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Zirconium in PDB 1xc1: Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)

Protein crystallography data

The structure of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp), PDB code: 1xc1 was solved by W.Zhong, D.Alexeev, I.Harvey, M.Guo, D.J.B.Hunter, H.Zhu, D.J.Campopiano, P.J.Sadler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.51
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 146.200, 146.200, 113.558, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 27.5

Zirconium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Zirconium atom in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) (pdb code 1xc1). This binding sites where shown within 5.0 Angstroms radius around Zirconium atom.
In total 27 binding sites of Zirconium where determined in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp), PDB code: 1xc1:
Jump to Zirconium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zirconium binding site 1 out of 27 in 1xc1

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Zirconium binding site 1 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 1 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr400

b:23.4
occ:1.00
ZR1 A:ZRC400 0.0 23.4 1.0
OH A:TYR195 2.1 14.4 1.0
O00 A:ZRC400 2.1 23.2 1.0
O1B A:ZRC400 2.1 21.9 1.0
O1A A:ZRC400 2.2 20.7 1.0
OP1 A:ZRC400 2.2 23.1 1.0
O31 A:ZRC400 2.3 23.3 1.0
O12 A:ZRC400 2.4 22.6 1.0
CZ A:TYR195 3.1 17.7 1.0
P A:ZRC400 3.3 27.5 1.0
ZR3 A:ZRC400 3.5 23.0 1.0
ZR2 A:ZRC400 3.5 24.7 1.0
OP2 A:ZRC400 3.6 24.2 1.0
CE2 A:TYR195 3.7 15.0 1.0
OP3 A:ZRC400 3.7 24.9 1.0
O A:HOH477 4.0 23.6 1.0
O A:HOH522 4.0 30.6 1.0
OH A:TYR196 4.0 17.7 1.0
O A:HOH518 4.1 29.4 1.0
CE1 A:TYR195 4.1 15.0 1.0
OE2 A:GLU57 4.3 33.6 1.0
O2B A:ZRC400 4.4 21.9 1.0
ND2 A:ASN193 4.4 16.1 1.0
NH2 A:ARG262 4.4 29.0 1.0
O3A A:ZRC400 4.5 22.3 1.0
O23 A:ZRC400 4.5 22.8 1.0
OP4 A:ZRC400 4.6 26.4 1.0
CZ A:TYR196 4.6 18.8 1.0
CE1 A:TYR196 4.6 19.0 1.0
OB2 A:ZRC400 4.7 21.5 1.0

Zirconium binding site 2 out of 27 in 1xc1

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Zirconium binding site 2 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 2 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr400

b:24.7
occ:1.00
ZR2 A:ZRC400 0.0 24.7 1.0
OB2 A:ZRC400 2.1 21.5 1.0
O00 A:ZRC400 2.2 23.2 1.0
O2A A:ZRC400 2.3 23.9 1.0
OP2 A:ZRC400 2.3 24.2 1.0
O2B A:ZRC400 2.3 21.9 1.0
O23 A:ZRC400 2.3 22.8 1.0
O12 A:ZRC400 2.3 22.6 1.0
P A:ZRC400 3.4 27.5 1.0
ZR3 A:ZRC400 3.5 23.0 1.0
ZR1 A:ZRC400 3.5 23.4 1.0
OP3 A:ZRC400 3.7 24.9 1.0
OP1 A:ZRC400 3.8 23.1 1.0
OH A:TYR196 4.2 17.7 1.0
ND2 A:ASN175 4.3 18.6 1.0
O A:HOH522 4.3 30.6 1.0
N A:GLY140 4.4 17.9 1.0
ND2 A:ASN193 4.4 16.1 1.0
OH A:TYR195 4.5 14.4 1.0
N A:ALA141 4.6 16.3 1.0
O3B A:ZRC400 4.6 24.9 1.0
O31 A:ZRC400 4.6 23.3 1.0
OG A:SER139 4.6 21.6 1.0
OP4 A:ZRC400 4.6 26.4 1.0
O1A A:ZRC400 4.7 20.7 1.0
CA A:GLY140 4.8 16.9 1.0
CB A:ALA141 5.0 15.4 1.0

