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Copper in PDB 1lnl: Structure of Deoxygenated Hemocyanin From Rapana Thomasiana

Protein crystallography data

The structure of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana, PDB code: 1lnl was solved by M.Perbandt, E.W.Guthoehrlein, W.Rypniewski, K.Idakieva, S.Stoeva, W.Voelter, N.Genov, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.486, 105.486, 374.988, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 28.8

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana (pdb code 1lnl). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana, PDB code: 1lnl:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1lnl

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Copper binding site 1 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5001

b:77.9
occ:1.00
NE2 A:HIS41 1.8 43.1 1.0
NE2 A:HIS70 2.0 43.1 1.0
CE1 A:HIS70 2.4 43.1 1.0
CE1 A:HIS41 2.5 43.1 1.0
NE2 A:HIS61 2.7 43.1 1.0
CU A:CU5012 2.9 77.9 1.0
CD2 A:HIS41 3.0 43.1 1.0
CE1 A:HIS61 3.0 43.1 1.0
CD2 A:HIS70 3.3 43.1 1.0
SG A:CYS59 3.5 43.1 1.0
ND1 A:HIS41 3.7 43.1 1.0
ND1 A:HIS70 3.7 43.1 1.0
CD2 A:HIS61 3.9 43.1 1.0
CG A:HIS41 4.0 43.1 1.0
CG A:HIS70 4.2 43.1 1.0
ND1 A:HIS61 4.2 43.1 1.0
CB A:CYS59 4.3 43.1 1.0
CG A:HIS61 4.6 43.1 1.0
NE2 A:HIS185 4.6 43.1 1.0
NE2 A:HIS212 4.7 43.1 1.0
CZ A:PHE208 4.8 43.1 1.0
CE1 A:HIS212 4.8 43.1 1.0
CE1 A:HIS185 4.8 43.1 1.0
CE1 A:PHE208 4.9 43.1 1.0
CE1 A:PHE66 4.9 43.1 1.0
NE2 A:HIS181 4.9 43.1 1.0
CD1 A:LEU199 4.9 43.1 1.0

Copper binding site 2 out of 9 in 1lnl

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Copper binding site 2 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5012

b:77.9
occ:1.00
NE2 A:HIS185 2.1 43.1 1.0
NE2 A:HIS212 2.2 43.1 1.0
NE2 A:HIS181 2.3 43.1 1.0
CE1 A:HIS212 2.3 43.1 1.0
CE1 A:HIS185 2.7 43.1 1.0
NE2 A:HIS70 2.8 43.1 1.0
CE1 A:HIS181 2.9 43.1 1.0
CU A:CU5001 2.9 77.9 1.0
CD2 A:HIS70 3.1 43.1 1.0
CD2 A:HIS185 3.3 43.1 1.0
CD2 A:HIS212 3.5 43.1 1.0
CD2 A:HIS181 3.5 43.1 1.0
ND1 A:HIS212 3.6 43.1 1.0
ND1 A:HIS185 3.9 43.1 1.0
CE1 A:HIS70 4.0 43.1 1.0
NE2 A:HIS41 4.1 43.1 1.0
ND1 A:HIS181 4.2 43.1 1.0
CG A:HIS212 4.2 43.1 1.0
CG A:HIS185 4.2 43.1 1.0
CE1 A:PHE208 4.3 43.1 1.0
CG A:HIS70 4.4 43.1 1.0
CE1 A:HIS41 4.4 43.1 1.0
CZ A:PHE208 4.5 43.1 1.0
CG A:HIS181 4.5 43.1 1.0
CE1 A:PHE66 4.8 43.1 1.0
ND1 A:HIS70 4.8 43.1 1.0
CZ A:PHE66 4.9 43.1 1.0

Copper binding site 3 out of 9 in 1lnl

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Copper binding site 3 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu5503

b:77.9
occ:1.00
CE1 B:HIS117 1.9 43.1 1.0
NE2 B:HIS117 2.4 43.1 1.0
ND1 B:HIS117 3.2 43.1 1.0
CD2 B:HIS117 3.7 43.1 1.0
CG B:HIS117 4.0 43.1 1.0

