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Copper in PDB 4nqq: Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2

Protein crystallography data

The structure of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2, PDB code: 4nqq was solved by J.Brasch, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.085, 188.700, 53.150, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.9

Other elements in 4nqq:

The structure of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 also contains other interesting chemical elements:

Calcium (Ca) 14 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 (pdb code 4nqq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2, PDB code: 4nqq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 4nqq

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Copper binding site 1 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu305

b:72.3
occ:1.00
 HD1 A:HIS63 1.3 79.5 1.0
ND1 A:HIS63 2.1 66.2 1.0
HB3 A:HIS63 2.8 59.1 1.0
HG3 A:PRO18 3.0 51.1 1.0
CG A:HIS63 3.1 54.8 1.0
CE1 A:HIS63 3.1 50.0 1.0
HE1 A:HIS63 3.3 60.0 1.0
CB A:HIS63 3.3 49.3 1.0
HA A:HIS63 3.6 58.3 1.0
CG A:PRO18 3.9 42.6 1.0
CA A:HIS63 4.1 48.5 1.0
HB3 A:PRO18 4.1 46.5 1.0
O A:HOH401 4.1 24.1 1.0
HB2 A:HIS63 4.2 59.1 1.0
NE2 A:HIS63 4.2 40.4 1.0
CD2 A:HIS63 4.2 40.1 1.0
O A:HIS63 4.3 54.6 1.0
HD3 A:PRO18 4.4 48.6 1.0
HG2 A:PRO18 4.5 51.1 1.0
CB A:PRO18 4.5 38.8 1.0
HB3 A:PHE17 4.5 39.6 1.0
HA A:PRO18 4.6 51.0 1.0
CD A:PRO18 4.7 40.5 1.0
C A:HIS63 4.7 46.9 1.0
N A:PRO18 4.8 40.7 1.0
CA A:PRO18 4.9 42.5 1.0
HE2 A:HIS63 5.0 48.5 1.0

Copper binding site 2 out of 9 in 4nqq

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Copper binding site 2 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu306

b:52.8
occ:1.00
 HE1 A:HIS151 1.1 31.0 1.0
CE1 A:HIS151 2.0 25.8 1.0
O C:HOH412 2.3 17.6 1.0
O A:HOH422 2.3 24.0 1.0
O A:HOH423 2.3 16.2 1.0
O A:HOH421 2.5 31.7 1.0
NE2 A:HIS151 2.8 28.8 1.0
O A:HOH418 2.9 30.4 1.0
HE2 A:HIS151 2.9 34.6 1.0
ND1 A:HIS151 3.0 41.1 1.0
HD1 A:HIS151 3.3 49.4 1.0
CD2 A:HIS151 4.0 28.4 1.0
CG A:HIS151 4.1 28.2 1.0
HB3 A:SER152 4.5 49.9 1.0
OD2 C:ASP197 4.5 39.7 1.0
HB3 C:ASP197 4.6 31.4 1.0
HD2 A:HIS151 4.9 34.1 1.0
OE2 C:GLU199 5.0 34.5 1.0

Copper binding site 3 out of 9 in 4nqq

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Copper binding site 3 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu304

b:0.4
occ:1.00
 HG3 B:PRO18 2.6 54.7 1.0
O B:HOH430 2.9 38.2 1.0
ND1 B:HIS63 2.9 26.1 1.0
HD3 B:PRO18 3.4 42.1 1.0
HB3 B:HIS63 3.4 66.9 1.0
CG B:PRO18 3.5 45.6 1.0
CE1 B:HIS63 3.6 38.5 1.0
HE1 B:HIS63 3.7 46.2 1.0
CG B:HIS63 3.8 65.9 1.0
CD B:PRO18 3.8 35.1 1.0
HG2 B:PRO18 4.0 54.7 1.0
CB B:HIS63 4.1 55.8 1.0
N B:PRO18 4.2 37.4 1.0
HA B:HIS63 4.3 49.1 1.0
HB3 B:PRO18 4.3 34.6 1.0
CB B:PRO18 4.4 28.8 1.0
NE2 B:HIS63 4.6 73.0 1.0
HA B:PRO18 4.7 40.4 1.0
HB3 B:PHE17 4.7 27.9 1.0
CD2 B:HIS63 4.7 66.3 1.0
C B:PHE17 4.7 30.2 1.0
HD2 B:PRO18 4.7 42.1 1.0
CA B:HIS63 4.7 40.9 1.0
CA B:PRO18 4.8 33.6 1.0
O B:PHE17 4.8 34.8 1.0
HB2 B:HIS63 4.9 66.9 1.0

Copper binding site 4 out of 9 in 4nqq

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Copper binding site 4 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu305

b:77.5
occ:1.00
 HE2 B:HIS151 1.4 80.8 1.0
NE2 B:HIS151 2.2 67.4 1.0
O B:HOH415 2.6 29.8 1.0
HD2 B:HIS151 2.9 90.8 1.0
CD2 B:HIS151 2.9 75.6 1.0
CE1 B:HIS151 3.4 78.6 1.0
HE1 B:HIS151 3.7 94.3 1.0
HG B:SER152 4.1 0.8 1.0
HB3 B:SER152 4.2 0.6 1.0
CG B:HIS151 4.2 77.7 1.0
ND1 B:HIS151 4.4 72.9 1.0
OG B:SER152 4.7 94.8 1.0
CB B:SER152 4.9 97.2 1.0