Zirconium binding site 3 out of 27 in 1xc1

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Zirconium binding site 3 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 3 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zr400

b:23.0
occ:1.00
ZR3 A:ZRC400 0.0 23.0 1.0
OH A:TYR196 2.0 17.7 1.0
O00 A:ZRC400 2.2 23.2 1.0
O3B A:ZRC400 2.2 24.9 1.0
OP3 A:ZRC400 2.2 24.9 1.0
O3A A:ZRC400 2.3 22.3 1.0
O31 A:ZRC400 2.3 23.3 1.0
O23 A:ZRC400 2.4 22.8 1.0
CZ A:TYR196 3.3 18.8 1.0
P A:ZRC400 3.3 27.5 1.0
ZR1 A:ZRC400 3.5 23.4 1.0
ZR2 A:ZRC400 3.5 24.7 1.0
OP1 A:ZRC400 3.6 23.1 1.0
OP2 A:ZRC400 3.6 24.2 1.0
O A:HOH527 3.9 32.2 1.0
CE2 A:TYR196 4.0 19.0 1.0
O A:HOH508 4.0 28.3 1.0
O A:HOH458 4.2 22.8 1.0
CE1 A:TYR196 4.2 19.0 1.0
O A:HOH536 4.2 38.9 1.0
O A:HOH453 4.3 21.6 1.0
O2A A:ZRC400 4.3 23.9 1.0
OH A:TYR195 4.4 14.4 1.0
O12 A:ZRC400 4.5 22.6 1.0
ND2 A:ASN175 4.5 18.6 1.0
OP4 A:ZRC400 4.5 26.4 1.0
O1B A:ZRC400 4.7 21.9 1.0
OB2 A:ZRC400 4.7 21.5 1.0

Zirconium binding site 4 out of 27 in 1xc1

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Zirconium binding site 4 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 4 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zr400

b:27.7
occ:1.00
ZR1 B:ZRC400 0.0 27.7 1.0
O00 B:ZRC400 2.0 27.6 1.0
OP1 B:ZRC400 2.2 27.9 1.0
O1A B:ZRC400 2.2 25.0 1.0
OH B:TYR195 2.2 28.5 1.0
O31 B:ZRC400 2.3 27.1 1.0
O1B B:ZRC400 2.3 24.8 1.0
O12 B:ZRC400 2.4 28.0 1.0
P B:ZRC400 3.3 33.5 1.0
CZ B:TYR195 3.3 30.2 1.0
ZR3 B:ZRC400 3.5 30.4 1.0
ZR2 B:ZRC400 3.5 32.5 1.0
OP2 B:ZRC400 3.6 27.9 1.0
OP3 B:ZRC400 3.7 29.6 1.0
CE2 B:TYR195 3.8 29.0 1.0
O B:HOH470 4.0 28.1 1.0
O B:HOH462 4.1 27.0 1.0
OH B:TYR196 4.1 25.6 1.0
OD1 B:ASN193 4.3 24.5 1.0
CE1 B:TYR195 4.4 27.9 1.0
OB2 B:ZRC400 4.4 25.3 1.0
CE1 B:TYR196 4.4 22.6 1.0
O B:HOH455 4.5 24.5 1.0
O2B B:ZRC400 4.5 26.6 1.0
O23 B:ZRC400 4.5 26.9 1.0
OP4 B:ZRC400 4.5 31.1 1.0
NH2 B:ARG262 4.6 31.0 1.0
O3A B:ZRC400 4.6 29.1 1.0
CZ B:TYR196 4.7 22.7 1.0

Zirconium binding site 5 out of 27 in 1xc1

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Zirconium binding site 5 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 5 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zr400

b:32.5
occ:1.00
ZR2 B:ZRC400 0.0 32.5 1.0
OB2 B:ZRC400 2.1 25.3 1.0
O00 B:ZRC400 2.2 27.6 1.0
O12 B:ZRC400 2.2 28.0 1.0
OP2 B:ZRC400 2.2 27.9 1.0
O2A B:ZRC400 2.3 26.7 1.0
O23 B:ZRC400 2.3 26.9 1.0
O2B B:ZRC400 2.3 26.6 1.0
P B:ZRC400 3.4 33.5 1.0
ZR1 B:ZRC400 3.5 27.7 1.0
ZR3 B:ZRC400 3.6 30.4 1.0
OP1 B:ZRC400 3.7 27.9 1.0
OP3 B:ZRC400 3.8 29.6 1.0
OG B:SER139 4.0 24.8 1.0
O B:HOH500 4.3 45.3 1.0
OD1 B:ASN193 4.3 24.5 1.0
N B:GLY140 4.3 17.2 1.0
OH B:TYR196 4.4 25.6 1.0
O31 B:ZRC400 4.5 27.1 1.0
NZ B:LYS174 4.5 24.9 1.0
N B:ALA141 4.6 14.3 1.0
OP4 B:ZRC400 4.6 31.1 1.0
OH B:TYR195 4.7 28.5 1.0
O3B B:ZRC400 4.8 27.9 1.0
CA B:GLY140 4.8 16.6 1.0
O1A B:ZRC400 4.8 25.0 1.0

