0
CG L:ASP185 3.7 80.2 1.0
CD L:LYS188 3.9 82.4 1.0
OD1 L:ASP185 4.1 67.0 1.0
HD2 L:LYS188 4.3 98.9 1.0
HG2 L:LYS188 4.3 89.7 1.0
HD3 L:LYS188 4.4 98.9 1.0
CG L:HIS189 4.6 66.9 1.0
ND1 L:HIS189 4.6 67.8 1.0
HB3 L:LYS188 4.6 88.2 1.0
CG L:LYS188 4.6 74.7 1.0
HA L:ASP185 4.7 85.7 1.0
CB L:ASP185 4.9 71.3 1.0

Nickel binding site 2 out of 3 in 6x5e

Go back to Nickel Binding Sites List in 6x5e
Nickel binding site 2 out of 3 in the Crystal Structure of A Lewis-Binding Fab (CH88.2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Lewis-Binding Fab (CH88.2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni302

b:0.7
occ:1.00
HE2 L:HIS30 2.4 98.5 1.0
NE2 L:HIS30 2.8 82.1 1.0
O L:HOH407 2.8 58.5 1.0
HE1 L:HIS30 2.9 0.2 1.0
HD22 L:ASN28 3.0 0.5 1.0
CE1 L:HIS30 3.1 87.6 1.0
ND2 L:ASN28 3.5 88.7 1.0
HD21 L:ASN28 3.6 0.5 1.0
CD2 L:HIS30 3.9 75.1 1.0
HB3 L:ASN28 4.1 88.1 1.0
ND1 L:HIS30 4.2 79.8 1.0
OE2 L:GLU27 4.3 1.0 1.0
HD2 L:HIS30 4.4 90.2 1.0
CG L:ASN28 4.5 67.2 1.0
O L:ASN28 4.5 85.0 1.0
CG L:HIS30 4.7 74.3 1.0
HZ2 L:TRP92 4.8 95.3 1.0
CB L:ASN28 4.8 73.4 1.0

Nickel binding site 3 out of 3 in 6x5e

Go back to Nickel Binding Sites List in 6x5e
Nickel binding site 3 out of 3 in the Crystal Structure of A Lewis-Binding Fab (CH88.2)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of A Lewis-Binding Fab (CH88.2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:84.0
occ:1.00
HZ2 A:LYS188 1.5 90.0 1.0
HZ1 A:LYS188 2.0 90.0 1.0
NZ A:LYS188 2.1 75.0 1.0
NE2 A:HIS189 2.2 69.1 1.0
OD1 A:ASP185 2.6 81.5 1.0
HZ3 A:LYS188 2.7 90.0 1.0
CE1 A:HIS189 3.0 62.7 1.0
HE1 A:HIS189 3.0 75.3 1.0
CE A:LYS188 3.2 74.9 1.0
HE2 A:LYS188 3.2 89.8 1.0
CD2 A:HIS189 3.3 68.5 1.0
CG A:ASP185 3.4 76.9 1.0
OD2 A:ASP185 3.4 78.5 1.0
HE3 A:LYS188 3.5 89.8 1.0
HD2 A:HIS189 3.6 82.2 1.0
ND1 A:HIS189 4.2 62.6 1.0
CG A:HIS189 4.4 60.8 1.0
HD3 A:LYS188 4.5 86.7 1.0
CD A:LYS188 4.5 72.2 1.0
HA A:ASP185 4.7 82.5 1.0
CB A:ASP185 4.8 77.0 1.0
HD1 A:HIS189 4.9 75.2 1.0
HD2 A:LYS188 4.9 86.7 1.0
HB3 A:LYS188 4.9 84.0 1.0
O A:ASP185 5.0 74.9 1.0

Reference:

C.Soliman, A.J.Guy, J.X.Chua, M.Vankemmelbeke, R.S.Mcintosh, S.Eastwood, V.K.Truong, A.Elbourne, I.Spendlove, L.G.Durrant, P.A.Ramsland. Molecular and Structural Basis For Lewis Glycan Recognition By A Cancer-Targeting Antibody. Biochem.J. V. 477 3219 2020.
ISSN: ESSN 1470-8728
PubMed: 32789497
DOI: 10.1042/BCJ20200454
Page generated: Wed Dec 16 01:57:08 2020

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