Copper binding site 5 out of 9 in 4nqq

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Copper binding site 5 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu304

b:51.3
occ:1.00
 HE2 C:HIS151 1.4 38.8 1.0
O A:HOH425 2.2 19.6 1.0
NE2 C:HIS151 2.2 32.3 1.0
O A:HOH426 2.3 16.9 1.0
O A:HOH420 2.4 23.8 1.0
O A:HOH419 2.7 16.5 1.0
CD2 C:HIS151 3.1 35.6 1.0
HD2 C:HIS151 3.1 42.8 1.0
CE1 C:HIS151 3.3 42.9 1.0
HE1 C:HIS151 3.6 51.4 1.0
OE2 A:GLU199 4.1 52.7 1.0
OD2 A:ASP197 4.2 44.9 1.0
HB3 A:ASP197 4.3 32.2 1.0
CG C:HIS151 4.3 31.1 1.0
ND1 C:HIS151 4.4 42.0 1.0
CD A:GLU199 4.6 50.4 1.0
HG C:SER152 4.7 43.1 1.0
HB3 C:SER152 4.8 59.3 1.0
OE1 A:GLU199 4.9 57.0 1.0

Copper binding site 6 out of 9 in 4nqq

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Copper binding site 6 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu305

b:70.3
occ:1.00
 HD1 C:HIS166 1.6 33.6 1.0
O C:HOH409 2.2 48.2 1.0
ND1 C:HIS166 2.3 28.0 1.0
O C:HOH407 2.9 36.6 1.0
CE1 C:HIS166 3.1 42.0 1.0
HE1 C:HIS166 3.1 50.4 1.0
HB3 C:HIS166 3.3 33.4 1.0
CG C:HIS166 3.4 37.0 1.0
CB C:HIS166 3.9 27.9 1.0
NE2 C:HIS166 4.2 31.3 1.0
HD11 A:LEU161 4.3 87.7 1.0
CD2 C:HIS166 4.4 29.4 1.0
HA C:HIS166 4.5 25.1 1.0
HB2 C:HIS166 4.6 33.4 1.0
CA C:HIS166 4.8 20.9 1.0
HG C:SER168 4.8 58.9 1.0
OG C:SER168 4.9 49.1 1.0
H C:LYS167 4.9 18.1 1.0
HE2 C:HIS166 5.0 37.5 1.0

Copper binding site 7 out of 9 in 4nqq

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Copper binding site 7 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu306

b:86.5
occ:1.00
 HD1 C:HIS63 1.7 79.0 1.0
ND1 C:HIS63 2.3 65.8 1.0
HB3 C:HIS63 2.5 91.3 1.0
CG C:HIS63 3.0 71.5 1.0
CB C:HIS63 3.2 76.1 1.0
CE1 C:HIS63 3.3 76.1 1.0
HG3 C:PRO18 3.6 82.9 1.0
HE1 C:HIS63 3.6 91.3 1.0
HA C:HIS63 3.8 75.3 1.0
HB2 C:HIS63 3.9 91.3 1.0
CD2 C:HIS63 4.1 67.2 1.0
CA C:HIS63 4.1 62.7 1.0
NE2 C:HIS63 4.2 70.1 1.0
O C:HIS63 4.3 66.3 1.0
CG C:PRO18 4.5 69.1 1.0
HD3 C:PRO18 4.6 88.0 1.0
C C:HIS63 4.7 59.6 1.0
HD2 C:HIS63 4.9 80.6 1.0
HB3 C:PHE17 4.9 86.0 1.0
HB3 C:PRO18 4.9 76.7 1.0
CD C:PRO18 5.0 73.3 1.0
HE2 C:HIS63 5.0 84.1 1.0

Copper binding site 8 out of 9 in 4nqq

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Copper binding site 8 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu305

b:74.3
occ:1.00
 HE2 D:HIS151 1.4 0.1 1.0
NE2 D:HIS151 2.2 88.4 1.0
CD2 D:HIS151 3.2 96.2 1.0
CE1 D:HIS151 3.2 97.5 1.0
HD2 D:HIS151 3.3 0.4 1.0
HE1 D:HIS151 3.4 1.0 1.0
ND1 D:HIS151 4.3 0.6 1.0
CG D:HIS151 4.4 0.3 1.0
HB3 D:SER152 4.6 0.1 1.0
HG D:SER152 4.9 0.3 1.0

Copper binding site 9 out of 9 in 4nqq

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Copper binding site 9 out of 9 in the Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Mouse P-Cadherin Extracellular Domains EC1-EC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu306

b:0.6
occ:1.00
 HB3 D:HIS63 2.0 0.5 1.0
CB D:HIS63 2.9 0.6 1.0
HD1 D:HIS63 3.0 0.9 1.0
HB2 D:HIS63 3.4 0.5 1.0
O D:HIS63 3.4 0.4 1.0
ND1 D:HIS63 3.5 0.7 1.0
CG D:HIS63 3.5 0.3 1.0
CA D:HIS63 3.9 0.5 1.0
HA D:HIS63 3.9 0.4 1.0
C D:HIS63 4.0 0.4 1.0
CE1 D:HIS63 4.7 0.2 1.0
CD2 D:HIS63 4.8 0.9 1.0
HG3 D:PRO18 4.8 0.1 1.0

Reference:

J.Vendome, K.Felsovalyi, H.Song, Z.Yang, X.Jin, J.Brasch, O.J.Harrison, G.Ahlsen, F.Bahna, A.Kaczynska, P.S.Katsamba, D.Edmond, W.L.Hubbell, L.Shapiro, B.Honig. Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins. Proc.Natl.Acad.Sci.Usa V. 111 E4175 2014.
ISSN: ISSN 0027-8424
PubMed: 25253890
DOI: 10.1073/PNAS.1416737111
Page generated: Wed Jul 31 03:17:58 2024

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