Zirconium binding site 6 out of 27 in 1xc1

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Zirconium binding site 6 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 6 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zr400

b:30.4
occ:1.00
ZR3 B:ZRC400 0.0 30.4 1.0
OH B:TYR196 2.0 25.6 1.0
O00 B:ZRC400 2.1 27.6 1.0
OP3 B:ZRC400 2.1 29.6 1.0
O3B B:ZRC400 2.2 27.9 1.0
O31 B:ZRC400 2.2 27.1 1.0
O3A B:ZRC400 2.3 29.1 1.0
O23 B:ZRC400 2.3 26.9 1.0
P B:ZRC400 3.2 33.5 1.0
CZ B:TYR196 3.3 22.7 1.0
OP2 B:ZRC400 3.5 27.9 1.0
ZR1 B:ZRC400 3.5 27.7 1.0
OP1 B:ZRC400 3.6 27.9 1.0
ZR2 B:ZRC400 3.6 32.5 1.0
NZ B:LYS174 3.7 24.9 1.0
O B:HOH441 4.0 21.8 1.0
CE1 B:TYR196 4.1 22.6 1.0
CE2 B:TYR196 4.1 24.4 1.0
O B:HOH487 4.2 33.1 1.0
OB2 B:ZRC400 4.4 25.3 1.0
OP4 B:ZRC400 4.5 31.1 1.0
O12 B:ZRC400 4.5 28.0 1.0
OH B:TYR195 4.6 28.5 1.0
CE B:LYS174 4.7 26.5 1.0
O2A B:ZRC400 5.0 26.7 1.0
CD B:LYS174 5.0 27.5 1.0
O1B B:ZRC400 5.0 24.8 1.0
O B:HOH470 5.0 28.1 1.0

Zirconium binding site 7 out of 27 in 1xc1

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Zirconium binding site 7 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 7 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zr400

b:23.5
occ:1.00
ZR1 C:ZRC400 0.0 23.5 1.0
OH C:TYR195 2.1 25.6 1.0
O00 C:ZRC400 2.2 25.8 1.0
O1A C:ZRC400 2.2 23.4 1.0
OP1 C:ZRC400 2.2 23.5 1.0
O12 C:ZRC400 2.3 24.8 1.0
O1B C:ZRC400 2.3 22.5 1.0
O31 C:ZRC400 2.4 24.5 1.0
CZ C:TYR195 3.0 24.8 1.0
P C:ZRC400 3.4 26.7 1.0
ZR3 C:ZRC400 3.5 24.7 1.0
ZR2 C:ZRC400 3.5 24.1 1.0
CE2 C:TYR195 3.6 23.5 1.0
OP3 C:ZRC400 3.8 25.8 1.0
OP2 C:ZRC400 3.8 25.6 1.0
CE1 C:TYR195 3.9 23.3 1.0
O C:HOH443 4.0 24.3 1.0
O C:HOH509 4.1 47.8 1.0
OH C:TYR196 4.2 25.5 1.0
O C:HOH437 4.3 23.0 1.0
O2B C:ZRC400 4.4 22.9 1.0
NH2 C:ARG262 4.5 30.1 1.0
ND2 C:ASN193 4.5 20.5 1.0
O23 C:ZRC400 4.6 25.2 1.0
OP4 C:ZRC400 4.6 24.8 1.0
OB2 C:ZRC400 4.7 24.2 1.0
CE1 C:TYR196 4.7 23.9 1.0
O3A C:ZRC400 4.8 24.7 1.0
CD2 C:TYR195 4.8 20.9 1.0
NH1 C:ARG101 4.9 45.1 1.0
CZ C:TYR196 4.9 22.4 1.0

Zirconium binding site 8 out of 27 in 1xc1

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Zirconium binding site 8 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 8 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zr400

b:24.1
occ:1.00
ZR2 C:ZRC400 0.0 24.1 1.0
OB2 C:ZRC400 2.1 24.2 1.0
O00 C:ZRC400 2.2 25.8 1.0
O2B C:ZRC400 2.3 22.9 1.0
O12 C:ZRC400 2.3 24.8 1.0
OP2 C:ZRC400 2.3 25.6 1.0
O23 C:ZRC400 2.3 25.2 1.0
O2A C:ZRC400 2.4 23.3 1.0
P C:ZRC400 3.4 26.7 1.0
ZR3 C:ZRC400 3.5 24.7 1.0
ZR1 C:ZRC400 3.5 23.5 1.0
OP1 C:ZRC400 3.6 23.5 1.0
OP3 C:ZRC400 3.7 25.8 1.0
O C:HOH443 4.0 24.3 1.0
OH C:TYR195 4.2 25.6 1.0
N C:GLY140 4.3 18.9 1.0
O C:HOH477 4.3 29.0 1.0
OD1 C:ASN175 4.3 22.1 1.0
OG C:SER139 4.4 19.2 1.0
O31 C:ZRC400 4.6 24.5 1.0
N C:ALA141 4.6 13.5 1.0
OP4 C:ZRC400 4.6 24.8 1.0
ND2 C:ASN193 4.6 20.5 1.0
O3B C:ZRC400 4.7 25.9 1.0
O1A C:ZRC400 4.7 23.4 1.0
OH C:TYR196 4.8 25.5 1.0
CA C:GLY140 4.8 18.1 1.0