Copper binding site 4 out of 9 in 1lnl

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Copper binding site 4 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu5004

b:77.9
occ:1.00
NE2 B:HIS41 1.9 43.1 1.0
NE2 B:HIS70 2.0 43.1 1.0
NE2 B:HIS61 2.3 43.1 1.0
CU B:CU5015 2.6 77.9 1.0
CE1 B:HIS41 2.6 43.1 1.0
CE1 B:HIS70 2.9 43.1 1.0
CD2 B:HIS70 3.1 43.1 1.0
CD2 B:HIS41 3.1 43.1 1.0
CE1 B:HIS61 3.1 43.1 1.0
CD2 B:HIS61 3.5 43.1 1.0
ND1 B:HIS41 3.8 43.1 1.0
CE1 B:HIS181 3.9 43.1 1.0
NE2 B:HIS212 3.9 43.1 1.0
ND1 B:HIS70 4.0 43.1 1.0
NE2 B:HIS181 4.1 43.1 1.0
CG B:HIS41 4.1 43.1 1.0
CG B:HIS70 4.1 43.1 1.0
SG B:CYS59 4.1 43.1 1.0
CE1 B:PHE208 4.2 43.1 1.0
ND1 B:HIS61 4.3 43.1 1.0
NE2 B:HIS185 4.5 43.1 1.0
CG B:HIS61 4.5 43.1 1.0
CZ B:PHE208 4.5 43.1 1.0
CD2 B:HIS212 4.6 43.1 1.0
CE1 B:HIS212 4.6 43.1 1.0
CE2 B:PHE66 4.6 43.1 1.0
CD2 B:LEU343 4.7 43.1 1.0
CB B:CYS59 4.8 43.1 1.0
CE1 B:HIS185 4.8 43.1 1.0
CD1 B:LEU199 4.9 43.1 1.0

Copper binding site 5 out of 9 in 1lnl

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Copper binding site 5 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu5015

b:77.9
occ:1.00
NE2 B:HIS181 1.7 43.1 1.0
NE2 B:HIS212 1.7 43.1 1.0
CE1 B:HIS181 2.1 43.1 1.0
NE2 B:HIS185 2.4 43.1 1.0
CE1 B:HIS212 2.5 43.1 1.0
CU B:CU5004 2.6 77.9 1.0
CD2 B:HIS212 2.9 43.1 1.0
CD2 B:HIS181 3.0 43.1 1.0
NE2 B:HIS70 3.2 43.1 1.0
CE1 B:HIS185 3.2 43.1 1.0
ND1 B:HIS181 3.4 43.1 1.0
CD2 B:HIS70 3.4 43.1 1.0
CD2 B:HIS185 3.5 43.1 1.0
ND1 B:HIS212 3.7 43.1 1.0
CE1 B:PHE208 3.8 43.1 1.0
CG B:HIS181 3.8 43.1 1.0
CG B:HIS212 3.9 43.1 1.0
NE2 B:HIS41 4.2 43.1 1.0
CE1 B:HIS70 4.3 43.1 1.0
CZ B:PHE208 4.3 43.1 1.0
CE1 B:HIS41 4.4 43.1 1.0
NE2 B:HIS61 4.4 43.1 1.0
ND1 B:HIS185 4.5 43.1 1.0
CG B:HIS70 4.5 43.1 1.0
CE2 B:PHE66 4.6 43.1 1.0
CG B:HIS185 4.6 43.1 1.0
CD1 B:PHE208 4.7 43.1 1.0
O B:HIS181 4.7 43.1 1.0
CZ B:PHE66 4.8 43.1 1.0
CD2 B:HIS61 5.0 43.1 1.0

Copper binding site 6 out of 9 in 1lnl

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Copper binding site 6 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu5506

b:77.9
occ:1.00
NH1 B:ARG-1 0.2 77.9 1.0
CZ B:ARG-1 1.3 77.9 1.0
NH2 B:ARG-1 2.2 77.9 1.0
CE1 B:HIS-2 2.3 77.9 1.0
NE B:ARG-1 2.4 77.9 1.0
NE2 B:HIS-2 2.6 77.9 1.0
CG B:ARG-1 2.7 77.9 1.0
CD B:ARG-1 2.9 77.9 1.0
ND1 B:HIS-2 3.2 77.9 1.0
CD2 B:HIS-2 3.6 77.9 1.0
CG B:HIS-2 3.9 77.9 1.0
CB B:ARG-1 4.1 77.9 1.0
CA B:ARG-1 4.5 77.9 1.0
O B:HIS-2 4.7 77.9 1.0
C B:HIS-2 4.7 77.9 1.0
N B:ARG-1 4.8 77.9 1.0

