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Copper in PDB 1gmw: Structure of Uree

Protein crystallography data

The structure of Structure of Uree, PDB code: 1gmw was solved by H.K.Song, S.B.Mulrooney, R.Huber, R.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17 / 1.5
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.756, 129.905, 56.419, 90.00, 91.21, 90.00
R / Rfree (%) 22.3 / 26.1

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Uree (pdb code 1gmw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Uree, PDB code: 1gmw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1gmw

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Copper binding site 1 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1139

b:62.6
occ:1.00
NE2 A:HIS110 2.3 54.9 1.0
O A:HOH2034 2.3 43.8 1.0
CD2 A:HIS110 3.1 53.0 1.0
CD2 A:HIS112 3.2 65.5 1.0
NE2 A:HIS112 3.2 65.9 1.0
CE1 A:HIS110 3.4 54.4 1.0
CG A:HIS110 4.3 54.9 1.0
CE1 A:HIS112 4.4 66.2 1.0
CG A:HIS112 4.4 65.7 1.0
ND1 A:HIS110 4.4 54.6 1.0
ND1 A:HIS112 5.0 66.1 1.0

Copper binding site 2 out of 6 in 1gmw

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Copper binding site 2 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1139

b:48.8
occ:1.00
NE2 D:HIS96 2.1 32.2 1.0
NE2 B:HIS96 2.1 40.9 1.0
CE1 D:HIS96 3.0 33.8 1.0
CE1 B:HIS96 3.1 36.7 1.0
CD2 D:HIS96 3.1 31.6 1.0
CD2 B:HIS96 3.1 37.6 1.0
ND1 D:HIS96 4.2 31.7 1.0
ND1 B:HIS96 4.2 38.5 1.0
CG D:HIS96 4.2 33.8 1.0
CG B:HIS96 4.2 38.8 1.0
O D:ASN94 4.7 38.0 1.0

Copper binding site 3 out of 6 in 1gmw

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Copper binding site 3 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1140

b:54.5
occ:1.00
NE2 B:HIS110 2.3 42.0 1.0
NE2 B:HIS112 2.3 54.3 1.0
CD2 B:HIS110 3.0 39.7 1.0
CD2 B:HIS112 3.2 53.2 1.0
CE1 B:HIS112 3.2 53.8 1.0
CE1 B:HIS110 3.3 41.6 1.0
ND1 B:HIS112 4.2 53.8 1.0
CG B:HIS112 4.3 53.1 1.0
CG B:HIS110 4.3 41.1 1.0
ND1 B:HIS110 4.4 41.6 1.0

Copper binding site 4 out of 6 in 1gmw

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Copper binding site 4 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1139

b:47.3
occ:1.00
NE2 C:HIS96 2.0 29.0 1.0
NE2 A:HIS96 2.0 35.2 1.0
CE1 C:HIS96 2.7 25.9 1.0
CE1 A:HIS96 3.0 33.0 1.0
CD2 A:HIS96 3.0 31.9 1.0
CD2 C:HIS96 3.2 23.8 1.0
O C:HOH2023 3.8 41.3 1.0
ND1 C:HIS96 3.9 27.2 1.0
ND1 A:HIS96 4.1 32.0 1.0
CG A:HIS96 4.1 32.1 1.0
CG C:HIS96 4.2 27.7 1.0
O C:ASN94 4.7 36.2 1.0

Copper binding site 5 out of 6 in 1gmw

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Copper binding site 5 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1140

b:38.1
occ:1.00
NE2 C:HIS112 2.1 30.8 1.0
NE2 C:HIS110 2.1 27.4 1.0
CD2 C:HIS112 3.0 29.8 1.0
CE1 C:HIS112 3.0 29.4 1.0
CE1 C:HIS110 3.1 26.1 1.0
CD2 C:HIS110 3.1 27.5 1.0
ND1 C:HIS112 4.2 29.8 1.0
CG C:HIS112 4.2 31.8 1.0
ND1 C:HIS110 4.2 27.7 1.0
CG C:HIS110 4.2 27.2 1.0
O C:HOH2033 4.7 23.9 1.0
CD2 C:PHE127 4.8 36.2 1.0

Copper binding site 6 out of 6 in 1gmw

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Copper binding site 6 out of 6 in the Structure of Uree


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Uree within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1139

b:62.0
occ:1.00
NE2 D:HIS112 1.9 61.4 1.0
O D:HOH2026 2.2 47.5 1.0
NE2 D:HIS110 2.2 52.5 1.0
O D:HOH2027 2.3 50.0 1.0
CD2 D:HIS112 2.5 60.4 1.0
CE1 D:HIS112 3.0 61.5 1.0
CD2 D:HIS110 3.2 53.0 1.0
CE1 D:HIS110 3.2 51.7 1.0
CG D:HIS112 3.6 60.7 1.0
ND1 D:HIS112 3.9 61.7 1.0
ND1 D:HIS110 4.3 52.3 1.0
CG D:HIS110 4.3 51.9 1.0
CB D:HIS112 4.9 58.1 1.0
CD2 D:PHE127 5.0 50.7 1.0

Reference:

H.K.Song, S.B.Mulrooney, R.Huber, R.Hausinger. Crystal Structure of Klebsiella Aerogenes Uree, A Nickel-Binding Metallochaperone For Urease Activation J.Biol.Chem. V. 276 49359 2001.
ISSN: ISSN 0021-9258
PubMed: 11591723
DOI: 10.1074/JBC.M108619200
Page generated: Sun Dec 13 10:58:57 2020

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