Zirconium binding site 9 out of 27 in 1xc1

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Zirconium binding site 9 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 9 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zr400

b:24.7
occ:1.00
ZR3 C:ZRC400 0.0 24.7 1.0
OH C:TYR196 2.0 25.5 1.0
O3B C:ZRC400 2.1 25.9 1.0
O00 C:ZRC400 2.2 25.8 1.0
O31 C:ZRC400 2.3 24.5 1.0
OP3 C:ZRC400 2.3 25.8 1.0
O3A C:ZRC400 2.3 24.7 1.0
O23 C:ZRC400 2.4 25.2 1.0
P C:ZRC400 3.3 26.7 1.0
CZ C:TYR196 3.4 22.4 1.0
ZR1 C:ZRC400 3.5 23.5 1.0
ZR2 C:ZRC400 3.5 24.1 1.0
OP1 C:ZRC400 3.6 23.5 1.0
OP2 C:ZRC400 3.7 25.6 1.0
OH C:TYR195 4.1 25.6 1.0
O C:HOH477 4.1 29.0 1.0
CE1 C:TYR196 4.1 23.9 1.0
O C:HOH453 4.2 26.2 1.0
O C:HOH411 4.2 17.1 1.0
CE2 C:TYR196 4.3 20.5 1.0
O C:HOH508 4.4 44.1 1.0
O12 C:ZRC400 4.4 24.8 1.0
O C:HOH509 4.4 47.8 1.0
OD1 C:ASN175 4.4 22.1 1.0
O1B C:ZRC400 4.6 22.5 1.0
OP4 C:ZRC400 4.6 24.8 1.0
OB2 C:ZRC400 4.6 24.2 1.0
O2A C:ZRC400 4.6 23.3 1.0
O C:HOH497 4.7 36.0 1.0
CE2 C:TYR195 4.9 23.5 1.0
CZ C:TYR195 5.0 24.8 1.0

Zirconium binding site 10 out of 27 in 1xc1

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Zirconium binding site 10 out of 27 in the Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp)


Mono view


Stereo pair view

A full contact list of Zirconium with other atoms in the Zr binding site number 10 of Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (Fbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zr400

b:23.4
occ:1.00
ZR1 D:ZRC400 0.0 23.4 1.0
OH D:TYR195 1.9 16.6 1.0
O1B D:ZRC400 2.1 22.4 1.0
O00 D:ZRC400 2.1 24.0 1.0
OP1 D:ZRC400 2.1 24.2 1.0
O1A D:ZRC400 2.3 23.1 1.0
O12 D:ZRC400 2.3 24.2 1.0
O31 D:ZRC400 2.4 23.0 1.0
CZ D:TYR195 3.0 21.5 1.0
P D:ZRC400 3.3 26.8 1.0
ZR2 D:ZRC400 3.5 23.0 1.0
ZR3 D:ZRC400 3.6 24.7 1.0
CE2 D:TYR195 3.6 19.9 1.0
OP3 D:ZRC400 3.7 24.4 1.0
OP2 D:ZRC400 3.8 24.3 1.0
O D:HOH407 4.0 15.5 1.0
CE1 D:TYR195 4.1 21.4 1.0
OH D:TYR196 4.1 17.0 1.0
NH2 D:ARG262 4.3 29.3 1.0
OD1 D:ASN193 4.5 26.6 1.0
OP4 D:ZRC400 4.5 25.9 1.0
O23 D:ZRC400 4.6 23.5 1.0
O3A D:ZRC400 4.6 23.6 1.0
CZ D:TYR196 4.7 18.8 1.0
O D:HOH445 4.7 22.5 1.0
CE1 D:TYR196 4.7 19.6 1.0
O2B D:ZRC400 4.8 22.6 1.0
OB2 D:ZRC400 4.9 23.6 1.0
CD2 D:TYR195 4.9 20.4 1.0

Reference:

W.Zhong, D.Alexeev, I.Harvey, M.Guo, D.J.B.Hunter, H.Zhu, D.J.Campopiano, P.J.Sadler. Assembly of An Oxo-Zirconium(IV) Cluster in A Protein Cleft Angew.Chem.Int.Ed.Engl. V. 43 5914 2004.
ISSN: ISSN 1433-7851
PubMed: 15472987
DOI: 10.1002/ANIE.200460806
Page generated: Wed Dec 16 14:05:32 2020

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