Copper binding site 7 out of 9 in 1lnl

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Copper binding site 7 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu5007

b:77.9
occ:1.00
NE2 C:HIS41 1.8 43.1 1.0
NE2 C:HIS70 2.0 43.1 1.0
NE2 C:HIS61 2.1 43.1 1.0
CU C:CU5018 2.5 77.9 1.0
CE1 C:HIS41 2.6 43.1 1.0
CE1 C:HIS70 2.7 43.1 1.0
CE1 C:HIS61 2.7 43.1 1.0
CD2 C:HIS41 2.9 43.1 1.0
CD2 C:HIS70 3.3 43.1 1.0
CD2 C:HIS61 3.3 43.1 1.0
ND1 C:HIS41 3.7 43.1 1.0
CE1 C:HIS181 3.8 43.1 1.0
CG C:HIS41 3.9 43.1 1.0
ND1 C:HIS61 3.9 43.1 1.0
ND1 C:HIS70 3.9 43.1 1.0
SG C:CYS59 4.0 43.1 1.0
NE2 C:HIS212 4.2 43.1 1.0
CG C:HIS70 4.2 43.1 1.0
CG C:HIS61 4.2 43.1 1.0
NE2 C:HIS185 4.3 43.1 1.0
CB C:CYS59 4.5 43.1 1.0
NE2 C:HIS181 4.5 43.1 1.0
CZ C:PHE208 4.6 43.1 1.0
CE2 C:PHE66 4.6 43.1 1.0
CE1 C:PHE208 4.7 43.1 1.0
ND1 C:HIS181 4.7 43.1 1.0
CE1 C:HIS185 4.8 43.1 1.0
CE1 C:HIS212 4.9 43.1 1.0
CD2 C:HIS212 5.0 43.1 1.0

Copper binding site 8 out of 9 in 1lnl

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Copper binding site 8 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu5018

b:77.9
occ:1.00
CE1 C:HIS181 1.7 43.1 1.0
NE2 C:HIS181 2.0 43.1 1.0
NE2 C:HIS185 2.3 43.1 1.0
NE2 C:HIS212 2.3 43.1 1.0
CU C:CU5007 2.5 77.9 1.0
ND1 C:HIS181 3.0 43.1 1.0
NE2 C:HIS70 3.0 43.1 1.0
CE1 C:HIS185 3.0 43.1 1.0
CE1 C:HIS212 3.1 43.1 1.0
CD2 C:HIS212 3.3 43.1 1.0
CD2 C:HIS181 3.3 43.1 1.0
CD2 C:HIS185 3.4 43.1 1.0
CD2 C:HIS70 3.4 43.1 1.0
CG C:HIS181 3.8 43.1 1.0
NE2 C:HIS41 4.1 43.1 1.0
CE1 C:HIS70 4.2 43.1 1.0
NE2 C:HIS61 4.3 43.1 1.0
ND1 C:HIS185 4.3 43.1 1.0
ND1 C:HIS212 4.3 43.1 1.0
CG C:HIS185 4.4 43.1 1.0
CG C:HIS212 4.5 43.1 1.0
CE1 C:HIS41 4.5 43.1 1.0
CZ C:PHE208 4.7 43.1 1.0
CE2 C:PHE66 4.7 43.1 1.0
CE1 C:PHE208 4.7 43.1 1.0
CG C:HIS70 4.7 43.1 1.0
CZ C:PHE66 4.8 43.1 1.0
CE1 C:HIS61 4.9 43.1 1.0

Copper binding site 9 out of 9 in 1lnl

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Copper binding site 9 out of 9 in the Structure of Deoxygenated Hemocyanin From Rapana Thomasiana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Structure of Deoxygenated Hemocyanin From Rapana Thomasiana within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu5509

b:77.9
occ:1.00
NE2 C:HIS-2 0.8 77.9 1.0
CE1 C:HIS-2 1.1 77.9 1.0
CD2 C:HIS-2 1.6 77.9 1.0
ND1 C:HIS-2 1.9 77.9 1.0
NH2 C:ARG-1 2.0 77.9 1.0
CG C:HIS-2 2.1 77.9 1.0
NE C:ARG-1 2.6 77.9 1.0
CZ C:ARG-1 2.6 77.9 1.0
CB C:HIS-2 3.5 77.9 1.0
O C:HIS-2 3.7 77.9 1.0
NH1 C:ARG-1 3.9 77.9 1.0
CD C:ARG-1 4.0 77.9 1.0
CA C:HIS-2 4.1 77.9 1.0
C C:HIS-2 4.2 77.9 1.0
CG C:ARG-1 4.6 77.9 1.0

Reference:

M.Perbandt, E.W.Guthoehrlein, W.Rypniewski, K.Idakieva, S.Stoeva, W.Voelter, N.Genov, C.Betzel. The Structure of A Functional Unit From the Wall of A Gastropod Hemocyanin Offers A Possible Mechanism For Cooperativity Biochemistry V. 42 6341 2003.
ISSN: ISSN 0006-2960
PubMed: 12767214
DOI: 10.1021/BI020672X
Page generated: Wed Oct 28 14:15:39 2020
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