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Copper in PDB 1qd0: Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens

Protein crystallography data

The structure of Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens, PDB code: 1qd0 was solved by S.Spinelli, L.G.J.Frenken, P.Hermans, T.Verrips, K.Brown, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 46.700, 46.700, 121.100, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 28

Copper Binding Sites:

The binding sites of Copper atom in the Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens (pdb code 1qd0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens, PDB code: 1qd0:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1qd0

Go back to Copper Binding Sites List in 1qd0
Copper binding site 1 out of 2 in the Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1001

b:25.5
occ:1.00
O28 A:RR61003 2.0 31.8 1.0
N1 A:RR61003 2.0 43.5 1.0
O29 A:RR61003 2.2 45.2 1.0
NE2 A:HIS34 2.3 16.8 1.0
N2 A:RR61003 2.6 36.4 1.0
C4 A:RR61003 2.8 47.0 1.0
C10 A:RR61003 2.9 46.7 1.0
C5 A:RR61003 3.0 29.0 1.0
C3 A:RR61003 3.2 33.1 1.0
CE1 A:HIS34 3.3 18.0 1.0
CD2 A:HIS34 3.4 15.6 1.0
C14 A:RR61003 4.2 48.7 1.0
C11 A:RR61003 4.2 47.2 1.0
C6 A:RR61003 4.3 28.0 1.0
ND1 A:HIS34 4.5 16.8 1.0
CZ2 A:TRP56 4.5 7.4 1.0
CG A:HIS34 4.5 15.3 1.0
C9 A:RR61003 4.6 32.0 1.0
C15 A:RR61003 4.8 23.3 1.0

Copper binding site 2 out of 2 in 1qd0

Go back to Copper Binding Sites List in 1qd0
Copper binding site 2 out of 2 in the Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Camelid Heavy Chain Variable Domains Provide Efficient Combining Sites to Haptens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1002

b:13.4
occ:1.00
N52 A:RR61003 1.9 11.1 1.0
O78 A:RR61003 2.0 16.2 1.0
O79 A:RR61003 2.1 9.4 1.0
NE2 A:HIS32 2.2 12.8 1.0
C54 A:RR61003 2.7 4.7 1.0
C60 A:RR61003 2.8 5.4 1.0
N51 A:RR61003 2.8 10.1 1.0
C55 A:RR61003 3.1 12.7 1.0
CD2 A:HIS32 3.2 14.8 1.0
CE1 A:HIS32 3.2 10.7 1.0
C53 A:RR61003 3.4 12.2 1.0
ND1 A:HIS34 3.6 16.8 1.0
CB A:HIS34 3.9 16.3 1.0
C64 A:RR61003 4.0 4.2 1.0
CG A:HIS34 4.1 15.3 1.0
C61 A:RR61003 4.2 4.2 1.0
O A:HOH1035 4.3 27.6 1.0
ND1 A:HIS32 4.3 10.8 1.0
C56 A:RR61003 4.3 14.0 1.0
CG A:HIS32 4.3 13.6 1.0
CE1 A:HIS34 4.7 18.0 1.0
C65 A:RR61003 4.7 14.3 1.0
C59 A:RR61003 4.8 12.7 1.0

Reference:

S.Spinelli, L.G.Frenken, P.Hermans, T.Verrips, K.Brown, M.Tegoni, C.Cambillau. Camelid Heavy-Chain Variable Domains Provide Efficient Combining Sites to Haptens. Biochemistry V. 39 1217 2000.
ISSN: ISSN 0006-2960
PubMed: 10684599
DOI: 10.1021/BI991830W
Page generated: Wed Oct 28 14:16:48 2020
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